Article

The PROSITE dictionary of sites and patterns in proteins, its current status

BAIROCH, Amos Marc

Reference

BAIROCH, Amos Marc. The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Research, 1993, vol. 21, no. 13, p. 3097-103

DOI : 10.1093/nar/21.13.3097 PMID : 8332530

Available at: http://archive-ouverte.unige.ch/unige:36853

Disclaimer: layout of this document may differ from the published version.

1 / 1 .-., 1993 Oxford University Press Nucleic Acids Research, 1993, Vol. 21, No. 13 3097-3103 The PROSITE dictionary of sites and patterns in proteins, its current status

Amos Bairoch Department of Medical Biochemistry, University of Geneva, 1 rue Michel Servet, 1211 Geneva 4, Switzerland

BACKGROUND FORMAT PROSITE is a compilation of sites and patterns found in protein The PROSITE database is composed of two ASCII (text) files. sequences; it can be used as a method ofdetermining the function The first file (PROSITE.DAT) is a computer-readable file that of uncharacterized proteins translated from genomic or cDNA contains all the information necessary for programs that make sequences. In some cases the sequence of an unknown protein use of PROSITE to scan sequence(s) for the occurrence of the is too distantly related to any protein ofknown structure to detect patterns. This file also includes, for each ofthe patterns described, its resemblance by overall sequence alignment, but relationships statistics on the number of hits obtained while scanning for that can be revealed by the occurrence in its sequence of a particular pattern in the SWISS-PROT protein sequence data bank [8]. cluster of residue types which is variously known as a pattern, Cross-references to the corresponding SWISS-PROT entries are motif, signature, or fingerprint. These motifs arise because also present in the file. The second file (PROSITE.DOC), which specific region(s) of a protein which may be important, for we call the textbook, contains textual information that documents example, for their binding properties or for their enzymatic each pattern. A user manual (PROSUSER.TXT) is distributed activity are conserved in both structure and sequence. These with the database; it fully describes the format of both files. A structural requirements impose very tight constraints on the sample textbook entry is shown in Figure 1 with the evolution of these small but important portion(s) of a protein corresponding data from the pattern file. sequence. The use ofprotein sequence patterns to determine the function ofproteins is becoming very rapidly one of the essential tools of . This reality has been recognized by CONTENT OF THE CURRENT RELEASE many authors [1,2]. While there have been a number of reviews of published patterns [3,4,5], no attempt had been made until Release 10.1 of PROSITE (April 1993) contains 635 very recently [6,7] to systematically collect biologically significant documentation entries describing 803 different patterns. The list patterns or to discover new ones. Based on these observations, ofthese entries is provided in Appendix 1. The database requires we decided in 1988, to actively pursue the development of a about 2 Mb of disk storage space. database of patterns which would be used to search against sequences of unknown function. This database, called PROSITE, contains some patterns which have been published in the COMPUTER PROGRAMS THAT MAKE USE OF literature, but the majority have been developed in the last four PROSITE years by the author. Many academic groups and commercial companies have developed computer programs that make use of PROSITE. We LEADING CONCEPTS list here some ofthese programs (a fuill descriptive list is included The design of PROSITE follows four leading concepts: with the database and is stored in a file called 'PROSITE.PRG'). Completeness. For such a compilation to be helpful in the determination of protein function, it is important that it contains as many biologically meaningful patterns as possible. ACADEMIC High specificity of the patterns. In the majority of cases we Program Operating system Author have chosen that are that do not patterns specific enough they MacPattern Apple McIntosh Rainer Fuchs [9] detect too many unrelated sequences, yet they will detect most, prosite.c IBM 3090400E and Unix Klaus Hartmuth if not all, sequences that clearly belong to the set in ProSearch Unix and DOS (AWK) Lee Kolakowski [10] consideration. cregex Unix and DOS Jack Leunissen dbsite/mksite Unix J.-M. Claverie Documentation. Each of the patterns is fully documented; the PROINDEX VAX VMS Steve Clark documentation includes a concise description of the protein Quelsite VAX VMS Claude Valencien family that it is designed to detect as well as a summary of Scrutineer VAX VMS and Unix Peter Sibbald [11] the reasons leading to the development of the pattern. PATTERN Unix Olivier Boulot PIP and PIPI VAX VMS and Unix Roger Staden [12] Periodic reviewing. It is important that each pattern be PATMAT OS and Unix Steven Henikoff [13] periodically reviewed to insure that it is still valid. PROTOMAT OS and Unix Steven Henikoff [14] 3098 Nucleic Acids Research, 1993, Vol. 21, No. 13

COMMERCIAL Program Package Supplier Operatng system MOTIF GCG Genetics Comp. Group Vax VMS and Unix QUEST IG-Suite IntelliGenetics Vax VMS and Unix PROMOT OML Vax VMS and Unix PROSITE PC/Gene IntelliGenetics DOS PROSITE GeneWorks IntelliGenetics Apple McIntosh Protean LaserGene DNASTAR Apple McIntosh PROTSITE National Biosciences DOS SEQ/Pattern ProExplore Biostructure Unix

FUTURE DEVELOPMENTS Basel Biozentrum Biocomputing server (EMBnet SWISS node) address: unibas.ch There are a number of protein families as well as functional or Internet bioftp. (or 131.152.8.1) structural domains that cannot be detected due using patterns to ExPASy (Expert Protein Analysis System server, University their extreme sequence divergence. Typical examples of of Geneva, Switzerland) important functional domains which are weakly conserved are Internet address: the immunoglobulin domains, the SH2 and SH3 domains, and .hcuge.ch (129.195.254.61) the fibronectin type I domain. In such domains there are only National Institute of Genetics (Japan) FTP server a few sequence positions which are well conserved. Any attempt Internet address: ftp.nig.ac.jp (133.39.16.66) to build a consensus pattern for such regions will either fail to pick up a significant proportion of the protein sequences that You can also browse through PROSITE using various Internet contain such a region (false negatives) or will pick up too many Gopher servers that specialize in biosciences (biogophers) [19]. proteins that do not contain the region (false positives). Gopher is a distributed document delivery service that allows Techniques based on the use ofweight matrices [15,16,17] allows a neophyte user to access various types of data residing on the detection of such proteins or domains. We plan to collaborate multiple hosts in a seamless fashion. closely with Dr P. Bucher ofthe Swiss Cancer Research Institute The present distribution frequency is four releases per year. (ISREC) in Lausanne and with Dr T.K. Attwood of the No restrictions are placed on use or redistribution of the data. University of Leeds to develop such methods and to integrate them into PROSITE. REFERENCES HOW TO OBTAIN PROSITE 1. Doolittle R.F. (In) Of URFs and ORFs: a primer on how to analyze derived sequences., University Science Books, Mill Valley, California, PROSrTE is distributed on magnetic tape and on CD-ROM by (1986). the EMBL Data Library. For all enquiries regarding the 2. Lesk A.M. (In) Computational Molecular Biology, Lesk A.M., Ed., subscription and distribution of PROSITE one should contact: ppl7-26, Oxford University Press, Oxford (1988). 3. Barker W.C., Hunt T.L., George D.G. Protein Seq. Data Anal. EMBL Data Library 1:363-373(1988). European Molecular Biology Laboratory 4. Hodgman T.C. Comput. Appl. Biosci. 5:1-13(1989). Postfach 10.2209, Meyerhofstrasse 1 5. Taylor W.R., Jones D.T. Curr. Opin. Struct. Biol. 1:327-333(1991). 6. Bork P. FEBS Lett. 257:191-195(1989). 6900 Heidelberg, Germany 7. Smith H.O., Annau T.M., Chandrasegaran S. Proc. Natl. Acad. Sci. USA Telephone: (+49 6221) 387 258 87:826-830(1990). Telefax: (+49 6221) 387 519 or 387 306 8. Bairoch A., Boeckmann B. Nucleic Acids Res. 20:2019-2022(1992). Electronic network address: [email protected] 9. Fuchs R. Comput. Appl. Biosci. 7:105-106(1991). 10. Kolakowski L.F. Jr., Leunissen J.A.M., Smith J.E. Biotechniques PROSITE can be obtained from the EMBL File Server [18]. 13:919-921(1992). Detailed instructions on how to make the best use ofthis service, 11. Sibbald P.R., Sommerfeldt H., Argos P. Comput. Appl. Biosci. and in 7:535-536(1991). particular on how to obtain PROSITE, can be obtained 12. Staden R. DNA Sequence 1:369-374(1991). by sending to the network address [email protected] 13. Wallace J.C., Henikoff S. Comput. Appl. Biosci. 8:249-254(1992). the following message: 14. Henikoff S., Henikoff J. Nucleic Acids Res. 19:6565-6572(1991). 15. Staden R. Nucleic Acids Res. 12:505-519(1984). HELP 16. Gribskov M., Luethy R., Eisenberg D. Meth. Enzymol. 183:146-159(1990). HELP PROSITE 17. Attwood T.K., Eliopoulos E.E., Findlay J.B.C. Gene 98:153-159(1991). 18. Stoehr P.J., Omond R.A. Nucleic Acids Res. 17:6763-6764(1989). If you have access to a computer system linked to the Internet 19. Gilbert D. Trends Biochem. Sci. 18:107-108(1993). you can obtain PROSITE using FTP (File Transfer Protocol), from the following file servers: EMBL anonymous FTP server Internet address: fip.EMBL-heidelberg.de (or 192.54.41.33) NCBI Repository (National Library of Medicine, NIH, Washington D.C., U.S.A.) Internet address: ncbi.nlm.nih.gov (130.14.20.1) Nucleic Acids Research, 1993, Vol. 21, No. 13 3099 a (PDOC00107) (PS00116; DNA POLYNERASEB) (BEGIN) - DNA otzerise f_1ty S slrnature* Replicative DNA polymerases (EC 2.7.7.7) are the key cataLyzing the accurate replication of DNA. They require either a sut RUA molecule or a protein as a primr for the de novo synthesis of a DNA chain. On the basis of sequence sImIlarities a nuwer of DNA polymera have been grouped together Cl to 7] under the designation of DNA polywrase fmily B. The polyerases that belong to thIs faellymare: - Higher eukaryotes polymfrases alpha. - Higher aukaryotes polymerises delta. - Yeast polywrise I/alpha (gene POLI), polyerase Il/epsilon (gene POL2), polyerae" ll/delta (gene POL3) and polyeraseREV3. - polymerase ll (gene diA or polC). Polymerses of viruses fram the herpesviridie family. - Polywraes fram Adenoviruses. Polymerases from Bsculoviruses. Polywrases from Chlorella virutes. Polywrases from Poxvlruses. Bacteriophage T4 polywrase. Podoviridie becteriophages Phi-29, M2, and PZA polywrase. Tectiviridae bacteriophage PRDI polymerase. Polymerases encoded on eukiryotic linear DNA plasmids such as lulyveromyces lactis pGKL1 and pGKL2 Agaricus bitorquis pEN, Ascobolus imersus pA 2, Cltviceps purpuree pCLKI and Mize S-1. Six regions of similarity (nuilered from I to VI) are found in all or a b subset of the above polymerises. The ost conserved region (I) includes a ID DNA POLYNERASE-B; PATTERN. perfectly conserved tetr tide which contains two ispartate residues. The AC PS0O 16- function of this consrvi region Is not yet known, however it has been DT APR-1996 (CREATED)- MAY-1993 (DATA UPDATE); AY-1993 (INFO UPDATE). suggested C3l that it my be involved in binding a magnsiu Ion. We use this DE DNA poltmrise famIly S sa ture. conserved region as a signature for this fmily of DNA polymerses. PA CYA- CGLIVNSTAC -D-T-D-CSG]-CLIVNFTC]-x-CL VNSTAC]. NR /RELEASEn24 28154* -Consensus pattern: EYA]- EGLIVNSTAC] -D-T-D- ESG]- ELIVNFTC] -x- CLIVNSTACI NR /TOTAL42(4fi- /P6SITIVE=41(41); /UNKNOWN0(0); /FALSE POS=1(1); Sequences known to belong to this class detected by the pttern: ALL, except NR /FALSE NEGu2(2) for yeast polywrase II/epsilon nd Agaricus bitorquis MEN. CC /TAXO-ANMGEAEV-/AX-REPEATu1- -Other sequence(s) detected In SWISS-PROT: chicken vitalI1ogenin 2. DR P26019, DP0 DR0NM, T; P0968, Dh T P280, D SCNPO, T -Last update: Nay 1993 / Pattern and text revised. DR P27727, DOARYU, T; P13382, DPOAYEAST, T P28339, DmDmOVIN, DR P28340, DPDNUNAN P15436, DPODEAST, P14284 D EST T- E11 Jung G., Leavitt N.C., Hsieh J.-C. Ito J. DR P21189, DPOZECOLI, T- P26811, DPOL-ULSO, P03261 DPOL-ADE2: T- Proc. IltI. Aced. Sci. U.S.A. 84:8o87-8291C1987). DR P04495, DPOL ADE05, T; DPOLADE07, T P06538, DPOLADEI2, T- E2] Bernad A., Zabillos A. Silas N., Blenco L. DR P03196, DPOL-ESV, T; , DPOL-NCNVA, T P04293, DPOLNSV11, T- ENBO J. 6:4219-4225(1967). DR P07917, DPOL NSVIA, P04292, DPOL NSV1K, ;P04, DPOL NSV1S, T; C 3] Argos P. DR P07918, DPOLNSV21, T; P2887, DPOLNSV6U, T; P , DPOL-NSVES, T;- Mucleic Acids Res. 16:9909-9916(1968). DR P2M59, DPOL NSVI1, T; P24907, DPOLNSVSA, T; P09252, DPOLTZVD, 7; E4] Wang T.S.-F. Wong S.W., Korn D. DR P094, DPOIPLULA,T P05468, DPO2kLULA, T; P2233, DPOL CAU, FASEB J. 3:14-21(0989). DR P10582, DPOL)IIZE, T; P18131, DPOL PVAC, P20509, DPOLVACCC, T; C 5] Delarue N., Poch 0., Todro N., Moras D., Argos P. DR P06856, DPOL VACCV, T- P21402, DPOL FOWPV, T 0, DPOLDPN2, T; Protein Engineering 3:461-467(1990). DR P06950, DPOL-BPPZA, T; P19694, DPOL2, P10479, DPOL RD, T; C 6] Ito J., Braithwaite D.K. DR P04415, DPOL-BPT4,T, Nucleic Acids Res. 19:4045-4057(1991). DR P22374, DPOL ASCIN, N; P21951, DPOE YEAST, N; n7 Braithwaite D.K., Ito J. DR P02845 VIT2:CHICK, F; - Nucleic Acids Res. 21:787-802(1993). DO PDOCO0O07; (END)

Figure 1. Sample data from PROSITE. a) A documentation (textbook) entry. b) The corresponding entry in the pattern file.

Appendix 1. List of patterns documentation entries in release 10.1 of PROS1TE

Post-translational modifications EGF-like domain cysteine pattern signature N-glycosylation site Fibrinogen beta and gamma chains C-terminal domain signature Glycosaminoglycan attachment site Type II fibronectin collagen-binding domain Tyrosine sulfatation site Hemopexin domain signature cAMP- and cGMP-dependent protein kinase phosphorylation site C-type lectin domain signature Protein kinase C phosphorylation site Osteonectin domain signatures Casein kinase II phosphorylation site Somatomedin B domain signature phosphorylation site Thyroglobulin type-1 repeat signature N-myristoylation site 'Trefoil' domain signature Amidation site Cellulose-binding domain, bacterial type Aspartic acid and asparagine hydroxylation site Cellulose-binding domain, fungal type Vitamin K-dependent carboxylation domain Chitin recognition or binding domain signature Phosphopantetheine attachment site Barwin domain signatures Prokaryotic membrane lipoprotein lipid attachment site WAP-type 'four-disulfide core' domain signature Prokaryotic N-terminal methylation site Phorbol esters/diacylglycerol binding domain Farnesyl group (CAAX box) C2 domain signature ZP domain signature Domains Endoplasmic reticulum targeting sequence DNA or RNA associated proteins Microbodies C-terminal targeting signal 'Homeobox' domain signature Gram-positive cocci surface proteins 'anchoring' hexapeptide 'Homeobox' antennapedia-type protein signature Bipartite nuclear targeting sequence 'Homeobox' engrailed-type protein signature Cell attachment sequence 'Paired box' domain signature ATP/GTP-binding site motif A (P-loop) 'POU' domain signatures EF-hand calcium-binding domain , C2H2 type, domain Actinin-type -binding domain signatures Zinc finger, C3HC4 type, signature Cofilin/tropomyosin-type actin-binding domain Nuclear hormones receptors DNA-binding region signature Apple domain GATA-type zinc finger domain Band 4.1 family domain signatures Poly(ADP-ribose) polymerase zinc finger domain Kringle domain signature Fungal Zn(2)-Cys(6) binuclear cluster domain 3100 Nucleic Acids Research, 1993, Vol. 21, No. 13

Appendix 1. continued

Leucine zipper pattern Ribosomal protein SI I signature Fos/jun DNA-binding basic domain signature Ribosomal protein S12 signature Myb DNA-binding domain repeat signatures Ribosomal protein S13 signature Myc-type, 'helix-loop-helix' putative DNA-binding domain signature Ribosomal protein S14 signature p53 tumor antigen signature Ribosomal protein S15 signature CBF/NF-Y subunits signatures Ribosomal protein S16 signature 'Cold-shock' DNA-binding domain signature Ribosomal protein S17 signature CTF/NF-I signature Ribosomal protein S18 signature Ets-domain signatures Ribosomal protein Si9 signature Fork head domain signatures Ribosomal protein S4e signaure HSF-type DNA-binding domain signature Ribosomal protein S6e signature IRF family signature Ribosomal protein S17e signature LIM domain Ribosomal protein S19e signature SRF-type transcription factors DNA-binding and dimerization domain Ribosomal protein S24e signature TEA domain signature Ribosomal protein S26e signature Transcription factor TFIIB repeat signature DNA mismatch repair proteins mutL/hexB/PMSI signature Transcription factor TFIID repeat signature DNA mismatch repair proteins mutS family signature TFIIS cysteine-rich domain signature RecF protein signatures DEAD and DEAH box families ATP-dependent helicases signature Small, acid-soluble spore proteins, alpha/beta type, signatures Eukaryotic putative RNA-binding region RNP-1 signature Fibrillarin signature Enzymes XPAC protein signatures Bacterial regulaory proteins, araC family signature Zinc-containing alcohol dehydrogenases signature Bacterial regulatory proteins, asnC family signature Iron-containing alcohol dehydrogenases signature Bacterial regulatory proteins, crp family signature Short-chain family signature Bacterial regulatory proteins, gntR family signature Aldo/keto reductase family signatures Bacterial regulatory proteins, lacl family signature Bacterial regulatory proteins, luxR family signature L- active site Bacterial regulatory proteins, lysR family signature D-isomer specific 2-hydroxyacid dehydrogenases signatures Bacterial regulatory proteins, merR family signature Hydroxymethylglutaryl-coenzyme A reductases signatures Transcriptional antiterminators bglG family signature 3-hydroxyacyl-CoA dehydrogenase signature Sigma-54 factors family signatures active site signature Sigma-70 factors family signaus Malic enzymes signature Sigma-54 interaction domain signatures Isocitrate and isopropyimalate dehydrogenases signature Single-strand binding signatures 6-phosphogluconate dehydrogenase signature Bacterial histone-like DNA-binding proteins signature Glucose-6-phosphate dehydrogenase active site Histone H2A signature IMP dehydrogenase/GMP reductase signature Histone H2B signature Bacterial quinoprotein dehydrogenases signatures Histone H3 signature FMN-dependent alpha-hydroxy acid dehydrogenases active site Histone H4 signature GMC oxidoreductases signatures HMGI/2 signature Eukaryotic molybdopterin oxidoreductases signature HMG-I and HMG-Y DNA-binding domain (A T-hook) Prokaryotic molybdopterin oxidoreductases signatures HMG14 and HMG17 signature Aldehyde dehydrogenases active sites Bromodomain Glyceraldehyde 3-phosphate dehydrogenase active site Chromo domain Fumarate reductase/succinate dehydrogenase FAD-binding site Regulator of chromosome condensation signatures Acyl-CoA dehydrogenases signatues Protamine P1 signature Glutamate/Leucine/Phenylalanine dehydrogenases active site Nuclear transition protein 1 signature D-amino acid oxidase signature Ribosomal protein L2 signature Delta I-pyrroline-5-carboxylate reductase signature Ribosomal protein L3 signature signature Ribosomal protein L5 signature Tetrahydrofolate dehydrogene/cyclohydrolase signatures Ribosomal protein L6 signatures Pyridine nucleotide-disulphide oxidoreductases class-I active site Ribosomal protein L9 signature Pyridine nucleotide-disulphide oxidoreductases class-II active site Ribosomal protein Lii signature Respiratory-chain NADH dehydrogenase subunit 1 signatures Ribosomal protein L13 signaure Respiratory-chain NADH dehydrogenase 30 Kd subunit signature Ribosomal protein L14 signature Respiratory-chain NADH dehydrogenase 49 Kd subunit signature Ribosomal protein L15 signature Respiratory-chain NADH dehydrogenase 51 Kd subunit signatures Ribosomal protein L16 signatures Respiratory-chain NADH dehydrogenase 75 Kd subunit signatures Ribosomal protein L22 signature Nitrite reductases and sulfite reductase putative siroheme-binding sites Ribosomal protein L23 signature Uricase signature Ribosomal protein L29 signature Cytochrome c oxidase subunit I, copper B binding region signature Ribosomal protein L30 signature Cytochrome c oxidase subunit II, copper A binding region signature Ribosomal protein L33 signature Multicopper oxidases signatures Ribosomal protein L34 signature Peroxidases signatures Ribosomal protein L19e signature signatures Ribosomal protein L30e signaure Glutathione peroxidases signatures Ribosomal protein L32e signature , putative iron-binding region signatures Ribosomal protein L46e signature Extradiol ring-cleavage signature Ribosomal protein S3 signatures Intradiol ring-cleavage dioxygenases signature Ribosomal protein S4 signature Bacterial ring hydroxylating dioxygenases alpha-subunit signature Ribosomal protein S5 signature Bacterial subunits signatre Ribosomal protein S7 signature Biopterin-dependent aromatic amino acid hydroxylases signature Ribosomal protein S8 signature Copper type II, ascorbate-dependent monooxygenases signatures Ribosomal protein S9 signature signatures Ribosomal protein S1O signature Fatty acid desaturases signatures Nucleic Acids Research, 1993, Vol. 21, No. 13 3101

Cytochrome P450 cysteine heme-iron ligand signature signature signature Carboxylesterases type-B active site Copper/Zinc signatures signatures Manganese and iron superoxide dismutases signature active site large subunit signature Histidine acid phosphatases signatures Ribonucleotide reductase small subunit signature 5'-nucleotidase signatures Nitrogenases component 1 alpha and beta subunits signatures Fructose-1-6-bisphosphatase active site NifH/frxC family signatures Serine/threonine specific protein phosphatases signature Nickel-dependent hydrogenases large subunit signatures Tyrosine specific protein phosphatases active site Glutamyl-tRNA reductase signature Inositol monophosphatase family signatures Prokaryotic zinc-dependent phospholipase C signature 3'5'-cyclic nucleotide phosphodiesterases signature active site cAMP phosphodiesterases class-Il signature Methylated-DNA--protein-cysteine methyltransferase active site Sulfatases signatures N-6 Adenine-specific DNA methylases signature AP endonucleases family 1 signatures N4 cytosine-specific DNA methylases signature AP endonucleases family 2 signatures C-5 cytosine-specific DNA methylases signatures Endonuclease HI iron-sulfur binding region signature Serine hydroxymethyltransferase pyridoxal-phosphate attachment site Ribonuclease III family signature Phosphoribosylglycinamide formyltransferase active site Bacterial Ribonuclease P protein component signature Aspartate and ornithine carbamoyltransferases signature Ribonuclease T2 family histidine active sites Transketolase signatures family signature Acyltransferases ChoActase/COT/CPT-II family signatures Beta-amylase signatures Thiolases signatures Polygalacturonase active site Chloramphenicol acetyltransferase active site Clostridium cellulases repeated domain signature cysE/lacA/nodL acetyltransferases signature Chitinases class I signatures Beta-ketoacyl synthases active site Alpha-lactalbumin/lysozyme C signature Chalcone and stilbene synthases active site Alpha-galactosidase signature Gamma-glutamyltranspeptidase signature Alpha-L-fucosidase putative active site active site Glycosyl family 1 signatures Phosphorylase pyridoxal-phosphate attachment site Glycosyl hydrolases family 2 signatures UDP-glucoronosyl and UDP-glucosyl transferases signature Glycosyl hydrolases family 3 active site Purine/pyrimidine phosphoribosyl transferases signature Glycosyl hydrolases family 5 signature Glutamine amidotransferases class-I active site Glycosyl hydrolases family 6 signatures Glutamine amidotransferases class-Il active site Glycosyl hydrolases family 9 active sites signatures Thymidine phosphorylase signature Glycosyl hydrolases family 10 active site S-Adenosylmethionine synthetase signatures Glycosyl hydrolases family 11 active site signatures Polyprenyl synthetases signatures Glycosyl hydrolases family 17 signature synthase alpha chain family Lum-binding site signature Glycosyl hydrolases family 31 signatures signatures Glycosyl hydrolases family 32 active site EPSP synthase active site Alkylbase DNA glycosidases aLkA family signature Aspartate aminotransferases pyridoxal-phosphate attachment site Uracil-DNA glycosylase signature Aminotransferases class-Il pyridoxal-phosphate attachment site S-adenosyl-L-homocysteine signatures Aminotransferases class-III pyridoxal-phosphate attachment site Cytosol aminopeptidase signature Aminotransferases class-IV signature Phosphoserine aminotransferase signature Aminopeptidase P and proline dipeptidase signature signature Methionine aminopeptidase signature Galactokinase signature Serine carboxypeptidases, active sites GHMP kinases putative ATP-binding domain Zinc carboxypeptidases, zinc-binding regions signatures signature Serine proteases, family, active sites kinases Serine proteases, subtilase family, active sites pfkB family of carbohydrate signatures Serine proteases, V8 family, active sites Phosphoribulokinase signature Prolyl endopeptidase family serine active site cellular-type signature ClpP proteases active sites Prokaryotic carbohydrate kinases signature Eukaryotic thiol (cysteine) proteases active sites Protein kinases signatures carboxyl-terminal hydrolase, putative active-site signature Pyruvate kinase active site signature Eukaryotic aspartyl proteases active site signature Neutral zinc metallopeptidases, zinc-binding region signature Aspartokinase signature Matrixins cysteine switch ATP:guanido phosphotransferases active site Insulinase family signature PTS Hpr component phosphorylation sites signatures recA signature PTS permeases phosphorylation sites signatures Proteasome subunits signature signature Signal peptidases I signatures Nucleoside diphosphate kinases active site signature Phosphoribosyl pyrophosphate synthetase signature Asparaginase/glutaminase active site 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature Urease active site Bacteriophage-type RNA polymerase family active site signature ArgE/dapE/CPG2 family signatures Eukaryotic RNA polymerase II heptapeptide repeat Dihydroorotase signatures Eukaryotic RNA polymerases 30 to 40 Kd subunits signature Beta-lactamases classes -A, -C, and -D active site DNA polymerase family A signature Beta-lactamases class B signatures DNA polymerase family B signature and agmatinase signatures DNA polymerase family X signature Adenosine and AMP deaminase signature Galactose-l-phosphate uridyl active site signature Inorganic pyrophosphatase signature CDP-alcohol phosphatidyltransferases signature signatures PEP-utilizing enzymes signatures ATP synthase alpha and beta subunits signature signatures ATP synthase gamma subunit signature Hydrolases ATP synthase delta (OSCP) subunit signature active sites signatures ATP synthase a subunit signature Lipases, serine active site ATP synthase c subunit signature 3102 Nucleic Acids Research, 1993, Vol. 21, No. 13 Appendix 1. confinued

E1-E2 ATPases phosphorylation site Cytochrome b/b6 signatures Sodium and potassium ATPases beta subunits signatus Cytochrome b559 subunits heme-binding site signature , serine active site Thioredoxin family active site Glutaredoxin active site Type-l copper (blue) proteins signature DDC/GAD/HDC pyridoxal-phosphate attachment site 2Fe-2S ferredoxins, iron-sulfur binding region signature Prokaryotic orihine and lysine decarboxylases pyridoxal-ps e attachment site 4Fe-4S ferredoxins, iron-sulfur binding region signature Orotidine 5'-phosphate decarboxylase active site High potential iron-sulfur proteins signature Phosphoenolpyruvate carboxylase active sites Rieske iron-sulfur protein signatures Phosphoenolpyruvate carboxykinase (GTP) signature Flavodoxin signature Phosphoenolpyruvate carboxykinase (ATP) signature Rubredoxin signature Indole-3-glycerol phosphate synthase signature Electron transfer flavoprotein alpha-subunit signature Ribulose bisphosphate carboxylase large chain active site Fructose-bisphosphate aldolase class-I active site Other transport proteins Fructose-bisphosphate aldolase class-H signatures Class I metallothioneins signature Malate synthase signature Ferritin iron-binding regions signatures Citrate synthase signature Bacterioferritin signature KDPG and KHG aldolases active site signatures Transfeffins signatures Isocitrate signature Plant hemoglobins signature DNA signatures Hemerythrins signature Eukaryotic-type carbonic anhydrases signature Arthropod hemocyanins/insect LSPs signatures Prokaryotic-type carbonic anhydrases signatures ATP-binding proteins 'active transport' family signature Fumarate lyases signature Binding-protein-ependent transport systems umer membrane component signatue family signature Serum albumin family signature Enolase signature Transthyretin signatures Serine/threonine dehydratases pyridoxal-phosphate attachment site Avidin/Streptavidin family signature Enoyl-CoA hydratase/ signature Eukaryotic cobalamin-binding proteins signature Tryptophan synthase alpha chain signature Lipocalin signature Tryptophan synthase beta chain pyridoxal-phosphate attachment site Cytosolic fatty-acid binding proteins signature Delta-aminolevulinic acid dehydratase active site LBP/BPI/CETP family signature Dihydrodipicolinate synthetase signatures Plant lipid transfer proteins signature Phenylalanine and histidine ammonia-lyases signature Uteroglobin family signatures Porphobilinogen deaminase -binding site Mitochondrial energy transfer proteins signature Guanylate cyclases signature Sugar transport proteins signatures signatures Sodium symporters signatures signature Prokaryotic sulfate- and thiosulfate-binding proteins signatures Amino acid penneases signature Aromatic amino acids permeases signature pyridoxal-phosphate attachment site Anion exchangers family signatrs Aldose I-epimerase putative active site Bacterial protein export pilT protein family signature Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature GltP/dctA family of transporters signatures FKBP-type peptidyl-prolyl cis-trans isomerase signatures MIP family signature Triosephosphate isomerase active site Neurotransmitters transporters signatures Xylose isomerase signatures General diffusion gram-negative porins signature Phosphoglucose isomerase signatures Eukaryotic porin signature family phosphohistidine signature Insulin-like growth factor binding proteins signature Phosphoglucomutase & phosphomannomutase phosphohistidine signature Methylmalonyl-CoA mutase signature Strctura proteins Eukaryotic DNA topoisomerase I active site 43 Kd postsynaptic protein signature Prokaryotic DNA topoisomerase I active site signatures DNA topoisomerase II signature Annexins repeated domain signature Clathrin light chains signatures Clusterin signatures Amioacyl-ueansfer RNA synthetases class-I signtr Connexins signatures Aminoacyl-transfer RNA synthetases class-I signatures Crystallins beta and gamma 'Greek key' motif signature WHEP-TRS domain signature Dynamin family signature ATP-citrate lyase and succinyl-CoA active site Intermediate filaments signature signatures Involucrin signature Ubiquitin-activating signature Kinesin motor domain signature Ubiquitin-conjugating enzymes active site Myelin basic protein signature Formate--tetrahydrofolate signatures Myelin P0 protein signature Adenylosuccinate synthetase active site Myelin proteolipid protein signature Argininosuccinate synthase signatures Neuromodulin (GAP-43) signatures Phosphoribosylglycinamide synthetase signature Profilin signature ATP-dependent DNA ligase signatures Surfactant associated polypeptide SP-C palmitoylation sites Others Synapsins signatures sopenicillin N synthetase signatures Synaptobrevin signature Site-specific recombinases signatues Synaptophysin/synaptoporin signature Thiamine pyrophosphate enzymes signature Tropomyosins signature Biotin-requiring enzymes attachment site Tubulin subunits alpha, beta, and gamma signature 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site Tubulin-beta mRNA autoregulation signal Putative AMP-binding domain signature Tau and MAP proteins repeated region signaure Neuraxin and MAP1B proteins repeated region signature Ekctron transport proteins F-actin capping protein alpha subunit signatures Cytochrome c family heme-binding site signature F-actin capping protein beta subunit signature Cytochrome b5 family, heme-binding domain signatue Vinculin family signatures Nucleic Acids Research, 1993, Vol. 21, No. 13 3103

Amyloidogenic glycoprotein signatures Myotoxins signature Cadherins extracellular repeated domain signature Heat-stable enterotoxins signature Insect flexible cuticle proteins signature Aerolysin type toxins signature Gas vesicles protein GVPa signatures Shiga/ ribosomal inactivating toxins active site signature Gas vesicles protein GVPc repeated domain signature Channel forming colicins signature Flagella basal body rod proteins signature Hok/gef family cell toxic proteins signature Plant viruses icosahedral capsid proteins 'S' region signature Staphyloccocal enterotoxins/Streptococcal pyrogenic exotoxins signatures Potexviruses and carlaviruses coat protein signature Thiol-activated cytolysins signature Receptors Membrane attack complex components/perforin signature Neurotransmitter-gated ion-channels signature Inhibitors G-protein coupled receptors signature Pancreatic trypsin inhibitor (Kunitz) family signature G-protein coupled receptors family 2 signatures Bowman-Birk serine protease inhibitors family signature Visual pigments (opsins) retinal binding site Kazal serine protease inhibitors family signature Bacterial rhodopsins retinal binding site Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature Receptor tyrosine kinase class II signature signature Receptor tyrosine kinase class III signature Potato inhibitor I family signature Receptor tyrosine kinase class V signatures Squash family of serine protease inhibitors signature Growth factor and cytokines receptors family signatures Cysteine proteases inhibitors signature TNFR/NGFR family cysteine-rich region signature Tissue inhibitors of metalloproteinases signature Integrins alpha chain signature Cereal trypsin/alpha-amylase inhibitors family signature Integrins beta chain cysteine-rich domain signature Alpha-2-macroglobulin family thiolester region signature Natriuretic peptides receptors signature Disintegrins signature Photosynthetic reaction center proteins signature Lambdoid phages regulatory protein CHI signature Photosystem I psaA and psaB proteins signature Others Phytochrome chromophore attachment site Pentaxin family signature Speract receptor repeated domain signature Immunoglobulins and major histocompatbility complex proteins signature TonB-dependent receptor proteins signature Gram-negative pili assembly chaperone signature Type-Il membrane antigens family signature Prion protein signatures Bacterial chemotaxis sensory transducers signature Cyclins signature Cytokines and growth factors Proliferating cell nuclear antigen signature Granulins signature Arrestins signature HBGF/FGF family signature Chaperonins cpn60 signature PTN/MK heparin-binding protein family signatures Chaperonins cpnlO signature Nerve growth factor family signature Chaperonins TCP-1 signatures Platelet-derived growth factor (PDGF) family signature Heat shock hsp7O proteins family signatures Small cytokines (intercrine/chemokine) signatures Heat shock hsp9O proteins family signature TGF-beta family signature DnaJ domains signatures TNF family signature Protein secY signatures Wnt-l family signature CDC48/PASl/SEC18 family signature Interferon alpha and beta family signature Ubiquitin signature Granulocyte-macrophage colony-stimulating factor signature Beta-transducin family Trp-Asp repeats signature Interleukin-l signature Ras GTPase-activating proteins signature Interleukin-2 signature Guanine-nucleotide dissociation stimulators CDC25 family signature Interleukin-6/G-CSF/MGF family signature Guanine-nucleotide dissociation stimulators CDC24 family signature Interleukin-7 signature family signature Interleukin-10 signature SRP54-type proteins GTP-binding domain signature LIF/OSM family signature GTP-binding elongation factors signature Eukaryotic initiation factor 5A hypusine signature Hormones and active peptides Prokaryotic-type peptide chain release factors signature Adipokinetic hormone family signature Calreticulin family signatures Bombesin-like peptides family signature S-100/ICaBP type calcium binding protein signature Calcitonin/CGRP/IAPP family signature Hemolysin-type putative calcium-binding region signature Corticotropin-releasing factor family signature HlyD family secretion proteins signature Granins signatures P-II protein signatures Gastrin/cholecystokinin family signature 14-3-3 proteins signatures Glucagon/GIP/secretin/VIP family signature Caseins alpha/beta signature Glycoprotein hormones alpha chain signatures Legume lectins signatures Glycoprotein hormones beta chain signatures Vertebrate galactoside-binding lectin signature Gonadotropin-releasing hormones signature Lysosome-associated membrane glycoproteins signatures Insulin family signature Glycophorin A signature Natriuretic peptides signature Seminal vesicle protein I repeats signature Neurohypophysial hormones signature Seminal vesicle protein II repeats signature Pancreatic hormone family signature Stress-induced proteins SRPl/T1Pl family signature Parathyroid hormone family signature Tissue factor signature Pyrokinins signature HCP repeats signature Somatotropin, prolactin and related hormones signatures Bacterial ice-nucleation proteins octamer repeat Tachykinin family signature Cell cycle proteins ftsW/rodA/spoVE signature Thymosin beta-4 family signature Enterobacterial virulence outer membrane protein signatures Cecropin family signature Staphylocoagulase repeat signature Mammalian defensins signature 11-S plant seed storage proteins signature Insect defensins signature Dehydrins signature Endothelins/sarafotoxins signature Germin family signature Toxins Small hydrophilic plant seed proteins signature Plant thionins signature Pathogenesis-related proteins BetvI family signature Snake toxins signature Thaumatin family signature