Online Supplementary Material s1

Supplementary Material

Two chaperonin systems in bacterial genomes with distinct ecological roles

Tom A. Williams1, Francisco M. Codoñer2, Christina Toft3, Mario A. Fares1*

1. Department of Genetics, University of Dublin, Trinity College, Dublin, Ireland

2. Laboratori de Retrovirología, Fundació IRSICaixa, Hospital Germans Trias i Pujol, Badalona,

3. Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala,

10 Sweden

Corresponding Author: Dr. Mario A. Fares

Department of Genetics

15 University of Dublin, Trinity College

Dublin 2, Dublin, Ireland

Email: [email protected]

Phone: +3538963521

25 Sequences and tree-building

To obtain all bacterial homologs of GroEL, we downloaded the complete set of fully sequenced

bacterial proteomes from NCBI on 8 July 2008 (622 proteomes) and used them to create a BLAST

30 database. This database was queried using Escherichia coli GroEL and all hits with an E-value

lower than 10−7 were retrieved. The list of hits was manually curated to remove spurious sequences

by removing proteins of length greater than 1.5 times that of the query sequence, and/or on the basis

of sequence annotation at NCBI, resulting in a final set of 840 GroEL homologues. These proteins

were aligned with MUSCLE 3.6 [1] using the default parameters, and a 100-bootstrap maximum

35 likelihood phylogenetic tree was created using RAxML 7 [2] under the WAG model of protein

sequence evolution [3], which was suggested by ProtTest [4]. The topology of the resulting tree was

then used to infer duplication events in GroEL evolution.

Sequences were obtained for the mitochondrial Hsp60 analysis by BLASTing the Homo sapiens

40 mitochondrial Hsp60 sequence against the NCBI non-redundant database. The resulting hits were

retrieved and both automatically and manually curated. Due to the large number of hits to partial or

otherwise suspect sequences, all sequences shorter than 450 residues were discarded (this is 120

residues shorter than the H. sapiens sequence). The remaining sequences were aligned with the

GroEL sequences of the Rickettsiales, a group of bacteria that may be closely related to the

45 ancestral mitochondrion [5], and with a putative outgroup, Bradyrhizobium japonicum. A 100-

bootstrap, maximum-likelihood phylogenetic tree was built from this alignment as described above

(see Supplementary Figure 1). The topology of this tree suggested that the sequences did indeed fall

into three clades (eukaryotic mitochondrial sequences, Rickettsiales, Bradyrhizobium japonicum).

Given the evidence supporting the monophyly of the mitochondrion and the Rickettsiales [6], we

50 proceeded with our use of Bradyrhizobium japonicum as the outgroup. These sequences were then

used in our analysis of functional divergence as described below. Figure S1: Phylogenetic tree of mitochondrial HSP60 sequences. Branches are coloured

55 according to the major clades that were compared in our analysis. In line with previous reports, the

mitochondrial and Rickettsial groups receive strong bootstrap support.

Archaeal homologs of the bacterial group II chaperonin genes were obtained by BLASTing the

Desulfotomaculum reducens group II sequence against all archaeal sequences in the NCBI non-

60 redundant database, using the default parameters. Non-chaperonin sequences were manually

removed from the list of hits, and the remaining sequences were used to construct a phylogeny as

described above for the GroEL genes, using the LG model of protein evolution [7]. 65 Figure S2: Phylogenetic tree of group II chaperonin sequences from archaea and bacteria.

Bacterial lineages are highlighted in red; major archaeal lineages are coloured to clearly delineate

groups. Nine of the ten bacterial sequences form a strongly-supported monophyletic cluster which

has two group II sequences from the methanogen Methanosarcina acetivorans as an outgroup. The

immediate outgroup of the group II sequence from Oligotropha carboxidivorans is encoded by the

70 archaeaon Nanoarchaeum equitans.

Testing the pseudogenization of group II chaperonin sequences in bacteria

We used the method of Yang and Nielsen [8] implemented in the yn00 program, which is part of the

PAML package [9], to compare the ratios of nonsynonymous and synonymous substitution rates

75 (dN/dS) between bacterial and archaeal group II chaperonin sequences. The difference between the

nonsynonymous and synonymous rate is mainly due to selection, because nonsynonymous changes

alter the encoded protein sequence whereas synonymous changes do not. Most protein-changing mutations are deleterious [10], so that the nonsynonymous rate is usually much lower than the

synonymous rate in proteins under selective constraint – that is, functional proteins. If the group II

80 chaperonin sequences in bacteria have become nonfunctional, then the mean pairwise dN/dS ratio

among bacterial sequences should be substantially higher than that among archaeal sequences. In

fact, these ratios were very similar (0.204 for bacteria; for archaea: 0.194), suggesting that the group

II chaperonins are evolving under comparable selective constraints in both domains. Under the

assumption that the archaeal group II chaperonin sequences are functional, this result suggests the

85 bacterial sequences are as well.

Horizontal gene transfer between group II chaperonin-possessing bacteria and methanogenic

archaea

Existing evidence from a variety of sources supports a substantial level of horizontal gene transfer

90 between the 10 bacteria possessing a group II chaperonin gene and the methanogenic archaea

(summarized in Supplementary Table 1). The DarkHorse database, which attempts to catalogue

horizontally transferred genes [11], suggests that horizontal transfer is ongoing between these

species and archaea, with a mean of 46 recently-transferred (DarkHorse LPI score < 0.25) archaeal

genes per bacterial genome which contains a group II chaperonin gene. Putative group II

95 chaperonin clients in bacteria would have been transferred somewhat earlier, and should be found in

bacterial species with a group II chaperonin gene and archaea, but not other bacteria. Ultimately,

experimental work is required to identify clients of the functional archaeal chaperonin in these

bacteria.

Species HGT(%)a Other archaeal Archaeal Lifestyle

genesb associationc Geobacillus sp. 12-15 - - Thermophile [18]

Y412MC10 Oligotropha - - - CO metabolism [19] carboxidovorans Thermosinus - - - CO metabolism [20] carboxydivorans Desulfotomaculum 16.3 - Syntrophy (Imachi et Sulfur-reducing [21] reducens al. 2006) Desulfotomaculum - - Syntrophy (Imachi et Sulfur-reducing [21] acetoxidans al. 2006) Pelotomaculum - Yes (Kosaka et Syntrophy (Kosaka et Thermophile, thermopropionicum al. 2008) al. 2008) propionate-oxidizing

[22] Heliobacterium - Yes (Sattley et al. - Thermophile, modesticaldum 2008) photoheterotroph [23] Gloeobacter 5.5 Yes (Karlin et al. - Photoautotroph [24] violaceus 2005) Candidatus - Yes (Chivian et - Sulfur-reducing [25]

Desulforudis al. 2008) audaxviator Carboxydothermus 14.6 - - Thermophile, hydrogenoformans hydrogenogenic CO

metabolism [26] 100 Supplementary Table 1: Evidence for horizontal transfer of group II chaperonins from

archaea into bacteria.

a HGT = Horizontal gene transfer, the percentage of genes estimated to be obtained laterally in that

species (not necessarily from archaea) and predicted by HGT-DB [27].

b “Other archaeal genes” indicates whether additional non-chaperonin archaeal genes have

105 previously been identified in this species.

c “Archaeal association” lists known ecological relationships between this species and archaea.

125 Detection of functional divergence

Figure S3: Branch-specific detection of functional divergence

To investigate lineage-specific functional divergence in our GroEL tree, we developed a new

method, which is detailed below. Starting with the tips of a phylogenetic tree, the software walks

130 down to the root, identifying all interior nodes at which a branch-specific analysis of functional

divergence can be performed (the analysis is performed if there are at least four sequences in each

descendant clade). A test for functional divergence at each of these nodes is then carried out. A node

is defined by two clades (clusters) and one or more outgroup sequences, and our method uses

BLOSUM scores [12] to identify conserved unexpected substitutions — that is, substitutions

135 associated with large, negative BLOSUM scores — in one protein cluster which are not observed in

the homologous cluster, or in an outgroup cluster. These sites are then taken to be under functional

divergence on the branch leading to that cluster. The procedure is illustrated in Supplementary

Figure 3 above: a section of the multiple sequence alignment being scanned by the method shows a

column in which functional divergence is detected. The amino acids are colour-coded following the

140 same principle as ClustalX and hence the colours correspond to amino acid properties. In the examples we identify a transition from an ancestral F/Y to a P, which is conserved thereafter,

indicating functional divergence (FD). In the next example, a charged amino acid (D/E) mutates to a

M/L, also indicating functional divergence. For each column of a protein multiple sequence

alignment for which the three clusters are already defined, we calculate four quantities: the mean

145 pairwise BLOSUM score between sequences in the first cluster and the outgroup cluster (C1); the

mean pairwise BLOSUM score between sequences in the second cluster and the outgroup cluster

(C2); and the standard errors (SEC1, SEC2). We then calculate a test score for that column as and

assess significance against a normal distribution. The method was previously applied to the

evolution of endosymbiotic bacteria [13], with the main improvement here being the ability to

150 perform branch-specific tests of functional divergence across a complex phylogenetic tree.

Here, we present both a branch-specific, whole phylogeny test (the analysis of all bacterial GroEL

genes), and a test of a single lineage (mitochondrial Hsp60). In the case of analyzing the entire tree,

we draw a distribution of numbers of sites under functional divergence on each branch, and

155 examine the top 5% of the distribution in order to isolate the most important patterns of functional

divergence in the dataset. With our analysis of mitochondrial Hsp60, we examine the specific sites

identified as being under functional divergence.

Importance of sites under functional divergence in mtHsp60

160 This section presents the detailed evidence for our claim that the detected functionally divergent

sites in mtHsp60 (the mitochondrial GroEL) are of considerable functional importance. Note that, in

the following discussion, all residue numbers are given according to their positions in E. coli

GroEL: this is due to the far greater body of GroEL mutagenesis experiments that have been

conducted in that organism.

Three of the sites under functional divergence are close to positions that maintain the inter-ring interaction in GroEL (marked in red in Figure 2). V438 is 2.9Å away from E434, L444 is directly

beside (1.3Å) R445, and Q453 is again directly beside (1.3Å) R452, all three of which form the

interface with the other ring of GroEL [14]. We also identified two other residues in this region,

170 V14 and K28, of currently unknown function. Radical change at the inter-ring interface makes

sense, since bacterial GroEL operates as a double-ring complex while mtHsp60 does not.

Sun et al. [15] isolated mutants of a single-ring GroEL variant (SR1) which restored chaperone

function but did not restore the double-ring quaternary structure. That is, they isolated mutations

175 resulting in active, single-ring variants of GroEL. Four of the sites detected as being under

functional divergence were close to several of these mutants: K390 (under functional divergence)

was directly beside (1.3Å) M389, E397 was close to both R395 and A399 (3.1Å in each case),

Q505 is close to A503 (3.3Å) and A507 (3.1Å), and I515 is directly between M514 (1.3Å) and

T516 (1.2Å). One or more mutations at each of these positions restore single-ring GroEL function

180 [56]. Again, the proximity of these sites under functional divergence to sites which, when mutated,

result in an active single-ring GroEL mutant makes biological sense in light of the functional

differences between mtHsp60 and GroEL.

Six additional functionally divergent sites are in positions, which suggest functional importance.

185 T210 forms the hinge of a substrate-binding loop in the GroEL apical domain, and also makes

contact with other subunits in the same ring [16]. Both this site and the adjacent G211 are under

functional divergence in mtHsp60. A239 is beside (1.3Å) E238, which is involved in GroES

binding [17]. A241 is involved in substrate binding [18]. R284 forms a salt bridge, which plays an

important role in the conformational changes which occur in one half of the GroEL complex upon

190 ATP binding [20]. E315 is beside (1.3A) L314, which is involved in substrate binding [16].

The mutagenesis experiments referenced here were performed on E. coli GroEL, and so cannot

provide direct information about the function of the homologous positions in mtHsp60. However, the location of these functionally divergent sites in important regions of the GroEL protein suggest

that our method has captured, at least partially, the amino acid-level changes responsible for the

195 observed differences in function between mtHsp60 and GroEL.

Escherichia coli site mtHsp60 (consensus) Rickettsiales (consensus) Bradyrhizobium V14 A E E K28 A K K D121 M D D T210 G K K G211 Q M M A239 L A A A241 N V V A243 Q S S R284 N R R K315 H K K K390 N K K E397 T E E V438 I A A L444 K I I Q453 T Q Q Q505 V Q Q I515 T I V -(179 aln) - M M -(1016 aln) T A A Supplementary Table 2: Sites under functional divergence in mitochondrial Hsp60 (mtHsp60).

200 Phylogenetic distribution of groES

We used BLASTP searches against each bacterial and archaeal genome containing one or more

groEL genes to check for the co-occurrence of the chaperonin with its accessory protein, GROES.

We first performed our search using E. coli GROES, re-running manual BLASTs using a GROES

205 query sequence from a more closely-related species if the initial search did not identify any

significant hits (defined as an E-value lower than 10-7, coupled with NCBI database annotation).

The accession numbers for the hits obtained are provided in Supplementary Table 6. All but four

groEL-encoding genomes were shown to contain at least one groES gene with this approach. We

reasoned that the remaining four species – the bacteria Escherichia coli APEC O1, Clostridium

210 tetani E88, Magnetospirillum magneticum AMB-1, and Lysinibacillus sphaericus C3-41 – might

contain an unannotated groES gene, because all four possess typical groEL genes as well as having

relatives possessing both groEL and groES. Indeed, TBLASTN searches using the E. coli GROES

sequence revealed significant hits in all four genomes. In the case of Lysinibacillus, the hit to the E.

coli sequence is at the limit of our criterion (E-value = 10-7), but the genomic location of the hit –

215 directly adjacent to groEL – suggests that this is a genuine groES gene. Among the bacteria and

archaea we surveyed, then, genomes containing one or more groEL genes also contained at least

one groES.

Co-occurrence of groEL and groES duplicates

220 Substantially more species contain duplicate groEL (163) than groES (69) genes. Although some

groups of bacteria possess elevated copy numbers of both genes (the Rhizobiales and the

Burkholderiales), there is no 1:1 ratio in the number of groEL and groES genes, and many species

with multiple, functionally divergent GROELs have only a single GROES (e.g. the Chlamydiae,

Mycobacteria, and Wolbachia species; see Supplementary Table 6). This result suggests that a

225 single GROES can perform its co-chaperonin function for multiple, functionally divergent GROEL

complexes.

Sequence accession numbers

230 The tables in this section are presented in the following order:

3. Accession numbers for GROEL phylogeny.

4. Accession numbers for group II chaperonin phylogeny.

5. Accession numbers for mitochondrial Hsp60 phylogeny.

6. Accession numbers for GROES sequences in genomes that contain GROEL.

Species No. NCBI accession numbers Bradyrhizobium japonicum USDA 110 7 NP_772266.1, NP_774173.1, NP_768699.1,

NP_773619.1, NP_771867.1, NP_771275.1,

NP_770323.1 Sinorhizobium medicae WSM419 5 YP_001326966.1, YP_001326100.1,

YP_001314661.1, YP_001326495.1,

YP_001312869.1 Mesorhizobium loti MAFF303099 5 NP_103751.1, NP_106407.1, NP_108345.1,

NP_085869.1, NP_103625.1 Bradyrhizobium sp. BTAi1 5 YP_001241176.1, YP_001239060.1,

YP_001237787.1, YP_001238586.1,

YP_001239628.1 Burkholderia xenovorans LB400 5 YP_557235.1, YP_558424.1, YP_558394.1,

YP_553745.1, YP_555410.1 Sinorhizobium meliloti 1021 5 NP_437546.1, NP_384898.1, NP_435641.1,

NP_385302.1, NP_435310.1 Corynebacterium glutamicum ATCC 5 NP_601912.1, YP_226955.1, NP_599834.1,

13032 YP_224891.1, YP_224889.1 Rhizobium etli CFN 42 4 YP_468366.1, YP_468771.1, YP_472947.1,

YP_468803.1 Bradyrhizobium sp. ORS278 4 YP_001204748.1, YP_001204938.1,

YP_001207982.1, YP_001206315.1 Frankia sp. EAN1pec 4 YP_001504548.1, YP_001508152.1, YP_001507661.1, YP_001510251.1 Frankia alni ACN14a 4 YP_716828.1, YP_716615.2, YP_711940.1,

YP_711392.2 Rhizobium leguminosarum bv. viciae 4 YP_766495.1, YP_765148.1, YP_767017.1,

3841 YP_765335.1 Frankia sp. CcI3 4 YP_483473.1, YP_481274.1, YP_479746.1,

YP_481609.1 Acinetobacter baumannii 4 YP_001706389.1, YP_001712779.1,

YP_001715367.1, YP_001715364.1 Nitrobacter hamburgensis X14 3 YP_577836.1, YP_576475.1, YP_578391.1 Burkholderia cenocepacia MC0-3 3 YP_001764131.1, YP_001774336.1,

YP_001777638.1 Methylobacterium sp. 4-46 3 YP_001768695.1, YP_001772319.1,

YP_001772213.1 Mycobacterium smegmatis str. MC2 155 3 YP_885283.1, YP_885962.1, YP_886342.1 Burkholderia ambifaria AMMD 3 YP_772626.1, YP_778270.1, YP_777152.1 Burkholderia thailandensis E264 3 YP_442004.1, YP_440132.1, YP_439113.1 Chlamydophila felis Fe/C-56 3 YP_515282.1, YP_514950.1, YP_515063.1 Chlamydophila pneumoniae TW-183 3 NP_876411.1, NP_877077.1, NP_877201.1 Rhodococcus sp. RHA1 3 YP_702111.1, YP_706125.1, YP_700442.1 Anabaena variabilis ATCC 29413 3 YP_324266.2, YP_324127.1, YP_320421.1 Chlamydia trachomatis A/HAR-13 3 YP_327911.1, YP_328428.1, YP_328583.1 Chlamydophila pneumoniae J138 3 NP_300193.1, NP_300834.1, NP_300955.1 Azoarcus sp. BH72 3 YP_932478.1, YP_933870.1, YP_932727.1 Syntrophus aciditrophicus SB 3 YP_461542.1, YP_460096.1, YP_461768.1 Chlamydophila caviae GPIC 3 NP_829507.1, NP_829841.1, NP_829733.1 Chlamydia muridarum Nigg 3 NP_296764.1, NP_297266.1, NP_296515.1 Burkholderia cenocepacia HI2424 3 YP_834506.1, YP_839876.1, YP_837154.1 Chlamydophila abortus S26/3 3 YP_220012.1, YP_220334.1, YP_220224.1 Methylobacterium extorquens PA1 3 YP_001642221.1, YP_001638224.1,

YP_001640792.1 Rhodopirellula baltica SH 1 3 NP_869524.1, NP_868643.1, NP_868641.1 Sphingopyxis alaskensis RB2256 3 YP_615506.1, YP_617121.1, YP_615469.1 Methylococcus capsulatus str. Bath 3 YP_113217.1, YP_114145.1, YP_113667.1 Rhodobacter sphaeroides 2.4.1 3 YP_352366.1, YP_355125.1, YP_352918.1 Gloeobacter violaceus PCC 7421 3 NP_925843.1, NP_923973.1, NP_926694.1 Chlamydophila pneumoniae CWL029 3 NP_224342.1, NP_224972.1, NP_225093.1 Chlamydia trachomatis D/UW-3/CX 3 NP_219613.1, NP_220120.1, NP_220274.1 Chlamydophila pneumoniae AR39 3 NP_445180.1, NP_445632.1, NP_445505.1 Mesorhizobium sp. BNC1 3 YP_675632.1, YP_672926.1, YP_674919.1 Psychromonas ingrahamii 37 3 YP_942286.1, YP_943818.1, YP_944097.1 Chlamydia trachomatis 434/Bu 3 YP_001654449.1, YP_001654936.1,

YP_001654215.1 Nitrobacter winogradskyi Nb-255 3 YP_318798.1, YP_318720.1, YP_319179.1 Acaryochloris marina MBIC11017 3 YP_001517526.1, YP_001518705.1,

YP_001522017.1 Burkholderia ambifaria MC40-6 3 YP_001807462.1, YP_001816085.1,

YP_001810134.1 Acidothermus cellulolyticus 11B 2 YP_871863.1, YP_872123.1 Anaeromyxobacter dehalogenans 2CP-C 2 YP_466797.1, YP_465601.1 Synechococcus sp. WH 8102 2 NP_896609.1, NP_897945.1 Streptococcus suis 98HAH33 2 YP_001199712.1, YP_001199711.1 Burkholderia multivorans ATCC 17616 2 YP_001580709.1, YP_001585215.1 Rhodopseudomonas palustris BisB5 2 YP_571247.1, YP_569363.1 Mycobacterium sp. JLS 2 YP_001068901.1, YP_001069475.1 Mycobacterium tuberculosis H37Ra 2 YP_001281728.1, YP_001284804.1 Rhodopseudomonas palustris HaA2 2 YP_485455.1, YP_486841.1 Synechococcus elongatus PCC 7942 2 YP_399704.1, YP_401330.1 Synechococcus sp. JA-2-3B'a(2-13) 2 YP_477934.1, YP_477842.1 Burkholderia cenocepacia AU 1054 2 YP_620263.1, YP_621458.1 Synechococcus sp. CC9311 2 YP_731479.1, YP_731337.1 Synechococcus sp. JA-3-3Ab 2 YP_473815.1, YP_474840.1 Thermosynechococcus elongatus BP-1 2 NP_680976.1, NP_682202.1 Streptomyces griseus subsp. griseus 2 YP_001824281.1, YP_001824737.1

NBRC 13350 Mycobacterium avium subsp. 2 NP_962870.1, NP_963199.1 paratuberculosis K-10 Roseiflexus sp. RS-1 2 YP_001278425.1, YP_001275436.1 Prochlorococcus marinus str. MIT 9312 2 YP_398025.1, YP_396948.1 Prochlorococcus marinus subsp. marinus 2 NP_875980.1, NP_874842.1 str. CCMP1375 Propionibacterium acnes KPA171202 2 YP_055163.1, YP_056459.1 Trichodesmium erythraeum IMS101 2 YP_720226.1, YP_723793.1 Corynebacterium efficiens YS-314 2 NP_739171.1, NP_737212.1 Nostoc sp. PCC 7120 2 NP_485936.1, NP_487702.1 Prochlorococcus marinus str. MIT 9313 2 NP_895276.1, NP_895161.1 Mycobacterium sp. MCS 2 YP_637784.2, YP_638323.1 Rhodopseudomonas palustris BisB18 2 YP_534567.1, YP_533033.1 Prochlorococcus marinus str. NATL2A 2 YP_292161.1, YP_292974.1 Salinibacter ruber DSM 13855 2 YP_446228.1, YP_444383.1 Burkholderia pseudomallei 1106a 2 YP_001067391.1, YP_001074682.1 Mycobacterium ulcerans Agy99 2 YP_905407.1, YP_904989.1 Mycobacterium sp. KMS 2 YP_936626.1, YP_937174.1 Bacillus cereus ATCC 10987 2 NP_976617.1, NP_976618.1 Paracoccus denitrificans PD1222 2 YP_918344.1, YP_917417.1 Nocardioides sp. JS614 2 YP_925166.1, YP_924833.1 Ehrlichia ruminantium str. Welgevonden 2 YP_180506.1, YP_197549.1 Saccharopolyspora erythraea NRRL 2338 2 YP_001102799.1, YP_001108805.1 Prochlorococcus marinus subsp. pastoris 2 NP_893553.1, NP_892570.1 str. CCMP1986 Candidatus Protochlamydia 2 YP_007029.1, YP_008258.1 amoebophila UWE25 Polaromonas naphthalenivorans CJ2 2 YP_980897.1, YP_980633.1 Vibrio vulnificus YJ016 2 NP_935899.1, NP_937715.1 Salinispora tropica CNB-440 2 YP_001157132.1, YP_001160649.1 Mycobacterium tuberculosis F11 2 YP_001286390.1, YP_001289378.1 Prochlorococcus marinus str. MIT 9301 2 YP_001091850.1, YP_001090700.1 Anaeromyxobacter sp. Fw109-5 2 YP_001380878.1, YP_001378663.1 Kineococcus radiotolerans SRS30216 2 YP_001363363.1, YP_001360489.1 Synechococcus sp. WH 7803 2 YP_001225721.1, YP_001225586.1 Synechococcus elongatus PCC 6301 2 YP_171554.1, YP_172499.1 Rhodopseudomonas palustris CGA009 2 NP_946491.1, NP_947509.1 Thermobifida fusca YX 2 YP_288289.1, YP_290654.1 Chromobacterium violaceum ATCC 2 NP_903684.1, NP_902903.1 12472 Renibacterium salmoninarum ATCC 2 YP_001623646.1, YP_001624917.1

33209 Chlamydia trachomatis L2b/UCH- 2 YP_001653948.1, YP_001653227.1

1/proctitis Synechococcus sp. PCC 7002 2 YP_001733417.1, YP_001735691.1 Heliobacterium modesticaldum Ice1 2 YP_001680010.1, YP_001680996.1 Prochlorococcus marinus str. NATL1A 2 YP_001015656.1, YP_001014333.1 Mycobacterium bovis AF2122/97 2 NP_854111.1, NP_857091.1 Prochlorococcus marinus str. MIT 9303 2 YP_001016521.1, YP_001016667.1 Vibrio cholerae O1 biovar eltor str. 2 NP_232292.1, NP_233206.1

N16961 Verminephrobacter eiseniae EF01-2 2 YP_997330.1, YP_999124.1 Escherichia coli APEC O1 2 YP_859815.1, YP_001481444.1 Pelotomaculum thermopropionicum SI 2 YP_001213155.1, YP_001211426.1 Vibrio parahaemolyticus RIMD 2210633 2 NP_799230.1, NP_799797.1 Roseobacter denitrificans OCh 114 2 YP_683684.1, YP_681139.1 Streptomyces avermitilis MA-4680 2 NP_826169.1, NP_825108.1 Streptococcus suis 05ZYH33 2 YP_001197518.1, YP_001197519.1 Arthrobacter sp. FB24 2 YP_830277.1, YP_832365.1 Erythrobacter litoralis HTCC2594 2 YP_457720.1, YP_459769.1 Gluconacetobacter diazotrophicus PAl 5 2 YP_001602294.1, YP_001602889.1 Rhodopseudomonas palustris BisA53 2 YP_779797.1, YP_781205.1 Vibrio vulnificus CMCP6 2 NP_760189.1, NP_763045.1 Corynebacterium urealyticum DSM 7109 2 YP_001801109.1, YP_001799788.1 Burkholderia vietnamiensis G4 2 YP_001118641.1, YP_001117599.1 Microcystis aeruginosa NIES-843 2 YP_001659622.1, YP_001655355.1 Streptomyces coelicolor A3(2) 2 NP_628920.1, NP_628468.1 Prochlorococcus marinus str. AS9601 2 YP_001010028.1, YP_001008902.1 Nocardia farcinica IFM 10152 2 YP_121491.1, YP_117096.1 Mycobacterium tuberculosis H37Rv 2 NP_214954.1, NP_217934.1 Burkholderia sp. 383 2 YP_368198.1, YP_373371.1 Ralstonia eutropha H16 2 YP_725222.1, YP_726465.1 Synechocystis sp. PCC 6803 2 NP_440731.1, NP_442170.1 Mycobacterium marinum M 2 YP_001849074.1, YP_001849437.1 Xanthobacter autotrophicus Py2 2 YP_001419142.1, YP_001416072.1 Roseiflexus castenholzii DSM 13941 2 YP_001431326.1, YP_001432868.1 Moorella thermoacetica ATCC 39073 2 YP_429419.1, YP_430964.1 Burkholderia pseudomallei 1710b 2 YP_334547.1, YP_337181.1 Rhodobacter sphaeroides ATCC 17029 2 YP_001042868.1, YP_001043384.1 Arthrobacter aurescens TC1 2 YP_946791.1, YP_948583.1 Corynebacterium jeikeium K411 2 YP_250037.1, YP_251523.1 Mycobacterium leprae TN 2 NP_301345.1, NP_301373.1 Mycobacterium avium 104 2 YP_883834.1, YP_883500.1 Prochlorococcus marinus str. MIT 9515 2 YP_001011929.1, YP_001010830.1 Synechococcus sp. CC9902 2 YP_376518.1, YP_377748.1 Rhodoferax ferrireducens T118 2 YP_522403.1, YP_524251.1 Azorhizobium caulinodans ORS 571 2 YP_001523340.1, YP_001525228.1 Corynebacterium diphtheriae NCTC 2 NP_940351.1, NP_938952.1

13129 Burkholderia pseudomallei K96243 2 YP_109293.1, YP_110499.1 Mycobacterium vanbaalenii PYR-1 2 YP_951608.1, YP_952333.1 Vibrio cholerae O395 2 YP_001218153.1, YP_001215255.1 Synechococcus sp. RCC307 2 YP_001228115.1, YP_001227513.1 Ralstonia eutropha JMP134 2 YP_296861.1, YP_299384.1 Methylibium petroleiphilum PM1 2 YP_001019625.1, YP_001020151.1 Salinispora arenicola CNS-205 2 YP_001535232.1, YP_001539003.1 Mycobacterium tuberculosis CDC1551 2 NP_334865.1, NP_338050.1 Opitutus terrae PB90-1 2 YP_001818937.1, YP_001818115.1 Chloroflexus aurantiacus J-10-fl 2 YP_001636330.1, YP_001636476.1 Myxococcus xanthus DK 1622 2 YP_633052.1, YP_632638.1 Corynebacterium glutamicum R 2 YP_001139535.1, YP_001137589.1 Synechococcus sp. CC9605 2 YP_382463.1, YP_380944.1 Burkholderia pseudomallei 668 2 YP_001060129.1, YP_001061737.1 Desulfotomaculum reducens MI-1 2 YP_001114202.1, YP_001113833.1 Rhodospirillum rubrum ATCC 11170 2 YP_425254.1, YP_425678.1 Mycobacterium bovis BCG str. Pasteur 2 YP_976577.1, YP_979566.1

1173P2 Mycobacterium gilvum PYR-GCK 2 YP_001131424.1, YP_001136178.1 Syntrophobacter fumaroxidans MPOB 2 YP_844259.1, YP_846461.1 Acidiphilium cryptum JF-5 2 YP_001235613.1, YP_001234506.1 Salmonella enterica subsp. enterica 1 YP_153200.1 serovar Paratyphi A str. ATCC

9150 Salmonella enterica subsp. enterica 1 YP_219196.1 serovar Choleraesuis str. SC-B67 Helicobacter hepaticus ATCC 51449 1 NP_860732.1 Escherichia coli str. K-12 substr. 1 YP_001732912.1

DH10B Streptococcus pyogenes MGAS9429 1 YP_597502.2 Exiguobacterium sibiricum 255-15 1 YP_001815231.1 Enterobacter sakazakii ATCC 1 YP_001436294.1

BAA-894 Leptothrix cholodnii SP-6 1 YP_001789523.1 Streptococcus pyogenes MGAS315 1 NP_665569.1 Escherichia coli UTI89 1 YP_543679.1 Prochlorococcus marinus str. MIT 1 YP_001483733.1

9215 Leifsonia xyli subsp. xyli str. CTCB07 1 YP_062649.1 Thermosipho melanesiensis BI429 1 YP_001305316.1 Brucella canis ATCC 23365 1 YP_001594160.1 Campylobacter jejuni subsp. doylei 1 YP_001397688.1

269.97 Candidatus Sulcia muelleri GWSS 1 YP_001597987.1 Leptospira borgpetersenii serovar 1 YP_801077.1

Hardjo-bovis JB197 Photobacterium profundum SS9 1 YP_131474.1 Buchnera aphidicola str. APS 1 NP_239860.1

(Acyrthosiphon pisum) Sulfurovum sp. NBC37-1 1 YP_001359264.1 Ochrobactrum anthropi ATCC 49188 1 YP_001371563.1 Mycobacterium abscessus 1 YP_001701402.1 Porphyromonas gingivalis W83 1 NP_904815.1 Parvibaculum lavamentivorans DS-1 1 YP_001411890.1 Petrotoga mobilis SJ95 1 YP_001568199.1 Staphylococcus aureus subsp. aureus 1 YP_186835.1 COL Yersinia pseudotuberculosis IP 31758 1 YP_001402629.1 Fervidobacterium nodosum Rt17-B1 1 YP_001411043.1 Staphylococcus aureus subsp. aureus JH1 1 YP_001317220.1 Staphylococcus aureus subsp. aureus 1 YP_041479.1

MRSA252 Caldicellulosiruptor saccharolyticus 1 YP_001180085.1

DSM 8903 Clostridium botulinum A str. ATCC 1 YP_001385616.1

19397 Streptococcus pneumoniae CGSP14 1 YP_001836598.1 Shewanella oneidensis MR-1 1 NP_716337.1 Geobacillus kaustophilus HTA426 1 YP_146102.1 Francisella tularensis subsp. tularensis 1 YP_001121346.1

WY96-3418 Polynucleobacter necessarius STIR1 1 YP_001798220.1 Bacillus licheniformis ATCC 1 YP_077851.1

14580 Lactococcus lactis subsp. lactis Il1403 1 NP_266550.1 Shigella flexneri 5 str. 8401 1 YP_691584.1 Methylobacterium radiotolerans JCM 1 YP_001753228.1

2831 Bartonella henselae str. Houston-1 1 YP_034075.1 Pseudomonas entomophila L48 1 YP_609927.1 Pseudomonas syringae pv. syringae 1 YP_237140.1

B728a Vibrio harveyi ATCC BAA-1116 1 YP_001443417.1 Campylobacter hominis ATCC BAA-381 1 YP_001406156.1 Candidatus Desulforudis audaxviator 1 YP_001718181.1

MP104C Erwinia carotovora subsp. atroseptica 1 YP_048741.1

SCRI1043 Bacillus subtilis subsp. subtilis str. 168 1 NP_388484.1 Agrobacterium tumefaciens str. C58 1 NP_353706.1 Yersinia pestis Nepal516 1 YP_649246.1 Mannheimia succiniciproducens 1 YP_087651.1

MBEL55E Magnetospirillum magneticum AMB-1 1 YP_419566.1 Tropheryma whipplei str. Twist 1 NP_787569.1 Onion yellows phytoplasma OY-M 1 NP_950373.1 Candidatus Desulforudis audaxviator 1 YP_001718130.1

MP104C Streptococcus pneumoniae TIGR4 1 NP_346336.1 Flavobacterium johnsoniae UW101 1 YP_001194193.1 Anaplasma marginale str. St. Maries 1 YP_154105.1 Francisella tularensis subsp. novicida 1 YP_899157.1

U112 Burkholderia mallei ATCC 23344 1 YP_103588.1 Neisseria meningitidis MC58 1 NP_274966.1 Citrobacter koseri ATCC BAA-895 1 YP_001455205.1 Xanthomonas campestris pv. vesicatoria 1 YP_362302.1 str. 85-10 Escherichia coli SMS-3-5 1 YP_001746539.1 Streptococcus pyogenes SSI-1 1 NP_803024.1 Mycoplasma genitalium G37 1 NP_073065.2 Neisseria meningitidis Z2491 1 NP_283296.1 Lactobacillus reuteri F275 1 YP_001270960.1 Leuconostoc mesenteroides subsp. 1 YP_819222.1 mesenteroides ATCC 8293 Psychrobacter sp. PRwf-1 1 YP_001279543.1 Clostridium botulinum A3 str. Loch 1 YP_001788614.1

Maree Pseudomonas aeruginosa PAO1 1 NP_253075.1 Bartonella tribocorum CIP 105476 1 YP_001610271.1 Bacteroides thetaiotaomicron VPI-5482 1 NP_810742.1 Haemophilus influenzae Rd KW20 1 NP_438701.1 Rickettsia felis URRWXCal2 1 YP_246425.1 Lactobacillus salivarius UCC118 1 YP_536102.1 Psychrobacter arcticus 273-4 1 YP_263848.1 Desulfovibrio vulgaris subsp. vulgaris 1 YP_011193.1 str. Hildenborough Haemophilus influenzae PittGG 1 YP_001292487.1 Bartonella quintana str. Toulouse 1 YP_032639.1 Clostridium novyi NT 1 YP_878933.1 Shewanella amazonensis SB2B 1 YP_928996.1 Xanthomonas axonopodis pv. citri str. 1 NP_640895.1

306 Xanthomonas campestris pv. campestris 1 YP_241636.1 str. 8004 Clostridium acetobutylicum ATCC 824 1 NP_349309.1 Burkholderia mallei SAVP1 1 YP_992252.1 Helicobacter pylori HPAG1 1 YP_626751.1 Francisella tularensis subsp. tularensis 1 YP_170601.1

SCHU S4 Marinobacter aquaeolei VT8 1 YP_959298.1 Thermus thermophilus HB27 1 YP_005683.1 Pelobacter propionicus DSM 2379 1 YP_902459.1 Escherichia coli W3110 1 AP_004644.1 Bacillus pumilus SAFR-032 1 YP_001485790.1 Staphylococcus aureus subsp. aureus str. 1 YP_001332971.1

Newman Nitrosococcus oceani ATCC 19707 1 YP_344897.1 Mycoplasma penetrans HF-2 1 NP_757486.1 Acidobacteria bacterium Ellin345 1 YP_590174.1 Streptococcus agalactiae NEM316 1 NP_736462.1 Psychrobacter cryohalolentis K5 1 YP_579808.1 Buchnera aphidicola str. Sg (Schizaphis 1 NP_660380.1 graminum) Maricaulis maris MCS10 1 YP_755835.1 Leptospira interrogans serovar 1 YP_001299.1

Copenhageni str. Fiocruz L1-130 Enterobacter sp. 638 1 YP_001175069.1 Thermoanaerobacter tengcongensis 1 NP_622247.1

MB4 Streptococcus thermophilus LMG 18311 1 YP_138744.1 Treponema pallidum subsp. pallidum str. 1 NP_218470.1

Nichols Caulobacter crescentus CB15 1 NP_419502.1 Clostridium kluyveri DSM 555 1 YP_001393866.1 Streptococcus pyogenes str. Manfredo 1 YP_001129237.1 Polaromonas sp. JS666 1 YP_547613.1 Streptococcus thermophilus CNRZ1066 1 YP_140633.1 Staphylococcus aureus subsp. aureus 1 YP_494633.1

USA300 Lawsonia intracellularis PHE/MN1-00 1 YP_595000.1 Clostridium botulinum A str. ATCC 3502 1 YP_001255782.1 Staphylococcus aureus subsp. aureus JH9 1 YP_001247425.1 Actinobacillus pleuropneumoniae 1 YP_001652030.1 serovar 3 str. JL03 Sorangium cellulosum 'So ce 56' 1 YP_001616555.1 Solibacter usitatus Ellin6076 1 YP_827953.1 Wolbachia endosymbiont strain TRS of 1 YP_198181.1

Brugia malayi Lactobacillus helveticus DPC 4571 1 YP_001576925.1 Rickettsia typhi str. Wilmington 1 YP_067563.1 Actinobacillus pleuropneumoniae L20 1 YP_001053711.1 Pseudomonas fluorescens Pf-5 1 YP_261919.1 Candidatus Vesicomyosocius okutanii 1 YP_001219359.1

HA Finegoldia magna ATCC 29328 1 YP_001692194.1 Bacillus anthracis str. Ames 1 NP_842820.1 Clostridium botulinum B str. Eklund 17B 1 YP_001884621.1 Helicobacter acinonychis str. Sheeba 1 YP_665399.1 Shewanella halifaxensis HAW-EB4 1 YP_001675975.1 Burkholderia mallei NCTC 10229 1 YP_001028694.1 Pseudomonas aeruginosa UCBPP-PA14 1 YP_792731.1 Rickettsia bellii RML369-C 1 YP_537760.1 Thermotoga lettingae TMO 1 YP_001469949.1 Pseudomonas putida F1 1 YP_001269670.1 Francisella tularensis subsp. holarctica 1 YP_514345.1 Lactobacillus gasseri ATCC 33323 1 YP_814252.1 Streptococcus pyogenes MGAS6180 1 YP_281212.2 Xylella fastidiosa Temecula1 1 NP_779731.1 Pseudomonas putida W619 1 YP_001747842.1 Methylobacillus flagellatus KT 1 YP_544476.1 Yersinia pestis Antiqua 1 YP_653837.1 Lactobacillus casei ATCC 334 1 YP_807425.1 Legionella pneumophila subsp. 1 YP_094724.1 pneumophila str. Philadelphia 1 Delftia acidovorans SPH-1 1 YP_001566674.1 Clostridium botulinum B1 str. Okra 1 YP_001782921.1 Desulfotalea psychrophila LSv54 1 YP_063926.1 Pseudoalteromonas atlantica T6c 1 YP_663309.1 Francisella tularensis subsp. tularensis 1 YP_667734.1

FSC198 Pseudomonas fluorescens PfO-1 1 YP_350229.1 Staphylococcus aureus subsp. aureus 1 YP_001575900.1

USA300_TCH1516 Helicobacter pylori J99 1 NP_222730.1 Serratia proteamaculans 568 1 YP_001476645.1 Staphylococcus aureus RF122 1 YP_417372.1 Bacteroides vulgatus ATCC 8482 1 YP_001297686.1 Pasteurella multocida subsp. multocida 1 NP_246044.1 str. Pm70 Candidatus Blochmannia floridanus 1 NP_878382.1 Streptococcus pyogenes MGAS2096 1 YP_601391.2 Shigella flexneri 2a str. 2457T 1 NP_839689.1 Acinetobacter sp. ADP1 1 YP_047391.1 Yersinia pestis CO92 1 NP_403999.1 Legionella pneumophila str. Corby 1 YP_001251867.1 Clostridium thermocellum ATCC 27405 1 YP_001039283.1 Listeria monocytogenes EGD-e 1 NP_465592.1 Bordetella avium 197N 1 YP_785112.1 Alkaliphilus metalliredigens QYMF 1 YP_001318718.1 Alkalilimnicola ehrlichei MLHE-1 1 YP_740868.1 Yersinia pseudotuberculosis IP 32953 1 YP_068948.1 Yersinia pestis biovar Microtus str. 91001 1 NP_991899.1 Lactobacillus plantarum WCFS1 1 NP_784483.1 Rickettsia rickettsii str. 'Sheila Smith' 1 YP_001495063.1 Rubrobacter xylanophilus DSM 9941 1 YP_643594.1 Chlamydia trachomatis L2b/UCH- 1 YP_001653461.1

1/proctitis Streptococcus pyogenes M1 GAS 1 NP_270006.1 Ehrlichia chaffeensis str. Arkansas 1 YP_507185.1 Haemophilus somnus 129PT 1 YP_718679.1 Salmonella enterica subsp. enterica 1 NP_458769.1 serovar Typhi str. CT18 Brucella melitensis biovar Abortus 2308 1 YP_418418.1 Geobacter metallireducens GS-15 1 YP_383004.1 Shigella dysenteriae Sd197 1 YP_405822.1 Parabacteroides distasonis ATCC 8503 1 YP_001305096.1 Haemophilus somnus 2336 1 YP_001784105.1 Bacillus amyloliquefaciens FZB42 1 YP_001420264.1 Pseudomonas putida KT2440 1 NP_743520.1 Bacillus halodurans C-125 1 NP_241428.1 Campylobacter jejuni RM1221 1 YP_179343.1 Colwellia psychrerythraea 34H 1 YP_267706.1 Candidatus Carsonella ruddii PV 1 YP_802448.1 Baumannia cicadellinicola str. Hc 1 YP_589019.1

(Homalodisca coagulata) Orientia tsutsugamushi Boryong 1 YP_001248602.1 Shigella boydii CDC 3083-94 1 YP_001882834.1 Staphylococcus aureus subsp. aureus 1 NP_375137.1

N315 Sphingomonas wittichii RW1 1 YP_001263860.1 Borrelia burgdorferi B31 1 NP_212783.1 Xylella fastidiosa M12 1 YP_001776227.1 Janthinobacterium sp. Marseille 1 YP_001354342.1 Bacillus licheniformis ATCC 14580 1 YP_090259.1 Yersinia pestis Angola 1 YP_001605299.1 Shigella boydii Sb227 1 YP_410558.1 Beijerinckia indica subsp. indica ATCC 1 YP_001834439.1

9039 Herpetosiphon aurantiacus ATCC 23779 1 YP_001546443.1 Streptococcus mutans UA159 1 NP_722255.1 Escherichia coli 536 1 YP_672232.1 Bacillus thuringiensis serovar konkukian 1 YP_034593.1 str. 97-27 Pseudomonas putida GB-1 1 YP_001670710.1 Nitrosomonas europaea ATCC 19718 1 NP_840129.1 Streptococcus pneumoniae Hungary19A- 1 YP_001695268.1

6 Shewanella sp. W3-18-1 1 YP_964835.1 Polynucleobacter sp. QLW-P1DMWA-1 1 YP_001156582.1 Streptococcus gordonii str. Challis 1 YP_001451151.1 substr. CH1 Buchnera aphidicola str. Cc (Cinara 1 YP_802589.1 cedri) Rickettsia akari str. Hartford 1 YP_001493749.1 Lactobacillus sakei subsp. sakei 23K 1 YP_394972.1 Bacillus cereus E33L 1 YP_081854.1 Yersinia enterocolitica subsp. 1 YP_001004730.1 enterocolitica 8081 Haemophilus influenzae PittEE 1 YP_001289936.1 Anaplasma phagocytophilum HZ 1 YP_504857.1 Hyphomonas neptunium ATCC 15444 1 YP_760663.1 Dehalococcoides sp. BAV1 1 YP_001214693.1 Rhodobacter sphaeroides ATCC 17025 1 YP_001168384.1 Pseudoalteromonas haloplanktis TAC125 1 YP_338801.1 Thermotoga petrophila RKU-1 1 YP_001244015.1 Chlorobium chlorochromatii CaD3 1 YP_379609.1 Clostridium phytofermentans ISDg 1 YP_001560382.1 Salmonella enterica subsp. 1 YP_001572277.1 arizonae serovar 62:z4,z23:-- Staphylococcus saprophyticus subsp. 1 YP_300938.1 saprophyticus ATCC 15305 Acholeplasma laidlawii PG-8A 1 YP_001621222.1 Gramella forsetii KT0803 1 YP_863601.1 Treponema denticola ATCC 35405 1 NP_971783.1 Prochlorococcus marinus str. MIT 1 YP_001550335.1

9211 Campylobacter curvus 525.92 1 YP_001408485.1 Streptococcus pyogenes MGAS10270 1 YP_599438.2 Carboxydothermus hydrogenoformans Z- 1 YP_359661.1

2901 Silicibacter sp. TM1040 1 YP_612592.1 Rickettsia rickettsii str. Iowa 1 YP_001650336.1 Bordetella bronchiseptica RB50 1 NP_887510.1 Leptospira interrogans serovar Lai str. 1 NP_712836.1

56601 Bacteroides fragilis NCTC 9343 1 YP_212835.1 Campylobacter jejuni subsp. jejuni 81116 1 YP_001482740.1 Listeria welshimeri serovar 6b str. 1 YP_850286.1

SLCC5334 Symbiobacterium thermophilum IAM 1 YP_076724.1

14863 Dehalococcoides sp. CBDB1 1 YP_308352.1 Sulfurimonas denitrificans DSM 1251 1 YP_393145.1 Staphylococcus epidermidis RP62A 1 YP_189050.1 Escherichia coli E24377A 1 YP_001465641.1 Gluconobacter oxydans 621H 1 YP_192296.1 Xylella fastidiosa 9a5c 1 NP_297905.1 Pediococcus pentosaceus ATCC 25745 1 YP_803959.1 Brucella ovis ATCC 25840 1 YP_001257246.1 Bacillus clausii KSM-K16 1 YP_174382.1 Borrelia afzelii PKo 1 YP_710100.1 Prochlorococcus marinus str. MIT 1 YP_001484903.1

9215 Oenococcus oeni PSU-1 1 YP_810923.1 Granulibacter bethesdensis CGDNIH1 1 YP_746001.1 Salmonella enterica subsp. enterica 1 NP_807973.1 serovar Typhi Ty2 Escherichia coli HS 1 YP_001460926.1 Desulfococcus oleovorans Hxd3 1 YP_001528437.1 Haemophilus ducreyi 35000HP 1 NP_874147.1 Pelobacter carbinolicus DSM 2380 1 YP_358175.1 Ralstonia metallidurans CH34 1 YP_582771.1 Desulfovibrio vulgaris subsp. vulgaris 1 YP_966643.1

DP4 Geobacillus thermodenitrificans NG80-2 1 YP_001124352.1 Xanthomonas oryzae pv. oryzae MAFF 1 YP_453072.1

311018 Alkaliphilus oremlandii OhILAs 1 YP_001513975.1 Streptococcus pyogenes MGAS5005 1 YP_283124.1 Clavibacter michiganensis subsp. 1 YP_001223222.1 michiganensis NCPPB 382 Neisseria meningitidis 053442 1 YP_001598403.1 Shewanella pealeana ATCC 700345 1 YP_001503535.1 Staphylococcus epidermidis ATCC 1 NP_765184.1

12228 Clostridium perfringens ATCC 13124 1 YP_696963.1 Francisella tularensis subsp. holarctica 1 YP_001429247.2

FTNF002-00 Oceanobacillus iheyensis HTE831 1 NP_691577.1 Clostridium beijerinckii NCIMB 8052 1 YP_001307473.1 Streptococcus agalactiae A909 1 YP_330603.1 Desulfitobacterium hafniense Y51 1 YP_520193.1 Lysinibacillus sphaericus C3-41 1 YP_001695899.1 Escherichia coli ATCC 8739 1 YP_001726800.1 Pseudomonas mendocina ymp 1 YP_001189168.1 Acidovorax avenae subsp. citrulli 1 YP_969317.1

AAC00-1 Nitrosospira multiformis ATCC 25196 1 YP_413027.1 Prochlorococcus marinus str. MIT 1 YP_001551440.1

9211 Carboxydothermus hydrogenoformans 1 YP_359274.1

Z-2901 Beijerinckia indica subsp. indica ATCC 1 YP_001832857.1

9039 Cytophaga hutchinsonii ATCC 33406 1 YP_678437.1 Staphylococcus aureus subsp. aureus 1 YP_044045.1

MSSA476 Shewanella sp. MR-7 1 YP_736615.1 Dehalococcoides ethenogenes 195 1 YP_182136.1 Lactobacillus johnsonii NCC 533 1 NP_964487.1 Bdellovibrio bacteriovorus HD100 1 NP_967123.1 Haemophilus influenzae 86-028NP 1 YP_248252.1 Prosthecochloris vibrioformis DSM 265 1 YP_001130110.1 Bacillus weihenstephanensis KBAB4 1 YP_001643142.1 Cyanothece sp. ATCC 51142 1 YP_001804744.1 Salmonella enterica subsp. 1 YP_001591564.1 enterica serovar Paratyphi B str. SPB7 Bacillus anthracis str. 'Ames Ancestor' 1 YP_016876.1 Bacillus cereus ATCC 14579 1 NP_830146.1 Escherichia coli CFT073 1 NP_757075.1 Geobacter sulfurreducens PCA 1 NP_954380.1 Streptococcus agalactiae 2603V/R 1 NP_689060.1 Candidatus Protochlamydia amoebophila 1 YP_008179.1

UWE25 Borrelia garinii PBi 1 YP_073092.1 Thermus thermophilus HB8 1 YP_143537.1 Staphylococcus aureus subsp. aureus 1 YP_500736.1

NCTC 8325 Candidatus Ruthia magnifica str. Cm 1 YP_903785.1 (Calyptogena magnifica) Dichelobacter nodosus VCS1703A 1 YP_001210205.1 Legionella pneumophila str. Lens 1 YP_126086.1 Arcobacter butzleri RM4018 1 YP_001489376.1 Clostridium botulinum F str. Langeland 1 YP_001392643.1 Acinetobacter baumannii ATCC 17978 1 YP_001085682.1 Clavibacter michiganensis subsp. 1 YP_001711394.1 sepedonicus Bacteroides fragilis YCH46 1 YP_100673.1 Pseudomonas syringae pv. tomato str. 1 NP_794131.1

DC3000 Thermoanaerobacter sp. X514 1 YP_001662157.1 Xylella fastidiosa M23 1 YP_001830305.1 Aeromonas salmonicida subsp. 1 YP_001143150.1 salmonicida A449 Lactococcus lactis subsp. cremoris 1 YP_001031761.1

MG1363 Escherichia coli O157:H7 EDL933 1 NP_290776.1 Caulobacter sp. K31 1 YP_001685772.1 Dechloromonas aromatica RCB 1 YP_283653.1 Bordetella parapertussis 12822 1 NP_883195.1 Shewanella baltica OS185 1 YP_001364869.1 Bacillus cereus subsp. cytotoxis NVH 1 YP_001373613.1

391-98 Buchnera aphidicola str. Bp (Baizongia 1 NP_777659.1 pistaciae) Aeromonas hydrophila subsp. hydrophila 1 YP_855402.1

ATCC 7966 Shewanella denitrificans OS217 1 YP_561438.1 Acidovorax sp. JS42 1 YP_985019.1 Brucella abortus biovar 1 str. 9-941 1 YP_222995.1 Desulfovibrio desulfuricans G20 1 YP_388965.1 Coxiella burnetii RSA 331 1 YP_001597541.1 Lactobacillus delbrueckii subsp. 1 YP_619403.1 bulgaricus ATCC 11842 Chlorobium phaeobacteroides DSM 266 1 YP_912376.1 Mycobacterium abscessus 1 YP_001704459.1 Clostridium tetani E88 1 NP_782944.2 Bacillus anthracis str. Sterne 1 YP_026537.1 Aster yellows witches'-broom 1 YP_456796.1 phytoplasma AYWB Shewanella putrefaciens CN-32 1 YP_001182230.1 Leptospira biflexa serovar Patoc 1 YP_001839711.1 strain 'Patoc 1 (Paris)' Enterococcus faecalis V583 1 NP_816272.1 Silicibacter pomeroyi DSS-3 1 YP_166140.1 Listeria innocua Clip11262 1 NP_471507.1 Geobacter uraniireducens Rf4 1 YP_001233023.1 Helicobacter pylori 26695 1 NP_206812.1 Pseudomonas syringae pv. phaseolicola 1 YP_276203.1

1448A Saccharophagus degradans 2-40 1 YP_526358.1 Xanthomonas oryzae pv. oryzae 1 YP_202927.1

KACC10331 Shewanella sp. MR-4 1 YP_735520.1 Rickettsia conorii str. Malish 7 1 NP_360605.1 Neisseria meningitidis FAM18 1 YP_975876.1 Klebsiella pneumoniae subsp. 1 YP_001338154.1 pneumoniae MGH 78578 Bifidobacterium adolescentis ATCC 1 YP_909428.1

15703 Wigglesworthia glossinidia 1 NP_871261.1 endosymbiont of Glossina brevipalpis Campylobacter fetus subsp. fetus 82-40 1 YP_891876.1 Chromohalobacter salexigens DSM 3043 1 YP_574210.1 Lactococcus lactis subsp. cremoris SK11 1 YP_808466.1 Sorangium cellulosum 'So ce 56' 1 YP_001613420.1 Fusobacterium nucleatum subsp. 1 NP_603572.1 nucleatum ATCC 25586 Streptococcus thermophilus LMD-9 1 YP_819765.1 Brucella melitensis 16M 1 NP_542026.1 Syntrophomonas wolfei subsp. wolfei 1 YP_754524.1 str. Goettingen Shewanella woodyi ATCC 51908 1 YP_001762657.1 Staphylococcus aureus subsp. aureus 1 NP_646770.1

MW2 Azoarcus sp. EbN1 1 YP_157650.1 Xanthomonas campestris pv. campestris 1 NP_635915.1 str. ATCC 33913 Photorhabdus luminescens subsp. 1 NP_931324.1 laumondii TTO1 Aquifex aeolicus VF5 1 NP_214512.1 Novosphingobium aromaticivorans DSM 1 YP_495318.1

12444 Shewanella sediminis HAW-EB3 1 YP_001472382.1 Shigella flexneri 2a str. 301 1 NP_710008.1 Candidatus Pelagibacter ubique 1 YP_265587.1

HTCC1062 Bacillus thuringiensis str. Al Hakam 1 YP_893164.1 Halorhodospira halophila SL1 1 YP_001003906.1 Wolbachia endosymbiont of Drosophila 1 NP_966107.1 melanogaster Idiomarina loihiensis L2TR 1 YP_156661.1 Bordetella pertussis Tohama I 1 NP_882014.1 Listeria monocytogenes str. 4b F2365 1 YP_014692.1 Vibrio fischeri ES114 1 YP_203588.1 Jannaschia sp. CCS1 1 YP_511300.1 Wolinella succinogenes DSM 1740 1 NP_906559.1 Lactobacillus fermentum IFO 3956 1 YP_001843142.1 Tropheryma whipplei TW08/27 1 NP_789261.1 Francisella philomiragia subsp. 1 YP_001677824.1 philomiragia ATCC 25017 Neorickettsia sennetsu str. Miyayama 1 YP_506520.1 Yersinia pestis KIM 1 NP_667946.1 Zymomonas mobilis subsp. mobilis ZM4 1 YP_163664.1 Magnetococcus sp. MC-1 1 YP_864228.1 Lactobacillus acidophilus NCFM 1 YP_193328.1 Thiomicrospira crunogena XCL-2 1 YP_390616.1 Streptococcus pneumoniae D39 1 YP_817135.1 Bartonella bacilliformis KC583 1 YP_989430.1 Ralstonia solanacearum GMI1000 1 NP_518763.1 Francisella tularensis subsp. 1 YP_001891089.1 mediasiatica FSC147 Rickettsia massiliae MTU5 1 YP_001499598.1 Leuconostoc citreum KM20 1 YP_001728706.1 Thermotoga maritima MSB8 1 NP_228316.1 Campylobacter concisus 13826 1 YP_001466610.1 Chlorobium tepidum TLS 1 NP_661430.1 Nitratiruptor sp. SB155-2 1 YP_001355980.1 Pseudomonas aeruginosa PA7 1 YP_001350292.1 Brucella suis ATCC 23445 1 YP_001622038.1 Escherichia coli str. K-12 substr. 1 NP_418567.1

MG1655 Escherichia coli O157:H7 str. Sakai 1 NP_313151.1 Thiobacillus denitrificans ATCC 1 YP_313849.1

25259 Burkholderia mallei NCTC 10247 1 YP_001081400.1 Streptococcus pyogenes MGAS10750 1 YP_603349.2 Shewanella baltica OS155 1 YP_001052051.1 Rickettsia prowazekii str. Madrid E 1 NP_220991.1 Shewanella frigidimarina NCIMB 400 1 YP_752326.1 Ehrlichia canis str. Jake 1 YP_303279.1 Staphylococcus aureus subsp. aureus 1 NP_372553.1

Mu50 Rickettsia canadensis str. McKiel 1 YP_001492054.1 Candidatus Blochmannia pennsylvanicus 1 YP_277589.1 str. BPEN Pseudomonas stutzeri A1501 1 YP_001173625.1 Streptococcus pyogenes MGAS8232 1 NP_608082.1 Staphylococcus aureus subsp. aureus 1 YP_001442604.1

Mu3 Campylobacter jejuni subsp. jejuni 1 NP_282368.1

NCTC 11168 Lactobacillus brevis ATCC 367 1 YP_794794.1 Shewanella sp. ANA-3 1 YP_871195.1 Actinobacillus succinogenes 130Z 1 YP_001343970.1 Deinococcus radiodurans R1 1 NP_294330.1 Thermoanaerobacter pseudethanolicus 1 YP_001665694.1

ATCC 33223 Shigella sonnei Ss046 1 YP_313050.1 Streptococcus pneumoniae R6 1 NP_359314.1 Campylobacter jejuni subsp. jejuni 81- 1 YP_001000895.1

176 Rickettsia bellii OSU 85-389 1 YP_001496071.1 Yersinia pestis Pestoides F 1 YP_001164945.1 Francisella tularensis subsp. holarctica 1 YP_764064.1

OSU18 Yersinia pseudotuberculosis YPIII 1 YP_001722541.1 Bifidobacterium longum NCC2705 1 NP_695233.1 Lactobacillus delbrueckii subsp. 1 YP_813427.1 bulgaricus ATCC BAA-365 Salmonella typhimurium LT2 1 NP_463194.1 Deinococcus geothermalis DSM 11300 1 YP_605694.1 Mycoplasma gallisepticum R 1 NP_853259.2 Clostridium botulinum A str. Hall 1 YP_001389022.1 Leptospira borgpetersenii serovar 1 YP_797549.1

Hardjo-bovis L550 Coxiella burnetii Dugway 5J108-111 1 YP_001423710.1 Sodalis glossinidius str. 'morsitans' 1 YP_453986.1 Streptococcus pyogenes MGAS10394 1 YP_061078.2 Brucella suis 1330 1 NP_699396.1 Neisseria gonorrhoeae FA 1090 1 YP_209108.1 Clostridium perfringens str. 13 1 NP_563205.1 Coxiella burnetii RSA 493 1 NP_820699.1 Nitrosomonas eutropha C91 1 YP_746457.1 Ehrlichia ruminantium str. Gardel 1 YP_196590.1 Dinoroseobacter shibae DFL 12 1 YP_001534253.1 Pelodictyon luteolum DSM 273 1 YP_374469.1 Staphylococcus haemolyticus JCSC1435 1 YP_252917.1 Mycoplasma pneumoniae M129 1 NP_110262.1 Legionella pneumophila str. Paris 1 YP_123081.1 Clostridium difficile 630 1 YP_001086664.1 Marinomonas sp. MWYL1 1 YP_001340894.1 Bordetella petrii DSM 12804 1 YP_001632546.1 Alcanivorax borkumensis SK2 1 YP_692354.1 Hahella chejuensis KCTC 2396 1 YP_435739.1 Herminiimonas arsenicoxydans 1 YP_001100795.1 Shewanella loihica PV-4 1 YP_001092603.1 Flavobacterium psychrophilum JIP02/86 1 YP_001296851.1 Shewanella baltica OS195 1 YP_001553110.1 Streptococcus sanguinis SK36 1 YP_001034236.1 235 Supplementary Table 3: Sequences used to build the GroEL phylogeny. “No.” refers to the

number of GroEL sequences in each genome.

Annotation Accession number Hsp60 [Methanosarcina acetivorans C2A] NP_619248.1 Hsp60 [Methanosarcina acetivorans C2A] NP_615816.1 chaperonin Cpn60/TCP-1 [Methanococcoides burtonii DSM 6242] YP_565663.1 thermosome subunit [Methanosarcina barkeri str. Fusaro] YP_306635.1 thermosome subunit [Methanosarcina mazei Go1] NP_632096.1 Hsp60 [Methanosarcina acetivorans C2A] NP_616609.1 ThsA [Methanosphaera stadtmanae DSM 3091] YP_447191.1 thermosome subunit [Haloquadratum walsbyi DSM 16790] YP_656951.1 thermosome subunit 3 [Natronomonas pharaonis DSM 2160] YP_326251.1 thermosome alpha subunit [Haloarcula marismortui ATCC 43049] YP_136410.1 hypothetical protein Mlab_0771 [Methanocorpusculum labreanum Z] YP_001030209.1 chaperonin Cpn60/TCP-1 [Methanospirillum hungatei JF-1] YP_502441.1 chaperonin Cpn60/TCP-1 [Methanoculleus marisnigri JR1] YP_001046187.1 chaperonin Cpn60/TCP-1 [Candidatus Methanosphaerula palustris E1-9c] YP_002467686.1 chaperonin Cpn60/TCP-1 [Candidatus Methanoregula boonei 6A8] YP_001405552.1 chaperonin Cpn60/TCP-1 [Candidatus Methanoregula boonei 6A8] YP_001403485.1 chaperonin Hsp60 (GroEL-like) [uncultured methanogenic archaeon RC-I] YP_684559.1 thermosome [Nitrosopumilus maritimus SCM1] YP_001583126.1 chaperonin GroEL (HSP60 family) [Cenarchaeum symbiosum A] YP_876765.1 thermosome [Nitrosopumilus maritimus SCM1] YP_001582911.1 chaperonin GroEL (HSP60 family) [Cenarchaeum symbiosum A] YP_876909.1 chaperonin GroEL [Candidatus Korarchaeum cryptofilum OPF8] YP_001737932.1 thermosome subunit gamma [Sulfolobus solfataricus P2] NP_344314.1 thermosome [Sulfolobus islandicus L.S.2.15] YP_002833127.1 thermosome [Sulfolobus islandicus M.16.4] YP_002915628.1 thermosome [Sulfolobus islandicus M.16.27] YP_002844331.1 thermosome [Sulfolobus islandicus M.14.25] YP_002830382.1 thermosome [Methanosaeta thermophila PT] YP_843163.1 thermosome [Candidatus Korarchaeum cryptofilum OPF8] YP_001737738.1 thermosome gamma subunit [Sulfolobus acidocaldarius DSM 639] YP_255843.1 hypothetical protein ST0820 [Sulfolobus tokodaii str. 7] NP_376724.1 thermosome beta subunit [Haloarcula marismortui ATCC 43049] YP_137380.1 thermosome subunit 2 (beta subunit) [Natronomonas pharaonis DSM 2160] YP_325945.1 thermosome subunit 2 [Halobacterium salinarum R1] YP_001689883.1 CctB [Halobacterium sp. NRC-1] NP_280760.1 thermosome [Halorubrum lacusprofundi ATCC 49239] YP_002565089.1 thermosome, beta subunit [Haloquadratum walsbyi DSM 16790] YP_657160.1 thermosome subunit [Picrophilus torridus DSM 9790] YP_023973.1 chaperonin GroEL [Thermoplasma volcanium GSS1] NP_111026.1 thermosome beta chain [Thermoplasma acidophilum DSM 1728] NP_394733.1 thermosome subunit [Picrophilus torridus DSM 9790] YP_023513.1 chaperonin GroEL [Thermoplasma volcanium GSS1] NP_111647.1 thermosome, alpha chain [Thermoplasma acidophilum DSM 1728] NP_394440.1 thermosome alpha subunit [Sulfolobus acidocaldarius DSM 639] YP_256024.1 thermosome, alpha subunit [Sulfolobus tokodaii str. 7] NP_377184.1 thermosome [Metallosphaera sedula DSM 5348] YP_001191789.1 thermosome subunit alpha [Sulfolobus solfataricus P2] NP_342362.1 thermosome [Sulfolobus islandicus Y.N.15.51] YP_002840521.1 thermosome [Sulfolobus islandicus M.14.25] YP_002829404.1 thermosome [Sulfolobus islandicus L.S.2.15] YP_002832092.1 thermosome alpha subunit [Hyperthermus butylicus DSM 5456] YP_001013111.1 Thermosome subunit alpha [Desulfurococcus kamchatkensis 1221n] YP_002428726.1 thermosome subunit [Staphylothermus marinus F1] YP_001041268.1 thermosome alpha subunit [Aeropyrum pernix K1] NP_147591.2 thermosome [Ignicoccus hospitalis KIN4/I] YP_001434687.1 thermosome [Thermofilum pendens Hrk 5] YP_919704.1 thermosome [Caldivirga maquilingensis IC-167] YP_001539851.1 thermosome [Pyrobaculum arsenaticum DSM 13514] YP_001153907.1 thermosome [Thermoproteus neutrophilus V24Sta] YP_001794895.1 thermosome [Pyrobaculum islandicum DSM 4184] YP_930022.1 thermosome subunit [Pyrobaculum calidifontis JCM 11548] YP_001056654.1 thermosome (chaperonin) beta subunit [Pyrobaculum aerophilum str. IM2] NP_560621.1 chaperonin Hsp60 (GroEL-like) [uncultured methanogenic archaeon RC-I] YP_686560.1 thermosome [Methanosaeta thermophila PT] YP_843344.1 thermosome subunit alpha [Methanobrevibacter smithii ATCC 35061] YP_001272793.1 thermosome beta subunit [Aeropyrum pernix K1] NP_148364.2 thermosome [Metallosphaera sedula DSM 5348] YP_001192326.1 thermosome [Sulfolobus islandicus M.14.25] YP_002829892.1 thermosome subunit beta [Sulfolobus solfataricus P2] NP_341830.1 thermosome beta subunit [Sulfolobus acidocaldarius DSM 639] YP_255343.1 thermosome, beta subunit [Sulfolobus tokodaii str. 7] NP_376188.1 thermosome [Ignicoccus hospitalis KIN4/I] YP_001435484.1 thermosome beta subunit [Hyperthermus butylicus DSM 5456] YP_001012688.1 Thermosome subunit beta [Desulfurococcus kamchatkensis 1221n] YP_002428954.1 thermosome subunit [Staphylothermus marinus F1] YP_001040915.1 thermosome [Thermofilum pendens Hrk 5] YP_920098.1 thermosome [Caldivirga maquilingensis IC-167] YP_001539871.1 thermosome [Thermoproteus neutrophilus V24Sta] YP_001794696.1 thermosome [Pyrobaculum islandicum DSM 4184] YP_930477.1 thermosome (chaperonin) alpha subunit [Pyrobaculum aerophilum str. IM2] NP_559775.1 thermosome [Pyrobaculum arsenaticum DSM 13514] YP_001154333.1 thermosome subunit [Pyrobaculum calidifontis JCM 11548] YP_001055943.1 thermosome subunit 1 [Halobacterium salinarum R1] YP_001689997.1 CctA [Halobacterium sp. NRC-1] NP_280871.1 thermosome alpha subunit [Haloarcula marismortui ATCC 43049] YP_137342.1 thermosome subunit 1 (alpha subunit) [Natronomonas pharaonis DSM 2160] YP_326163.1 thermosome [Halorubrum lacusprofundi ATCC 49239] YP_002567303.1 thermosome, alpha subunit [Haloquadratum walsbyi DSM 16790] YP_658748.1 hypothetical protein NEQ141 [Nanoarchaeum equitans Kin4-M] NP_963436.1 thermosome, subunit alpha (thsA) [Archaeoglobus fulgidus DSM 4304] NP_071063.1 thermosome, subunit beta (thsB) [Archaeoglobus fulgidus DSM 4304] NP_070280.1 Thermosome alpha subunit [Thermococcus sibiricus MM 739] YP_002995148.1 Thermosome alpha subunit (Thermosome subunit 1) (Chaperonin alpha YP_002958525.1 subunit) (thsA) [Thermococcus gammatolerans EJ3] chaperonin beta subunit [Thermococcus kodakarensis KOD1] YP_184716.1 chaperonin beta subunit [Thermococcus onnurineus NA1] YP_002308265.1 thermosome, single subunit [Pyrococcus furiosus DSM 3638] NP_579703.1 thermosome, subunit alpha [Pyrococcus abyssi GE5] NP_125709.1 thermosome subunit alpha [Pyrococcus horikoshii OT3] NP_142040.1 Thermosome beta subunit [Thermococcus sibiricus MM 739] YP_002994938.1 chaperonin, alpha subunit [Thermococcus onnurineus NA1] YP_002307092.1 chaperonin, alpha subunit [Thermococcus kodakarensis KOD1] YP_183091.1 Thermosome alpha subunit (Thermosome subunit 1) (Chaperonin alpha YP_002959378.1 subunit) (thsA) [Thermococcus gammatolerans EJ3] thermosome (ths) [Methanocaldococcus jannaschii DSM 2661] NP_247993.1 thermosome [Methanococcus aeolicus Nankai-3] YP_001325213.1 thermosome [Methanococcus vannielii SB] YP_001323346.1 chaperonin GroEL [Methanococcus maripaludis S2] NP_988635.1 thermosome [Methanococcus maripaludis C5] YP_001096592.1 thermosome [Methanococcus maripaludis C6] YP_001549202.1 thermosome [Methanococcus maripaludis C7] YP_001329979.1 HSP60 family chaperonin [Methanopyrus kandleri AV19] NP_614289.1 chaperonin [Methanothermobacter thermautotrophicus str. Delta H] NP_275361.1 ThsB [Methanosphaera stadtmanae DSM 3091] YP_447176.1 thermosome [Methanobrevibacter smithii ATCC 35061] YP_001273399.1 chaperonin [Methanothermobacter thermautotrophicus str. Delta H] NP_275933.1 thermosome subunit, group II chaperonin [Methanococcoides burtonii DSM YP_566590.1

6242] Hsp60 [Methanosarcina barkeri str. Fusaro] YP_304632.1 thermosome, alpha subunit [Methanosarcina mazei Go1] NP_633120.1 Hsp60 [Methanosarcina acetivorans C2A] NP_619275.1 thermosome, chaperonin Cpn60/TCP-1 [Methanococcoides burtonii DSM YP_566766.1

6242] Hsp60 [Methanosarcina barkeri str. Fusaro] YP_304748.1 thermosome, alpha subunit [Methanosarcina mazei Go1] NP_633403.1 Hsp60 [Methanosarcina acetivorans C2A] NP_615060.1 thermosome [Candidatus Methanoregula boonei 6A8] YP_001403480.1 ABC-type nitrate/sulfonate/bicarbonate transport systems periplasmic YP_001029649.1

components-like protein [Methanocorpusculum labreanum Z] thermosome [Methanoculleus marisnigri JR1] YP_001048251.1 thermosome [Methanospirillum hungatei JF-1] YP_503967.1 thermosome [Candidatus Methanosphaerula palustris E1-9c] YP_002465151.1 thermosome [Candidatus Methanoregula boonei 6A8] YP_001403365.1 thermosome [Methanosaeta thermophila PT] YP_843199.1 chaperonin Hsp60 (GroEL-like) [uncultured methanogenic archaeon RC-I] YP_687546.1 chaperonin Hsp60 (GroEL-like) [uncultured methanogenic archaeon RC-I] YP_686459.1 chaperonin Cpn60/TCP-1 [Halorubrum lacusprofundi ATCC 49239] YP_002566930.1 thermosome subunit 4 [Natronomonas pharaonis DSM 2160] YP_327729.1 thermosome alpha subunit [Haloarcula marismortui ATCC 43049] YP_134485.1 thermosome-like protein [Gloeobacter violaceus] NP_926694.1 thermosome, alpha subunit [Carboxydothermus hydrogenoformans Z-2901] YP_359274.1 thermosome subunit [Heliobacterium modesticaldum Ice1] YP_001680996.1 chaperonin Cpn60/TCP-1 [Candidatus Desulforudis audaxviator MP104C] YP_001718181.1 chaperonin GroEL [Pelotomaculum thermopropionicum SI] YP_001211426.1 chaperonin Cpn60/TCP-1 [Desulfotomaculum reducens MI-1] YP_001113833.1 chaperonin Cpn60/TCP-1 [Desulfotomaculum acetoxidans DSM 771] YP_003192586.1 chaperonin Cpn60/TCP-1 [Thermosinus carboxydivorans Nor1] ZP_01666619.1 chaperonin Cpn60/TCP-1 [Geobacillus sp. Y412MC10] ZP_03040692.1 thermosome alpha subunit [Oligotropha carboxidovorans OM5] YP_002288645.1 240 Supplementary Table 4: Group II sequences used to construct the group II phylogeny

(Supplementary Figure 2).

Annotation Accession number chaperonin GroEL [Bradyrhizobium japonicum USDA 110] NP_774173.1 CPN60 [Spironucleus barkhanus] AAK54394.1 Chaperonin 60 [Giardia lamblia ATCC 50803] XP_001705532.1 chaperonin, 60 kDa subunit [Methylococcus capsulatus str. Bath] YP_113667.1 GK15276 [Drosophila willistoni] XP_002065107.1 GA14234 [Drosophila pseudoobscura pseudoobscura] XP_001357321.1 GL25699 [Drosophila persimilis] XP_002018904.1 GF21637 [Drosophila ananassae] XP_001965046.1 GD22056 [Drosophila simulans] XP_002079345.1 Hsp60D, isoform A [Drosophila melanogaster] NP_609656.1 GE11569 [Drosophila yakuba] XP_002088604.1 GG10196 [Drosophila erecta] XP_001969615.1 chaperonin CPN60-2, mitochondrial precursor [Entamoeba dispar SAW760] XP_001737674.1 chaperonin 1 60 kDa [Entamoeba histolytica HM-1:IMSS] XP_656268.2 GA22285 [Drosophila pseudoobscura pseudoobscura] XP_002134578.1 GL22976 [Drosophila persimilis] XP_002027611.1 chaperonin HSP60CNP60 [Leishmania braziliensis MHOMBR75M2904] XP_001566905.1 chaperonin HSP60CNP60 [Leishmania major strain Friedlin] XP_001684887.1 chaperonin HSP60CNP60 [Leishmania infantum JPCM5] XP_001467129.1 chaperonin Hsp60, mitochondrial precursor [Trypanosoma brucei XP_845527.1

TREU927] chaperonin HSP60CNP60 [Trypanosoma cruzi strain CL Brener] XP_804030.1 chaperonin 60 [Trimastix pyriformis] ABW76102.1 chaperonin Hsp60 mitochondrial precursor [Trypanosoma brucei XP_829562.1

TREU927] chaperonin Hsp60, mitochondrial precursor [Leishmania braziliensis XP_001567558.1

MHOMBR75M2904] chaperonin Hsp60, mitochondrial precursor [Leishmania major strain XP_001685504.1

Friedlin] chaperonin Hsp60, mitochondrial precursor [Leishmania infantum JPCM5] XP_001467869.1 TCP-1cpn60 chaperonin family protein [Cryptosporidium muris RN66] XP_002142730.1 Hsp60; GroEL-like chaperone (ATpase), predicted mitochondrial XP_627821.1

[Cryptosporidium parvum Iowa II] Hsp60 [Cryptosporidium hominis TU502] XP_667723.1 chaperonin [Trichomonas vaginalis G3] XP_001582336.1 chaperonin 60 [Trichomonas vaginalis G3] XP_001316281.1 chaperonin 60 [Trichomonas vaginalis G3] XP_001312753.1 chaperonin 60 AAB39487.1 heat shock protein 60 [Nyctotherus ovalis] CAI62555.2 chaperonin 60 [Mastigamoeba balamuthi] ABQ85794.1 GH11219 [Drosophila grimshawi] XP_001988539.1 GJ17770 [Drosophila virilis] XP_002052822.1 GI21603 [Drosophila mojavensis] XP_002003671.1 GK23787 [Drosophila willistoni] XP_002064505.1 GA25838 [Drosophila pseudoobscura pseudoobscura] XP_002132552.1 GL18870 [Drosophila persimilis] XP_002014595.1 GF20641 [Drosophila ananassae] XP_001965381.1 GG24737 [Drosophila erecta] XP_001968203.1 GE17001 [Drosophila yakuba] XP_002087459.1 GH05807p [Drosophila melanogaster] AAK77276.1 heat shock protein 60 related [Drosophila melanogaster] NP_524925.1 GM16759 [Drosophila sechellia] XP_002041615.1 GD23041 [Drosophila simulans] XP_002077669.1 hypothetical protein [Monosiga brevicollis MX1] XP_001747265.1 PREDICTED: similar to predicted protein [Hydra magnipapillata] XP_002162506.1 heat shock protein 60 [Trichinella spiralis] AAM34755.1 hypothetical protein TRIADDRAFT_54071 [Trichoplax adhaerens] XP_002110795.1 mitochondrial 60 kDa heat shock protein [Anemonia viridis] AAR88509.1 predicted protein [Nematostella vectensis] XP_001641093.1 HSP60 [Strongyloides ratti] ABY65231.1 hypothetical protein CBG11701 [Caenorhabditis briggsae AF16] XP_001664603.1 homologous to chaperonin protein AAA28077.1 Heat Shock Protein family member (hsp-60) [Caenorhabditis elegans] NP_497429.1 heat shock protein 60 (HSP60) [Plectus acuminatus] CAA10230.1 AF121264_11-560 chaperonine protein HSP60 [Onchocerca volvulus] AAD27589.1 mitochondrial heat shock protein 60 [Tigriopus japonicus] ACA03522.1 PREDICTED: similar to AGAP004002-PA [Ciona intestinalis] XP_002132071.1 AF310263_11-549 heat shock protein HSP60 [Schistosoma mansoni] AAM69406.1 SJCHGC09129 protein [Schistosoma japonicum] AAW24883.1 PREDICTED: similar to mitochondrial chaperonin Hsp56 XP_795205.2

[Strongylocentrotus purpuratus] Chaperonin [Paracentrotus lividus] CAB56199.1 mitochondrial chaperonin Hsp56 [Paracentrotus lividus] ABE73686.1 heat shock protein 60 [Biomphalaria glabrata] ACL00842.1 hypothetical protein BRAFLDRAFT_115228 [Branchiostoma floridae] XP_002227630.1 hypothetical protein BRAFLDRAFT_118581 [Branchiostoma floridae] XP_002205256.1 hypothetical protein LOC100124945 [Xenopus (Silurana) tropicalis] NP_001096355.1 similar to heat shock 60kDa protein 1 (chaperonin) [Xenopus laevis] NP_001079654.1 similar to heat shock 60kDa protein 1 (chaperonin) [Xenopus laevis] NP_001083970.1 Hspd1 protein [Xenopus laevis] AAH41192.1 heat shock protein 60 [Alligator mississippiensis] BAF94141.1 PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_001370003.1 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60)

(HSP-60) (Mitochondrial matrix protein P1) (P60 lymphocyte protein)

(HuCHA60) [Monodelphis domestica] heat shock 60kDa protein 1 (chaperonin) [Gallus gallus] NP_001012934.1 PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_001071820.1 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60)

(HSP-60) (Mitochondrial matrix protein P1) (HSP-65) [Rattus norvegicus] mCG116284 [Mus musculus] EDL32336.1 PREDICTED: similar to Heat shock protein 1 (chaperonin) [Mus musculus] XP_484008.1 Hspd1 protein [Mus musculus] AAI06113.1 heat shock protein hsp60, hsp60=chaperonin [mice, Peptide, 573 aa] AAB21806.1 unnamed protein product [Mus musculus] CAA37653.1 heat shock protein 65 [Mus musculus] CAA38762.1 heat shock protein (hsp60) precursor [Rattus norvegicus] CAA38564.1 chaperonin 60 [Rattus norvegicus] AAC53362.1 unnamed protein product [Mus musculus] BAC40607.1 heat shock protein 1 (chaperonin) [Mus musculus] NP_034607.3 unnamed protein product [Rattus norvegicus] CAA37654.1 heat shock 60kDa protein 1 (chaperonin) [Pongo abelii] NP_001127086.1 PREDICTED: chaperonin isoform 4 [Pan troglodytes] XP_001169135.1 PREDICTED: heat shock 60kDa protein 1 (chaperonin) isoform 1 [Macaca XP_001082144.1 mulatta] PREDICTED: chaperonin isoform 2 [Macaca mulatta] XP_001082397.1 PREDICTED: chaperonin [Macaca mulatta] XP_001086546.1 unnamed protein product [Macaca fascicularis] BAE88661.1 unnamed protein product [Homo sapiens] BAH12542.1 unnamed protein product [Homo sapiens] BAG35173.1 unnamed protein product [Homo sapiens] BAH12833.1 PREDICTED: chaperonin isoform 5 [Pan troglodytes] XP_001169156.1 mitochondrial heat shock 60kD protein 1 variant 1 [Homo sapiens] ACE06961.1 PREDICTED: chaperonin isoform 9 [Pan troglodytes] XP_516008.2 PREDICTED: chaperonin isoform 2 [Pan troglodytes] XP_001169030.1 PREDICTED: chaperonin isoform 7 [Pan troglodytes] XP_001169231.1 chaperonin (HSP60) AAA36022.1 unnamed protein product [Homo sapiens] BAH12883.1 chaperonin [Homo sapiens] NP_002147.2 heat shock protein 60 [Homo sapiens] ABB01006.1 PREDICTED: heat shock 60kDa protein 1 (chaperonin) isoform 1 [Sus XP_001928634.1 scrofa] PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_001502715.1 precursor (Heat shock protein 60) (HSP-60) (Hsp60) (60 kDa chaperonin)

(Chaperonin 60) (CPN60) (Mitochondrial matrix protein P1) (P60 lymphocyte protein) (HuCHA60) [Equus caballus] PREDICTED: heat shock 60kDa protein 1 (chaperonin) [Bos taurus] XP_001249791.1 PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_857240.1 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60)

(HuCHA60) isoform 4 [Canis familiaris] PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_857282.1 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60)

(HuCHA60) isoform 5 [Canis familiaris] PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_536016.2 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60)

(HuCHA60) isoform 1 [Canis familiaris] 60 kDa heat shock protein, mitochondrial precursor [Salmo salar] ACI33148.1 HSP60 [Carassius auratus] ABI26641.1 heat shock 60 kD protein 1 [Danio rerio] NP_851847.1 unnamed protein product [Tetraodon nigroviridis] CAG02593.1 heat shock protein 60 kDa [Paralichthys olivaceus] ABB76381.1 heat shock protein 60 kDa [Paralichthys olivaceus] ABB76384.1 Hsp60 protein [Myzus persicae] CAB58441.1 PREDICTED: similar to Hsp60 protein [Acyrthosiphon pisum] XP_001951373.1 chaperonin subunit, putative [Ixodes scapularis] EEC05122.1 PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_971630.1 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60)

(HSP-60) (Mitochondrial matrix protein P1) [Tribolium castaneum] GK14688 [Drosophila willistoni] XP_002065398.1 GA28835 [Drosophila pseudoobscura pseudoobscura] XP_002133115.1 GJ15562 [Drosophila virilis] XP_002051422.1 GI17556 [Drosophila mojavensis] XP_002002753.1 GF15575 [Drosophila ananassae] XP_001962681.1 GG25088 [Drosophila erecta] XP_001968832.1 GE25548 [Drosophila yakuba] XP_002089193.1 AT16985p [Drosophila melanogaster] AAM29278.1 GM18564 [Drosophila sechellia] XP_002037978.1 GM11458 [Drosophila sechellia] XP_002041940.1 Hsp60 protein, putative [Pediculus humanus corporis] EEB15946.1 GH17925 [Drosophila grimshawi] XP_001995750.1 GJ15640 [Drosophila virilis] XP_002058167.1 GI16304 [Drosophila mojavensis] XP_002011005.1 GK16370 [Drosophila willistoni] XP_002067348.1 heat shock protein 60 [Lucilia cuprina] ABO09590.1 heat shock protein 60 [Drosophila melanogaster] CAA67720.1 heat shock protein 60, isoform A [Drosophila melanogaster] NP_511115.2 SD06594p [Drosophila melanogaster] AAQ23524.1 GD17003 [Drosophila simulans] XP_002106653.1 GE15908 [Drosophila yakuba] XP_002100912.1 GG18391 [Drosophila erecta] XP_001977170.1 heat shock protein 60 [Culicoides variipennis] AAB94640.1 PREDICTED: similar to ENSANGP00000014839 [Nasonia vitripennis] XP_001600045.1 PREDICTED: similar to 60 kDa heat shock protein, mitochondrial XP_392899.2 precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60) (HSP-60) (Mitochondrial matrix protein P1) [Apis mellifera] AGAP004002-PA [Anopheles gambiae str. PEST] XP_318461.2 chaperonin-60kD, ch60 [Aedes aegypti] XP_001661764.1 60 kDa heat shock protein, mitochondrial [Culex quinquefasciatus] XP_001850501.1 heat shock protein [Schizosaccharomyces japonicus yFS275] XP_002171843.1 heat-shock protein [Schizosaccharomyces pombe] BAA09171.1 mitochondrial heat shock protein Hsp60 [Schizosaccharomyces pombe NP_592894.1

972h-] heat shock protein [Cryptococcus neoformans var. neoformans JEC21] XP_569211.1 heat shock protein 60 [Glomus intraradices] ABE02805.1 heat shock protein 60 [Glomus intraradices] ABE02806.1 unnamed protein product [Podospora anserina] XP_001910071.1 heat shock protein 60, mitochondrial precursor [Chaetomium globosum XP_001228161.1

CBS 148.51] heat shock protein 60, mitochondrial precursor [Sclerotinia sclerotiorum XP_001597891.1

1980] heat shock protein 60 [Botryotinia fuckeliana B05.10] XP_001552177.1 HS60_AJECA Heat shock protein 60, mitochondrial precursor (Antigen XP_386422.1

HIS-62) [Gibberella zeae PH-1] heat shock protein 60, mitochondrial precursor [Magnaporthe grisea 70-15] XP_360622.2 heat shock protein 60, mitochondrial precursor [Pyrenophora tritici-repentis XP_001931555.1

Pt-1C-BFP] hypothetical protein SNOG_16475 [Phaeosphaeria nodorum SN15] XP_001806589.1 probable heat-shock protein hsp60 [Neurospora crassa] CAB91379.2 heat shock protein 60, mitochondrial precursor [Neurospora crassa OR74A] XP_956500.2 antigenic mitochondrial protein HSP60, putative [Penicillium marneffei XP_002149398.1

ATCC 18224] antigenic mitochondrial protein HSP60, putative [Talaromyces stipitatus EED14822.1

ATCC 10500] Pc16g11070 [Penicillium chrysogenum Wisconsin 54-1255] CAP93777.1 hypothetical protein [Aspergillus oryzae RIB40] XP_001826345.1 hypothetical protein An12g04940 [Aspergillus niger] XP_001395564.1 HS60_PARBR Heat shock protein 60, mitochondrial precursor (60 kDa XP_663693.1 chaperonin) (Protein Cpn60) [Aspergillus nidulans FGSC A4] heat shock protein 60, mitochondrial precursor [Aspergillus terreus XP_001218472.1

NIH2624] antigenic mitochondrial protein HSP60, putative [Aspergillus clavatus XP_001267850.1

NRRL 1] antigenic mitochondrial protein HSP60 [Aspergillus fumigatus Af293] XP_755263.1 antigenic mitochondrial protein HSP60, putative [Neosartorya fischeri XP_001260425.1

NRRL 181] heat shock protein 60, mitochondrial precursor [Ajellomyces capsulatus XP_001539356.1

NAm1] mitochondrial 60 kDa heat shock protein [Microsporum canis] ABJ97613.1 heat shock protein 60, mitochondrial precursor [Coccidioides immitis RS] XP_001242382.1 hypothetical protein Kpol_1037p35 [Vanderwaltozyma polyspora DSM XP_001645297.1

70294] unnamed protein product [Candida glabrata] XP_448482.1 AFR155Wp [Ashbya gossypii ATCC 10895] NP_985702.1 unnamed protein product [Kluyveromyces lactis] XP_455510.1 YALI0F02805p [Yarrowia lipolytica] XP_504920.1 hypothetical protein PICST_90190 [Pichia stipitis CBS 6054] XP_001385888.1 hypothetical protein DEHA0E06589g [Debaryomyces hansenii CBS767] XP_459575.1 heat shock protein 60, mitochondrial precursor [Pichia guilliermondii ATCC XP_001482545.1

6260] heat shock protein 60, mitochondrial precursor [Pichia guilliermondii ATCC EDK41467.2

6260] hypothetical protein UM05831.1 [Ustilago maydis 521] XP_761978.1 hypothetical protein CC1G_02564 [Coprinopsis cinerea okayama7#130] XP_001840101.1 predicted protein [Laccaria bicolor S238N-H82] XP_001880247.1 AF426026_11-582 heat shock protein 60 [Piromyces sp. E2] AAP33147.1 heat shock protein 60 precursor [Neocallimastix patriciarum] AAK61605.1 heat shock protein 60 [Euglena gracilis] CAA65238.1 chaperonin Hsp60, mitochondrial precursor [Leishmania major] XP_001686777.1 chaperonin Hsp60, mitochondrial precursor [Leishmania infantum] XP_001469793.1 chaperonin Hsp60, mitochondrial precursor [Leishmania braziliensis XP_001568845.1

MHOMBR75M2904] chaperonin Hsp60, mitochondrial precursor [Leishmania major] XP_001686778.1 chaperonin Hsp60, mitochondrial precursor [Leishmania infantum] XP_001469794.1 chaperonin 60; cpn60 [Leishmania braziliensis] AAC12772.1 chaperonin Hsp60, mitochondrial precursor [Leishmania braziliensis XP_001568844.1

MHOMBR75M2904] chaperonin Hsp60 [Trypanosoma brucei TREU927] XP_822882.1 chaperonin HSP60, mitochondrial precursor [Trypanosoma cruzi strain CL XP_819506.1

Brener] heat shock protein 60 AAA30203.1 chaperonin 60 [Dictyostelium discoideum AX4] XP_636839.1 AF359268_11-555 chaperonin 60 [Dictyostelium discoideum] AAK49534.1 TCP-1cpn60 chaperonin family protein [Tetrahymena thermophila SB210] XP_001017291.2 hsp60 [Paramecium caudatum] BAB33386.1 hypothetical protein [Paramecium tetraurelia strain d4-2] XP_001448270.1 hsp60, putative [Paramecium tetraurelia] CAI39019.1 hypothetical protein [Paramecium tetraurelia strain d4-2] XP_001424134.1 mitochondrial chaperonin [Thalassiosira pseudonana CCMP1335] ACI64273.1 chaperonin 60C [Chlamydomonas reinhardtii] XP_001691353.1 chaperonin 60, mitochondrial [Ostreococcus lucimarinus CCE9901] XP_001419890.1 chaperonin-60, mitochondrial precursor (IC) [Ostreococcus tauri] CAL55987.1 hypothetical protein OsJ_018592 [Oryza sativa (japonica cultivar-group)] EAZ35109.1 hypothetical protein OsI_20809 [Oryza sativa Indica Group] EEC79614.1 Os05g0540300 [Oryza sativa (japonica cultivar-group)] NP_001056181.1 chaperonin, putative [Arabidopsis thaliana] NP_566466.1 unnamed protein product [Vitis vinifera] CAO45704.1 hypothetical protein [Vitis vinifera] CAN78641.1 chaperonin, putative [Arabidopsis thaliana] NP_850203.1 mitochondrial chaperonin (HSP60) [Arabidopsis thaliana] AAC04902.1 chaperonin hsp60 [Arabidopsis thaliana] CAA77646.1 HSP60 (Heat shock protein 60); ATP binding protein binding unfolded NP_189041.1 protein binding [Arabidopsis thaliana] hypothetical protein OsJ_009026 [Oryza sativa (japonica cultivar-group)] EAZ25543.1 Os03g0143400 [Oryza sativa (japonica cultivar-group)] NP_001048938.1 Chaperonin CPN60-1, mitochondrial precursor, putative, expressed [Oryza AAP54159.2 sativa (japonica cultivar-group)] Os10g0462900 [Oryza sativa (japonica cultivar-group)] NP_001064784.1 mitochondrial chaperonin 60 [Zea mays] NP_001105690.1 mitochondrial chaperonin-60 [Zea mays] CAA78101.1 chaperonin hsp60 [Zea mays] CAA77645.1 mitochondrial chaperonin-60 [Zea mays] NP_001105716.1 chaperonin 60 AAA33450.1 GroEL-like chaperone, ATPase [Medicago truncatula] ABE86688.1 GroEL-like chaperone, ATPase [Medicago truncatula] ABE86687.1 heat shock protein 60 [Ageratina adenophora] ABX76300.1 heat shock protein 60 [Prunus dulcis] AAN63805.1 predicted protein [Physcomitrella patens subsp. patens] XP_001760735.1 predicted protein [Physcomitrella patens subsp. patens] XP_001762115.1 predicted protein [Physcomitrella patens subsp. patens] XP_001783814.1 predicted protein [Physcomitrella patens subsp. patens] XP_001772410.1 heat shock protein 60 [Babesia bovis T2Bo] XP_001610603.1 heat shock protein 60 [Theileria parva strain Muguga] XP_763701.1 chaperonin (HSP60) [Theileria annulata strain Ankara] XP_952758.1 heat shock protein 60 [Toxoplasma gondii ME49] EEA99981.1 heat shock protein 60 [Toxoplasma gondii] AAD38419.1 hsp60 [Plasmodium chabaudi chabaudi] XP_743319.1 heat shock protein 60 [Plasmodium yoelii yoelii str. 17XNL] XP_724940.1 heat shock protein 60 [Plasmodium yoelii] AAC78150.1 hsp60 [Plasmodium knowlesi strain H] XP_002258797.1 hsp60 [Plasmodium falciparum 3D7] XP_001347438.1 60 kDa heat-shock protein PfHsp60 AAC47497.1 hypothetical protein [Paramecium tetraurelia strain d4-2] XP_001432728.1 TCP-1cpn60 chaperonin family protein [Tetrahymena thermophila SB210] XP_001017588.2 chaperonin GroEL [Rickettsia bellii OSU 85-389] YP_001496071.1 chaperonin GroEL [Rickettsia bellii RML369-C] YP_537760.1 chaperonin GroEL [Rickettsia canadensis str. McKiel] YP_001492054.1 chaperonin GroEL [Rickettsia felis URRWXCal2] YP_246425.1 chaperonin GroEL [Rickettsia typhi str. Wilmington] YP_067563.1 chaperonin GroEL [Rickettsia prowazekii str. Madrid E] NP_220991.1 chaperonin GroEL [Rickettsia akari str. Hartford] YP_001493749.1 chaperonin GroEL [Rickettsia massiliae MTU5] YP_001499598.1 chaperonin GroEL [Rickettsia conorii str. Malish 7] NP_360605.1 chaperonin GroEL [Rickettsia rickettsii str. 'Sheila Smith'] YP_001495063.1 chaperonin GroEL [Rickettsia rickettsii str. Iowa] YP_001650336.1 Supplementary Table 5: Sequences used to construct the mitochondrial GROEL phylogeny.

Species No. Accession numbers Burkholderia xenovorans LB400 5 YP_558423.1, YP_558393.1, YP_557234.1,

YP_553746.1, YP_555411.1 Bradyrhizobium japonicum USDA 110 5 NP_774172.1, NP_773618.1, NP_772265.1,

NP_771866.1, NP_768700.1 Mesorhizobium loti MAFF303099 5 NP_103626.1, NP_103750.1, NP_106408.1,

NP_108346.1, NP_085868.1 Sinorhizobium meliloti 1021 4 YP_002122333.1, NP_435311.1, NP_384899.1,

NP_435642.1 Bradyrhizobium sp. BTAi1 4 YP_001241175.1, YP_001237788.1,

YP_001239059.1, YP_001238585.1 Rhizobium etli CFN 42 4 YP_472946.1, YP_468770.1, YP_468367.1,

YP_468802.1 Burkholderia pseudomallei K96243 3 YP_109294.1, YP_109513.1, YP_110498.1 Burkholderia pseudomallei 1106a 3 YP_001067662.1, YP_001067392.1,

YP_001074681.1 Nitrobacter winogradskyi Nb-255 3 YP_318721.1, YP_319178.1, YP_318797.1 Sinorhizobium medicae WSM419 3 YP_001326967.1, YP_001326101.1,

YP_001314660.1 Burkholderia pseudomallei 668 3 YP_001060402.1, YP_001060130.1,

YP_001061736.1 Rhizobium leguminosarum bv. viciae 3 YP_766496.1, YP_765149.1, YP_767016.1

3841 Rhodopirellula baltica SH 1 3 NP_869523.1, NP_868642.1, NP_863812.1 Nitrobacter hamburgensis X14 3 YP_576476.1, YP_577835.1, YP_578390.1 Burkholderia ambifaria AMMD 3 YP_778271.1, YP_772625.1, YP_777153.1 Methylobacterium extorquens PA1 3 YP_001642222.1, YP_001640793.1,

YP_001638223.1 Bradyrhizobium sp. ORS278 3 YP_001204939.1, YP_001207981.1,

YP_001204747.1 Burkholderia cenocepacia MC0-3 3 YP_001764130.1, YP_001774335.1, YP_001777637.1 Syntrophus aciditrophicus SB 3 YP_461541.1, YP_461767.1, YP_460097.1 Burkholderia cenocepacia HI2424 3 YP_834505.1, YP_839875.1, YP_837155.1 Methylobacterium sp. 4-46 3 YP_001768694.1, YP_001772320.1,

YP_001772214.1 Burkholderia pseudomallei 1710b 3 YP_334800.1, YP_334548.1, YP_337180.1 Burkholderia ambifaria MC40-6 3 YP_001807461.1, YP_001816086.1,

YP_001810135.1 Sorangium cellulosum 'So ce 56' 2 YP_001613419.1, YP_001616554.1 Candidatus Protochlamydia 2 YP_007030.1, YP_008178.1 amoebophila UWE25 Rhodopseudomonas palustris BisB5 2 YP_569364.1, YP_571246.1 Mesorhizobium sp. BNC1 2 YP_672927.1, YP_675633.1 Methylococcus capsulatus str. Bath 2 YP_113216.1, YP_114146.1 Burkholderia sp. 383 2 YP_368197.1, YP_373370.1 Moorella thermoacetica ATCC 39073 2 YP_430965.1, YP_429418.1 Azorhizobium caulinodans ORS 571 2 YP_001523341.1, YP_001525227.1 Vibrio parahaemolyticus RIMD 2210633 2 NP_799231.1, NP_799796.1 Burkholderia multivorans ATCC 17616 2 YP_001580710.1, YP_001585216.1 Burkholderia mallei NCTC 10247 2 YP_001081401.1, YP_001082142.1 Vibrio cholerae O1 biovar eltor str. 2 NP_233205.1, NP_232293.1

N16961 Chromobacterium violaceum ATCC 2 NP_903685.1, NP_902902.1

12472 Roseiflexus castenholzii DSM 13941 2 YP_001431327.1, YP_001432867.1 Rhodopseudomonas palustris CGA009 2 NP_946492.1, NP_947510.1 Candidatus Protochlamydia 2 YP_008178.1, YP_007030.1 amoebophila UWE25 Burkholderia mallei SAVP1 2 YP_992251.1, YP_991695.1 Chloroflexus aurantiacus J-10-fl 2 YP_001636475.1, YP_001636331.1 Roseiflexus sp. RS-1 2 YP_001275435.1, YP_001278424.1 Burkholderia vietnamiensis G4 2 YP_001117600.1, YP_001118640.1 Burkholderia thailandensis E264 2 YP_442003.1, YP_440133.1 Psychromonas ingrahamii 37 2 YP_943819.1, YP_942285.1 Anabaena variabilis ATCC 29413 2 YP_320422.1, YP_324128.1 Rhodopseudomonas palustris BisA53 2 YP_781206.1, YP_779798.1 Erythrobacter litoralis HTCC2594 2 YP_459770.1, YP_457721.1 Burkholderia cenocepacia AU 1054 2 YP_620262.1, YP_621459.1 Roseobacter denitrificans OCh 114 2 YP_681140.1, YP_683685.1 Gloeobacter violaceus PCC 7421 2 NP_925842.1, NP_923974.1 Rhodospirillum rubrum ATCC 11170 2 YP_425677.1, YP_425253.1 Vibrio vulnificus YJ016 2 NP_935900.1, NP_937716.1 Burkholderia mallei NCTC 10229 2 YP_001028693.1, YP_001027190.1 Bdellovibrio bacteriovorus HD100 2 NP_967122.1, NP_970095.1 Syntrophobacter fumaroxidans MPOB 2 YP_844258.1, YP_846462.1 Vibrio cholerae O395 2 YP_001218154.1, YP_001215256.1 Acaryochloris marina MBIC11017 2 YP_001518706.1, YP_001522016.1 Rhodopseudomonas palustris HaA2 2 YP_486840.1, YP_485456.1 Burkholderia mallei ATCC 23344 2 YP_103589.1, YP_103981.1 Solibacter usitatus Ellin6076 2 YP_826033.1, YP_827952.1 Azoarcus sp. BH72 2 YP_932477.1, YP_933869.1 Gluconacetobacter diazotrophicus PAl 5 2 YP_001602295.1, YP_001602890.1 Xanthobacter autotrophicus Py2 2 YP_001419143.1, YP_001416071.1 Mycoplasma genitalium G37 2 ZP_05405503.1, NP_073066.1 Sorangium cellulosum 'So ce 56' 2 YP_001613419.1, YP_001616554.1 Sphingopyxis alaskensis RB2256 2 YP_615507.1, YP_617120.1 Rhodopseudomonas palustris BisB18 2 YP_533032.1, YP_534566.1 Vibrio vulnificus CMCP6 2 NP_760188.1, NP_763046.1 Caulobacter crescentus CB15 1 NP_419503.1 Legionella pneumophila str. Paris 1 YP_123080.1 Leptospira interrogans serovar Lai str. 1 NP_712835.1

56601 Thermosynechococcus elongatus BP-1 1 NP_680977.1 Actinobacillus succinogenes 130Z 1 YP_001343971.1 Salmonella typhimurium LT2 1 NP_463193.1 Shewanella baltica OS155 1 YP_001052052.1 Chlamydia muridarum Nigg 1 NP_296765.1 Streptococcus pyogenes MGAS9429 1 YP_597503.2 Chlamydophila pneumoniae TW-183 1 NP_876412.1 Campylobacter jejuni subsp. jejuni 81- 1 YP_001000894.1

176 Shigella sonnei Ss046 1 YP_313049.1 Prochlorococcus marinus subsp. marinus 1 NP_875981.1 str. CCMP1375 Rickettsia bellii RML369-C 1 YP_537761.2 Synechococcus sp. WH 8102 1 NP_896608.1 Escherichia coli UTI89 1 YP_543678.1 Synechococcus sp. CC9311 1 YP_731480.1 Novosphingobium aromaticivorans 1 YP_495317.1

DSM 12444 Acidothermus cellulolyticus 11B 1 YP_872122.1 Rhodobacter sphaeroides 2.4.1 1 YP_352365.1 Corynebacterium efficiens YS-314 1 NP_737211.1 Enterococcus faecalis V583 1 NP_816273.1 Prochlorococcus marinus str. MIT 9312 1 YP_398026.1 Wigglesworthia glossinidia 1 NP_871262.1 endosymbiont of Glossina brevipalpis Nostoc sp. PCC 7120 1 YP_001864511.1 Yersinia enterocolitica subsp. 1 YP_001004729.1 enterocolitica 8081 Staphylococcus epidermidis ATCC 1 NP_765185.1

12228 Mycobacterium vanbaalenii PYR-1 1 YP_952332.1 Frankia sp. CcI3 1 YP_479745.1 Xylella fastidiosa M23 1 YP_001830304.1 Neisseria meningitidis MC58 1 NP_274967.1 Chlamydia trachomatis L2b/UCH- 1 YP_001653462.1

1/proctitis Thermotoga lettingae TMO 1 YP_001469950.1 Prochlorococcus marinus str. MIT 9301 1 YP_001091851.1 Dinoroseobacter shibae DFL 12 1 YP_001534254.1 Dechloromonas aromatica RCB 1 YP_283652.1 Verminephrobacter eiseniae EF01-2 1 YP_997329.1 Polaromonas naphthalenivorans CJ2 1 YP_980898.1 Prochlorococcus marinus str. MIT 9303 1 YP_001016520.1 Mycobacterium bovis AF2122/97 1 NP_857092.1 Chlamydophila caviae GPIC 1 NP_829506.1 Bartonella tribocorum CIP 105476 1 YP_001610272.1 Yersinia pestis Angola 1 YP_001605300.1 Frankia sp. EAN1pec 1 YP_001510252.1 Chlorobium chlorochromatii CaD3 1 YP_379608.2 Campylobacter hominis ATCC BAA- 1 YP_001406155.1

381 Synechococcus sp. RCC307 1 YP_001228116.1 Desulfovibrio vulgaris subsp. vulgaris 1 YP_966642.1

DP4 Synechococcus sp. PCC 7002 1 YP_001735690.1 Carboxydothermus hydrogenoformans 1 YP_359660.1

Z-2901 Anaeromyxobacter sp. Fw109-5 1 YP_001380877.1 Mycobacterium tuberculosis F11 1 YP_001289379.1 Francisella tularensis subsp. tularensis 1 YP_667733.1|

FSC198 Chlamydophila pneumoniae CWL029 1 NP_224343.1 Desulfovibrio desulfuricans G20 1 YP_388966.1 Klebsiella pneumoniae subsp. 1 YP_001338153.1 pneumoniae MGH 78578 Corynebacterium urealyticum DSM 1 YP_001799787.1

7109 Mycoplasma penetrans HF-2 1 NP_757485.1 Listeria monocytogenes EGD-e 1 NP_465593.1 Haemophilus influenzae PittGG 1 YP_001292486.1 Salinispora arenicola CNS-205 1 YP_001539004.1 Staphylococcus aureus subsp. aureus 1 YP_494634.1

USA300 Herminiimonas arsenicoxydans 1 YP_001100794.1 Shewanella denitrificans OS217 1 YP_561437.1 Flavobacterium johnsoniae UW101 1 YP_001194195.1 Streptococcus thermophilus LMD-9 1 YP_819764.1 Arthrobacter aurescens TC1 1 YP_948584.1 Nocardia farcinica IFM 10152 1 YP_117095.1 Prochlorococcus marinus str. AS9601 1 YP_001010029.1 Corynebacterium jeikeium K411 1 YP_251524.1 Streptomyces avermitilis MA-4680 1 NP_826168.1 Bordetella parapertussis 12822 1 NP_883196.1 Vibrio harveyi ATCC BAA-1116 1 YP_001443418.1 Streptococcus suis 98HAH33 1 YP_001199709.1 Agrobacterium tumefaciens str. C58 1 NP_353707.1 Escherichia coli CFT073 1 NP_757074.1 Corynebacterium diphtheriae NCTC 1 NP_938951.1

13129 Synechococcus sp. CC9902 1 YP_376517.1 Brucella melitensis 16M 1 NP_542025.1 Syntrophomonas wolfei subsp. wolfei 1 YP_754525.1 str. Goettingen Salmonella enterica subsp. enterica 1 NP_807972.1 serovar Typhi str. CT18 Clostridium acetobutylicum ATCC 824 1 NP_349310.1 Candidatus Desulforudis audaxviator 1 YP_001718131.1

MP104C Corynebacterium glutamicum R 1 YP_001137588.1 Chlamydia trachomatis A/HAR-13 1 YP_327912.1 Neisseria meningitidis 053442 1 YP_001598402.1 Myxococcus xanthus DK 1622 1 YP_633051.1 Bordetella bronchiseptica RB50 1 NP_887511.1 Streptomyces coelicolor A3(2) 1 NP_628919.1 Synechococcus sp. CC9605 1 YP_382464.1 Lactobacillus sakei subsp. sakei 23K 1 YP_394971.1 Mycobacterium sp. MCS 1 YP_638322.1 Mycobacterium tuberculosis CDC1551 1 NP_338051.1 Desulfotomaculum reducens MI-1 1 YP_001114203.1 Leifsonia xyli subsp. xyli str. CTCB07 1 YP_062808.1 Campylobacter jejuni subsp. doylei 1 YP_001397689.1

269.97 Xanthomonas axonopodis pv. citri str. 1 NP_640894.1 306 Acinetobacter baumannii 1 YP_001847568.1 Mycobacterium bovis BCG str. Pasteur 1 YP_979567.1

1173P2 Helicobacter hepaticus ATCC 51449 1 NP_860731.1 Mycobacterium tuberculosis H37Ra 1 YP_001284805.1 Streptococcus pyogenes MGAS315 1 NP_665570.1 Pediococcus pentosaceus ATCC 25745 1 YP_803958.1 Prochlorococcus marinus str. MIT 9515 1 YP_001011930.1 Escherichia coli E24377A 1 YP_001465640.1 Thermosipho melanesiensis BI429 1 YP_001305317.1 Pseudomonas aeruginosa PA7 1 YP_001350293.1 Synechococcus elongatus PCC 7942 1 YP_401331.1 Leptothrix cholodnii SP-6 1 YP_001789522.1 Saccharophagus degradans 2-40 1 YP_526357.1 Cyanothece sp. ATCC 51142 1 YP_001802759.1 Acidobacteria bacterium Ellin345 1 YP_590175.1 Porphyromonas gingivalis W83 1 NP_904816.1 Rhodococcus sp. RHA1 1 YP_706124.1 Pelobacter carbinolicus DSM 2380 1 YP_902460.1 Synechococcus sp. JA-3-3Ab 1 YP_474839.1 Campylobacter fetus subsp. fetus 82-40 1 YP_891875.1 Buchnera aphidicola str. APS 1 NP_239859.1

(Acyrthosiphon pisum) Staphylococcus aureus subsp. aureus 1 NP_646771.1

MW2 Pseudomonas aeruginosa UCBPP-PA14 1 YP_792732.1 Escherichia coli str. K-12 substr. 1 NP_418566.1

MG1655 Alcanivorax borkumensis SK2 1 YP_692353.1 Parvibaculum lavamentivorans DS-1 1 YP_001411891.1 Aquifex aeolicus VF5 1 NP_214511.1 Clostridium botulinum A str. ATCC 1 YP_001385617.1

19397 Candidatus Blochmannia floridanus 1 NP_878381.1 Fervidobacterium nodosum Rt17-B1 1 YP_001411044.1 Bacillus licheniformis ATCC 14580 1 YP_077850.1 Hyphomonas neptunium ATCC 15444 1 YP_760662.1 Staphylococcus aureus subsp. aureus 1 YP_044046.1

MSSA476 Renibacterium salmoninarum ATCC 1 YP_001624918.1

33209 Candidatus Vesicomyosocius okutanii 1 YP_001219358.1

HA Lactococcus lactis subsp. cremoris 1 YP_001031760.1

MG1363 Pseudomonas entomophila L48 1 YP_609928.1 Xanthomonas campestris pv. vesicatoria 1 YP_362301.1 str. 85-10 Prochlorococcus marinus str. NATL1A 1 YP_001015657.1 Ralstonia eutropha JMP134 1 YP_296862.1 Erwinia carotovora subsp. atroseptica 1 YP_048740.1

SCRI1043 Gluconobacter oxydans 621H 1 YP_192295.1 Mycobacterium leprae TN 1 NP_301372.1 Francisella tularensis subsp. tularensis 1 YP_001121347.1

WY96-3418 Streptococcus pneumoniae CGSP14 1 YP_001836599.1 Aeromonas hydrophila subsp. 1 YP_855401.1 hydrophila ATCC 7966 Geobacillus kaustophilus HTA426 1 YP_146101.1 Streptococcus pneumoniae TIGR4 1 NP_346337.1 Candidatus Desulforudis audaxviator 1 YP_001718131.1

MP104C Propionibacterium acnes KPA171202 1 YP_056460.1 Desulfovibrio vulgaris subsp. vulgaris 1 YP_011194.1 str. Hildenborough Bacillus thuringiensis serovar konkukian 1 YP_034592.1 str. 97-27 Mycobacterium gilvum PYR-GCK 1 YP_001136179.1 Helicobacter pylori J99 1 NP_222731.1 Hahella chejuensis KCTC 2396 1 YP_435740.1 Haemophilus somnus 2336 1 YP_001784104.1 Microcystis aeruginosa NIES-843 1 YP_001659621.1 Chlamydophila pneumoniae J138 1 NP_300194.1 Lactobacillus reuteri F275 1 YP_001270959.1 Haemophilus ducreyi 35000HP 1 NP_874148.1 Treponema denticola ATCC 35405 1 NP_971544.1 Dehalococcoides ethenogenes 195 1 YP_182135.1 Yersinia pestis Nepal516 1 YP_649247.1 Exiguobacterium sibiricum 255-15 1 YP_001815232.1 Idiomarina loihiensis L2TR 1 YP_156662.1 Rickettsia felis URRWXCal2 1 YP_246424.2 Yersinia pestis Pestoides F 1 YP_001164946.1 Psychrobacter sp. PRwf-1 1 YP_001279544.1 Deinococcus geothermalis DSM 11300 1 YP_605693.1 Streptococcus agalactiae NEM316 1 NP_736463.1 Chlamydia trachomatis L2b/UCH- 1 YP_001653462.1

1/proctitis Bacteroides thetaiotaomicron VPI-5482 1 NP_810743.1 Thermobifida fusca YX 1 YP_290655.1 Escherichia coli str. K-12 substr. DH10B 1 YP_001732911.1 Clostridium novyi NT 1 YP_878934.1 Serratia proteamaculans 568 1 YP_001476644.1 Shewanella oneidensis MR-1 1 NP_716336.1 Psychrobacter arcticus 273-4 1 YP_263847.1 Acinetobacter sp. ADP1 1 YP_047392.1 Pseudomonas aeruginosa PAO1 1 NP_253076.1 Bacillus pumilus SAFR-032 1 YP_001485789.1 Shewanella amazonensis SB2B 1 YP_928997.1 Pelobacter propionicus DSM 2379 1 YP_902460.1 Photobacterium profundum SS9 1 YP_131475.2 Pelotomaculum thermopropionicum SI 1 YP_001213157.1 Lactobacillus delbrueckii subsp. 1 YP_813428.1 bulgaricus ATCC BAA-365 Marinobacter aquaeolei VT8 1 YP_959299.1 Mycobacterium tuberculosis H37Rv 1 NP_217935.1 Pseudomonas syringae pv. syringae 1 YP_237141.1

B728a Streptococcus pneumoniae R6 1 NP_359315.1 Clostridium kluyveri DSM 555 1 YP_001393865.1 Nitrosococcus oceani ATCC 19707 1 YP_344898.1 Bacillus anthracis str. Ames 1 NP_842819.1 Chlamydophila pneumoniae AR39 1 NP_445179.1 Maricaulis maris MCS10 1 YP_755836.1 Leptospira interrogans serovar 1 YP_001300.1

Copenhageni str. Fiocruz L1-130 Bordetella pertussis Tohama I 1 NP_882015.1 Salmonella enterica subsp. enterica 1 YP_219195.2 serovar Choleraesuis str. SC-B67 Helicobacter pylori HPAG1 1 YP_626752.1 Staphylococcus aureus RF122 1 YP_417373.1 Tropheryma whipplei str. Twist 1 NP_787202.1 Citrobacter koseri ATCC BAA-895 1 YP_001455206.1 Treponema pallidum subsp. pallidum str. 1 NP_219450.1

Nichols Brucella ovis ATCC 25840 1 YP_001257247.1 Pseudomonas putida F1 1 YP_001269671.1 Escherichia coli ATCC 8739 1 YP_001726801.1 Streptococcus pyogenes MGAS6180 1 YP_281213.2 Xylella fastidiosa Temecula1 1 NP_779730.1 Ralstonia metallidurans CH34 1 YP_582770.1 Salinispora tropica CNB-440 1 YP_001160650.1 Actinobacillus pleuropneumoniae L20 1 YP_001053712.1 Kineococcus radiotolerans SRS30216 1 YP_001360488.1 Neisseria gonorrhoeae FA 1090 1 YP_209107.1 Wolbachia endosymbiont strain TRS of 1 YP_198180.1

Brugia malayi Shewanella baltica OS185 1 YP_001364868.1 Polaromonas sp. JS666 1 YP_547614.1 Colwellia psychrerythraea 34H 1 YP_267705.1 Aeromonas salmonicida subsp. 1 YP_001143151.1 salmonicida A449 Mycobacterium sp. KMS 1 YP_937173.1 Silicibacter pomeroyi DSS-3 1 YP_166139.1 Ehrlichia ruminantium str. Welgevonden 1 YP_197550.1 Yersinia pestis CO92 1 NP_403998.1 Escherichia coli SMS-3-5 1 YP_001746538.1 Salmonella enterica subsp. arizonae 1 YP_001572278.1 serovar 62 Shewanella sp. MR-4 1 YP_735521.1 Methylobacillus flagellatus KT 1 YP_544477.1 Synechococcus sp. JA-2-3B'a(2-13) 1 NP_896608.1 Bartonella quintana str. Toulouse 1 YP_032640.1 Pseudomonas fluorescens Pf-5 1 YP_261920.1 Enterobacter sakazakii ATCC BAA-894 1 YP_001436293.1 Prochlorococcus marinus str. MIT 9211 1 YP_001551441.1 Caldicellulosiruptor saccharolyticus 1 YP_001180084.1

DSM 8903 Marinomonas sp. MWYL1 1 YP_001340893.1 Pelodictyon luteolum DSM 273 1 YP_374468.1 Shewanella halifaxensis HAW-EB4 1 YP_001675976.1 Psychrobacter cryohalolentis K5 1 YP_579807.1 Mycoplasma pneumoniae M129 1 NP_110263.1 Rubrobacter xylanophilus DSM 9941 1 YP_645036.1 Clostridium botulinum B1 str. Okra 1 YP_001782922.1 Desulfotalea psychrophila LSv54 1 YP_063927.1 Bordetella petrii DSM 12804 1 YP_001632545.1 Haemophilus somnus 129PT 1 YP_718678.1 Clostridium botulinum F str. Langeland 1 YP_001392644.1 Photorhabdus luminescens subsp. 1 NP_931325.1 laumondii TTO1 Saccharopolyspora erythraea NRRL 1 YP_001108806.1

2338 Rickettsia rickettsii str. 'Sheila Smith' 1 YP_001495064.1 Lactococcus lactis subsp. lactis Il1403 1 NP_266549.1 Bacteroides vulgatus ATCC 8482 1 YP_001297687.1 Candidatus Blochmannia 1 YP_277588.1 pennsylvanicus str. BPEN Lactobacillus casei ATCC 334 1 YP_807426.1 Onion yellows phytoplasma OY-M 1 NP_950372.1 Vibrio fischeri ES114 1 YP_203587.1 Yersinia pestis Antiqua 1 YP_653838.1 Paracoccus denitrificans PD1222 1 YP_918345.1 Staphylococcus aureus subsp. aureus 1 YP_001247426.1

JH9 Desulfitobacterium hafniense Y51 1 YP_520194.1 Shewanella loihica PV-4 1 YP_001092602.1 Yersinia pseudotuberculosis IP 32953 1 YP_068947.1 Salmonella enterica subsp. enterica 1 NP_807972.1 serovar Typhi Ty2 Rickettsia typhi str. Wilmington 1 YP_067564.1 Bacillus thuringiensis str. Al Hakam 1 YP_893163.2 Clostridium botulinum A str. ATCC 3502 1 YP_001385617.1 Enterobacter sp. 638 1 YP_001175068.1 Bacillus cereus ATCC 10987 1 NP_976616.1 Yersinia pseudotuberculosis IP 31758 1 YP_001402630.1 Streptococcus pyogenes M1 GAS 1 NP_270007.1 Bacillus cereus subsp. cytotoxis NVH 1 YP_001373612.1

391-98 Alkaliphilus metalliredigens QYMF 1 YP_001318717.1 Alkalilimnicola ehrlichei MLHE-1 1 YP_740869.1 Shigella flexneri 2a str. 2457T 1 NP_839688.1 Synechococcus sp. WH 7803 1 YP_001225722.1 Nitrosomonas europaea ATCC 19718 1 NP_840128.1 Legionella pneumophila subsp. 1 YP_094723.1 pneumophila str. Philadelphia 1 Bacillus cereus E33L 1 YP_081853.1 Herpetosiphon aurantiacus ATCC 23779 1 YP_001546442.1 Leuconostoc citreum KM20 1 YP_001728707.1 Shigella boydii Sb227 1 YP_410559.1 Beijerinckia indica subsp. indica ATCC 1 YP_001832856.1

9039 Synechocystis sp. PCC 6803 1 NP_440730.1 Rickettsia akari str. Hartford 1 YP_001493750.1 Xylella fastidiosa 9a5c 1 NP_297906.1 Francisella tularensis subsp. holarctica 1 YP_001429248.1

FTNF002-00 Bacillus amyloliquefaciens FZB42 1 YP_001420263.1 Staphylococcus aureus subsp. aureus 1 YP_001575901.1

USA300_TCH1516 Streptococcus agalactiae A909 1 YP_330604.1 Shewanella sp. W3-18-1 1 YP_964836.1 Coxiella burnetii RSA 493 1 YP_001597542.1 Pseudomonas putida KT2440 1 NP_743519.1 Rickettsia massiliae MTU5 1 YP_001499599.1 Xylella fastidiosa M12 1 YP_001776226.1 Sphingomonas wittichii RW1 1 YP_001263859.1 Acidovorax sp. JS42 1 YP_985020.1 Chlamydophila abortus S26/3 1 YP_220011.1 Bacillus weihenstephanensis KBAB4 1 YP_001643141.1 Clavibacter michiganensis subsp. 1 YP_001223313.1 michiganensis NCPPB 382 Janthinobacterium sp. Marseille 1 YP_001354341.1 Chlamydia trachomatis 434/Bu 1 YP_001654450.1 Methylibium petroleiphilum PM1 1 YP_001019624.1 Francisella philomiragia subsp. 1 YP_001677823.1 philomiragia ATCC 25017 Haemophilus influenzae Rd KW20 1 NP_438700.1 Streptococcus mutans UA159 1 NP_722256.1 Carboxydothermus hydrogenoformans 1 YP_359660.1

Z-2901 Lactobacillus gasseri ATCC 33323 1 YP_814251.1 Oceanobacillus iheyensis HTE831 1 NP_691576.1 Nocardioides sp. JS614 1 YP_924834.1 Borrelia garinii PBi 1 YP_073180.1 Staphylococcus aureus subsp. aureus str. 1 YP_001332972.1

Newman Lactobacillus delbrueckii subsp. 1 YP_813428.1 bulgaricus ATCC 11842 Borrelia afzelii PKo 1 YP_710188.1 Staphylococcus epidermidis RP62A 1 YP_189051.1 Clostridium thermocellum ATCC 27405 1 YP_001039282.1 Clostridium difficile 630 1 YP_001086663.1 Rhodoferax ferrireducens T118 1 YP_522404.1 Chlamydophila felis Fe/C-56 1 YP_515283.1 Streptococcus pyogenes str. Manfredo 1 YP_001129238.1 Bartonella bacilliformis KC583 1 YP_989431.1 Thermotoga petrophila RKU-1 1 YP_001244016.1 Lactobacillus plantarum WCFS1 1 NP_784482.1 Haemophilus influenzae PittEE 1 YP_001289937.1 Dehalococcoides sp. BAV1 1 YP_001214692.1 Mycobacterium smegmatis str. MC2 155 1 YP_885961.1 Prochlorococcus marinus str. MIT 9215 1 YP_001484904.1 Rhodobacter sphaeroides ATCC 17025 1 YP_001168385.1 Mycobacterium sp. JLS 1 YP_001069474.1 Candidatus Carsonella ruddii PV 1 YP_802449.1 Bordetella avium 197N 1 YP_785113.1 Candidatus Sulcia muelleri GWSS 1 YP_001597988.1 Shigella boydii CDC 3083-94 1 YP_001882833.1 Clostridium botulinum A str. Hall 1 YP_001389023.1 Brucella melitensis biovar Abortus 2308 1 YP_418419.1 Geobacter metallireducens GS-15 1 YP_383003.1 Shigella dysenteriae Sd197 1 YP_405821.1 Synechococcus elongatus PCC 6301 1 YP_172498.1 Bacteroides fragilis NCTC 9343 1 YP_212836.1 Dehalococcoides sp. CBDB1 1 YP_308351.1 Sulfurimonas denitrificans DSM 1251 1 YP_393146.1 Silicibacter sp. TM1040 1 YP_612591.1 Campylobacter jejuni subsp. jejuni 1 YP_001482739.1 81116 Orientia tsutsugamushi Boryong 1 YP_001248601.1 Thermus thermophilus HB27 1 YP_005682.1 Streptococcus gordonii str. Challis 1 YP_001451152.1 substr. CH1 Nitratiruptor sp. SB155-2 1 YP_001355981.1 Francisella tularensis subsp. holarctica 1 YP_514346.1 Xanthomonas oryzae pv. oryzae MAFF 1 YP_453073.1

311018 Listeria welshimeri serovar 6b str. 1 YP_850287.1

SLCC5334 Candidatus Pelagibacter ubique 1 YP_265586.1

HTCC1062 Chlorobium tepidum TLS 1 NP_661429.1 Clostridium botulinum A3 str. Loch 1 YP_001788615.1

Maree Acidiphilium cryptum JF-5 1 YP_001235614.1 Campylobacter concisus 13826 1 YP_001466609.1 Lactobacillus helveticus DPC 4571 1 YP_001576924.1 Escherichia coli 536 1 YP_672231.1 Lawsonia intracellularis PHE/MN1-00 1 YP_594999.1 Geobacillus thermodenitrificans NG80-2 1 YP_001124351.1 Thermus thermophilus HB8 1 YP_143538.1 Methylobacterium radiotolerans JCM 1 YP_001753229.1

2831 Magnetococcus sp. MC-1 1 YP_864229.1 Bacteroides fragilis YCH46 1 YP_100674.1 Deinococcus radiodurans R1 1 NP_294329.2 Bacillus clausii KSM-K16 1 YP_174381.1 Leptospira borgpetersenii serovar 1 YP_801076.1

Hardjo-bovis JB197 Streptococcus pyogenes MGAS10394 1 YP_061079.2 Francisella tularensis subsp. novicida 1 YP_899158.1

U112 Legionella pneumophila str. Corby 1 YP_001251868.1 Escherichia coli O157 1 NP_290775.1 Polynucleobacter necessarius STIR1 1 YP_001798221.1 Mycobacterium avium subsp. 1 YP_883501.1 paratuberculosis K-10 Neisseria meningitidis FAM18 1 YP_975877.1 Rickettsia rickettsii str. Iowa 1 YP_001650337.1 Ehrlichia chaffeensis str. Arkansas 1 YP_507184.1 Leuconostoc mesenteroides subsp. 1 YP_819223.1 mesenteroides ATCC 8293 Opitutus terrae PB90-1 1 YP_001818936.1 Xanthomonas oryzae pv. oryzae 1 YP_202928.2

KACC10331 Borrelia burgdorferi B31 1 NP_212875.1 Xanthomonas campestris pv. campestris 1 YP_241635.1 str. 8004 Staphylococcus aureus subsp. aureus 1 NP_372554.1

Mu50 Streptococcus thermophilus CNRZ1066 1 YP_140632.2 Pseudomonas mendocina ymp 1 YP_001189167.1 Actinobacillus pleuropneumoniae 1 YP_001652031.1 serovar 3 str. JL03 Lactobacillus johnsonii NCC 533 1 NP_964486.1 Buchnera aphidicola str. Sg (Schizaphis 1 NP_660379.1 graminum) Streptococcus pneumoniae 1 YP_001695269.1

Hungary19A-6 Escherichia coli O157 1 NP_313150.1 Prosthecochloris vibrioformis DSM 265 1 YP_001130109.1 Parabacteroides distasonis ATCC 8503 1 YP_001305095.1 Frankia alni ACN14a 1 YP_711391.1 Shigella flexneri 5 str. 8401 1 YP_691583.1 Shewanella sp. MR-7 1 YP_736614.1 Streptococcus thermophilus LMG 18311 1 YP_138743.2 Bacillus cereus ATCC 14579 1 NP_830145.2 Staphylococcus aureus subsp. aureus 1 YP_186836.1

COL Haemophilus influenzae 86-028NP 1 YP_248251.1 Jannaschia sp. CCS1 1 YP_511301.1 Cytophaga hutchinsonii ATCC 33406 1 YP_678436.1 Coxiella burnetii RSA 331 1 YP_001597542.1 Yersinia pestis biovar Microtus str. 1 NP_991898.1

91001 Escherichia coli W3110 1 AP_004643.1 Legionella pneumophila str. Lens 1 YP_126085.1 Sulfurovum sp. NBC37-1 1 YP_001359263.1 Geobacter sulfurreducens PCA 1 NP_954379.1 Granulibacter bethesdensis CGDNIH1 1 YP_746002.1 Francisella tularensis subsp. 1 YP_001891090.1 mediasiatica FSC147 Anaplasma phagocytophilum HZ 1 YP_504858.1 Nitrosospira multiformis ATCC 25196 1 YP_413028.1 Neisseria meningitidis Z2491 1 NP_283295.1 Streptomyces griseus subsp. griseus 1 YP_001824282.1

NBRC 13350 Acidovorax avenae subsp. citrulli 1 YP_969318.1

AAC00-1 Alkaliphilus oremlandii OhILAs 1 YP_001513976.1 Yersinia pestis KIM 1 NP_667945.1 Candidatus Ruthia magnifica str. Cm 1 YP_903784.1

(Calyptogena magnifica) Staphylococcus aureus subsp. aureus 1 YP_500737.1

NCTC 8325 Chlamydia trachomatis D/UW-3/CX 1 NP_219614.1 Streptococcus pyogenes MGAS8232 1 NP_608083.1 Helicobacter pylori 26695 1 NP_206813.1 Salmonella enterica subsp. enterica 1 YP_153199.1 serovar Paratyphi A str. ATCC 9150 Ralstonia eutropha H16 1 YP_725221.1 Yersinia pseudotuberculosis YPIII 1 YP_001722542.1 Prochlorococcus marinus subsp. pastoris 1 NP_893554.1 str. CCMP1986 Mycobacterium ulcerans Agy99 1 YP_904988.1 Leptospira biflexa serovar Patoc strain 1 YP_001839710.1

'Patoc 1 (Paris)' Lactococcus lactis subsp. cremoris SK11 1 YP_808465.1 Streptococcus pyogenes MGAS2096 1 YP_601392.2 Thermoanaerobacter tengcongensis 1 NP_622246.1

MB4 Bacillus halodurans C-125 1 NP_241427.1 Pseudoalteromonas atlantica T6c 1 YP_663308.1 Streptococcus pyogenes MGAS5005 1 YP_283125.2 Pseudomonas putida GB-1 1 YP_001670711.1 Pseudomonas syringae pv. tomato str. 1 NP_794132.1

DC3000 Delftia acidovorans SPH-1 1 YP_001566673.1 Pasteurella multocida subsp. multocida 1 NP_246043.1 str. Pm70 Bacillus anthracis str. 'Ames Ancestor' 1 YP_026536.1 Shewanella frigidimarina NCIMB 400 1 YP_752327.1 Baumannia cicadellinicola str. Hc 1 YP_589020.1

(Homalodisca coagulata) Mycoplasma gallisepticum R 1 NP_853260.1 Brucella suis 1330 1 NP_699397.1 Thiomicrospira crunogena XCL-2 1 YP_390615.1 Lactobacillus salivarius UCC118 1 YP_536103.1 Sodalis glossinidius str. 'morsitans' 1 YP_453985.1 Pseudomonas syringae pv. phaseolicola 1 YP_276204.1

1448A Mycobacterium abscessus 1 YP_001704460.1 Campylobacter jejuni RM1221 1 YP_179342.1 Prochlorococcus marinus str. NATL2A 1 YP_292162.1 Listeria monocytogenes str. 4b F2365 1 YP_014693.1 Shewanella putrefaciens CN-32 1 YP_001182229.1 Bacillus subtilis subsp. subtilis str. 168 1 NP_388483.2 Petrotoga mobilis SJ95 1 YP_001568198.1 Chlorobium phaeobacteroides DSM 266 1 YP_912377.1 Mannheimia succiniciproducens 1 YP_087650.1

MBEL55E Rhodobacter sphaeroides ATCC 17029 1 YP_001042867.1 Fusobacterium nucleatum subsp. 1 NP_603573.1 nucleatum ATCC 25586 Mycobacterium abscessus 1 YP_001704460.1 Pseudomonas putida W619 1 YP_001747841.1 Wolinella succinogenes DSM 1740 1 NP_906560.1 Shewanella sp. ANA-3 1 YP_871196.1 Tropheryma whipplei TW08/27 1 NP_789032.1 Streptococcus pyogenes SSI-1 1 NP_803025.1 Xanthomonas campestris pv. campestris 1 NP_635914.1 str. ATCC 33913 Pseudoalteromonas haloplanktis 1 YP_338802.1

TAC125 Bacillus licheniformis ATCC 14580 1 YP_077850.1 Azoarcus sp. EbN1 1 YP_157651.1 Rickettsia conorii str. Malish 7 1 NP_360606.2 Ochrobactrum anthropi ATCC 49188 1 YP_001371564.1 Shewanella pealeana ATCC 700345 1 YP_001503536.1 Bifidobacterium adolescentis ATCC 1 YP_909155.1

15703 Halorhodospira halophila SL1 1 YP_001003905.1 Escherichia coli HS 1 YP_001460925.1 Helicobacter acinonychis str. Sheeba 1 YP_665398.1 Wolbachia endosymbiont of Drosophila 1 NP_966108.1 melanogaster Buchnera aphidicola str. Bp (Baizongia 1 NP_777658.1 pistaciae) Beijerinckia indica subsp. indica ATCC 1 YP_001832856.1

9039 Clostridium beijerinckii NCIMB 8052 1 YP_001307472.1 Flavobacterium psychrophilum JIP02/86 1 YP_001296850.1 Brucella abortus biovar 1 str. 9-941 1 YP_222996.1 Anaeromyxobacter dehalogenans 2CP-C 1 YP_466796.1 Neorickettsia sennetsu str. Miyayama 1 YP_506521.1 Ehrlichia ruminantium str. Gardel 1 YP_196591.1 Zymomonas mobilis subsp. mobilis 1 YP_163663.1

ZM4 Mycobacterium avium 104 1 YP_883501.1 Shigella flexneri 2a str. 301 1 NP_710007.1 Thermoanaerobacter sp. X514 1 YP_001662156.1 Brucella suis ATCC 23445 1 YP_001622039.1 Thermotoga maritima MSB8 1 NP_228315.1 Trichodesmium erythraeum IMS101 1 YP_723792.1 Lactobacillus brevis ATCC 367 1 YP_794793.1 Finegoldia magna ATCC 29328 1 YP_001692195.1 Acinetobacter baumannii ATCC 17978 1 YP_001085683.1 Salinibacter ruber DSM 13855 1 YP_446227.1 Rickettsia prowazekii str. Madrid E 1 NP_220992.1 Staphylococcus aureus subsp. aureus 1 NP_375138.1

N315 Streptococcus suis 05ZYH33 1 YP_001197517.1 Leptospira borgpetersenii serovar 1 YP_797550.1

Hardjo-bovis L550 Lactobacillus acidophilus NCFM 1 YP_193327.1 Clavibacter michiganensis subsp. 1 YP_001709297.1 sepedonicus Streptococcus pneumoniae D39 1 YP_817136.1 Anaplasma marginale str. St. Maries 1 YP_154104.2 Symbiobacterium thermophilum IAM 1 YP_076725.1

14863 Staphylococcus aureus subsp. aureus 1 YP_001442605.1 Mu3 Salmonella enterica subsp. enterica 1 YP_001591563.1 serovar Paratyphi B str. SPB7 Ralstonia solanacearum GMI1000 1 NP_518762.1 Clostridium phytofermentans ISDg 1 YP_001560383.1 Campylobacter curvus 525.92 1 YP_001408486.1 Streptococcus pyogenes MGAS10270 1 YP_599439.2 Nitrosomonas eutropha C91 1 YP_746458.1 Gramella forsetii KT0803 1 YP_863600.1 Streptococcus agalactiae 2603V/R 1 NP_689061.1 Oenococcus oeni PSU-1 1 YP_810924.1 Staphylococcus aureus subsp. aureus 1 YP_001317221.1

JH1 Prochlorococcus marinus str. MIT 9211 1 YP_001551441.1 Bartonella henselae str. Houston-1 1 YP_034076.1 Rickettsia canadensis str. McKiel 1 YP_001492053.1 Mycobacterium marinum M 1 YP_001849436.1 Streptococcus pyogenes MGAS10750 1 YP_603350.2 Streptococcus sanguinis SK36 1 YP_001034235.1 Staphylococcus saprophyticus subsp. 1 YP_300937.1 saprophyticus ATCC 15305 Acholeplasma laidlawii PG-8A 1 YP_001621223.1 Ehrlichia canis str. Jake 1 YP_303280.1 Rickettsia bellii OSU 85-389 1 YP_001496072.1 Prochlorococcus marinus str. MIT 9313 1 NP_895277.1 Pseudomonas stutzeri A1501 1 YP_001173626.1 Clostridium perfringens ATCC 13124 1 YP_696964.1 Bifidobacterium longum NCC2705 1 NP_696713.1 Shewanella baltica OS195 1 YP_001553109.1 Arthrobacter sp. FB24 1 YP_832366.1 Polynucleobacter sp. QLW-P1DMWA-1 1 YP_001156583.1 Pseudomonas fluorescens PfO-1 1 YP_350230.1 Shewanella sediminis HAW-EB3 1 YP_001472381.1 Buchnera aphidicola str. Cc (Cinara 1 YP_802588.1 cedri) Prochlorococcus marinus str. MIT 9215 1 YP_001484904.1 Coxiella burnetii Dugway 5J108-111 1 YP_001423709.2 Geobacter uraniireducens Rf4 1 YP_001233022.1 Francisella tularensis subsp. holarctica 1 YP_764065.1

OSU18 Chromohalobacter salexigens DSM 1 YP_574209.1

3043 Thermoanaerobacter pseudethanolicus 1 YP_001665695.1

ATCC 33223 Corynebacterium glutamicum ATCC 1 NP_599833.2

13032 Aster yellows witches'-broom 1 YP_456797.1 phytoplasma AYWB Staphylococcus aureus subsp. aureus 1 YP_041480.1

MRSA252 Francisella tularensis subsp. tularensis 1 YP_170600.1

SCHU S4 Campylobacter jejuni subsp. jejuni 1 YP_002344611.1

NCTC 11168 Heliobacterium modesticaldum Ice1 1 YP_001680009.1 Thiobacillus denitrificans ATCC 25259 1 YP_313850.1 Bacillus anthracis str. Sterne 1 YP_026536.1 Brucella canis ATCC 23365 1 YP_001594161.1 Listeria innocua Clip11262 1 NP_471508.1 Lactobacillus fermentum IFO 3956 1 YP_001843141.1 Clostridium perfringens str. 13 1 YP_696964.1 Clostridium botulinum B str. Eklund 1 YP_001884620.1

17B Desulfococcus oleovorans Hxd3 1 YP_001528436.1 Shewanella woodyi ATCC 51908 1 YP_001762658.1 Dichelobacter nodosus VCS1703A 1 YP_001210206.1 Caulobacter sp. K31 1 YP_001685773.1 Arcobacter butzleri RM4018 1 YP_001489375.1 Staphylococcus haemolyticus JCSC1435 1 YP_252916.1 Methanosarcina acetivorans C2A 2 NP_615593.2, AAM04073.1 Methanosarcina mazei Go1 1 NP_633821.1 Methanosarcina barkeri str. Fusaro 1 YP_305070.1 Methanospirillum hungatei JF-1 1 YP_502524.1 Lysinibacillus sphaericus C3-41 1 Unannotated; TBLASTN hit at E = 1x10-

7/genomic location Clostridium tetani E88 1 Unannotated; TBLASTN hit at E = 8x10-17 Magnetospirillum magneticum AMB-1 1 Unannotated; TBLASTN hit at E = 1x10-19 Escherichia coli APEC O1 1 Unannotated; TBLASTN hit at E = 9x10-50 Supplementary Table 6: GROES sequences in microbial genomes that contain GROEL. “No.”

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