Roseiflexus spp. Number of uniquely mapped transcripts

Homolog on the metagenome Roseiflexus sp. RS-1 transcription metagenome gene annotation genome category metagenome ORF scaffold 12AM 1AM 2AM 3AM 4AM 5AM 6AM 7AM 8AM 9AM 10AM 12PM 1PM 2PM 3PM 4PM 5PM 6PM 7PM 8PM 9PM 10PM 11PM TOTAL Polyglucose biosynthesis/degradation cellulose synthesis/degradation Cellulose synthase RoseRS_3768 0 – weak day JCVI_PEP_metagenomic.orf.20918351.1 1113211799089 15 28 14 1 13 13 16 7 19 30 63 25 53 24 41 29 49 35 25 23 17 9 10 559 cellulase cellulose synthase (UDP-forming) || Cellulose synthaseRoseRS_0349 (UDP-forming)4 – weak night JCVI_PEP_metagenomic.orf.21251219.1 1113211796958 79 121 114 279 52 57 170 52 58 58 62 37 84 56 106 65 94 113 83 91 125 62 91 2109 Peptidase family M20/M25/M40 || Cellulase Glycogen synthesis/degradation alpha-glucan phosphorylase || Phosphorylase RoseRS_4181 2 – constitutive JCVI_PEP_metagenomic.orf.21528461.1 1113211797823 24 31 10 24 25 18 19 5 24 17 25 44 43 26 62 31 62 84 50 50 24 25 46 alpha-glucan phosphorylase || Phosphorylase RoseRS_4181 2 – constitutive JCVI_PEP_metagenomic.orf.21519717.1 1113211797791 243 270 255 269 141 133 258 117 232 203 390 333 443 344 879 355 778 701 518 472 486 342 362 glycosyl , group 1 || Starch (bacterial glycogen)RoseRS_1630 synthase 0 – weak day JCVI_PEP_metagenomic.orf.21218182.1 1113211796818 0 11 0 11 2 4 4 7 2 27 31 6 24 12 34 10 22 24 14 10 13 2 1 271 glycosyl transferase, group 1 || Starch (bacterial glycogen)RoseRS_2339 synthase 0 – weak day JCVI_PEP_metagenomic.orf.21429671.1 1113211797712 2 11 8 3 1 1 2 2 6 12 33 13 12 13 9 7 9 14 2 6 0 2 0 168 glycosyl transferase, group 1 || Starch (bacterial glycogen)RoseRS_2841 synthase 0 – weak day JCVI_PEP_metagenomic.orf.21550500.1 1113211797772 9 20 8 6 12 8 13 8 14 23 49 33 34 15 24 14 35 39 25 19 16 7 27 458 glycosyl transferase, group 1 || Starch (bacterial glycogen)RoseRS_2502 synthase 2 – constitutive JCVI_PEP_metagenomic.orf.21393780.1 1113211797781 24 50 33 25 35 34 34 25 37 30 79 36 37 30 47 41 55 54 54 30 53 40 43 926 glycosyl transferase, group 1 || Starch (bacterial glycogen)RoseRS_2380 synthase 2 – constitutive JCVI_PEP_metagenomic.orf.21579900.1 1113211797738 14 47 14 12 17 6 16 2 10 13 23 14 24 14 13 11 23 38 18 9 8 17 24 387 glycosyl transferase, group 1 || Starch (bacterial glycogen)RoseRS_1065 synthase 2 – constitutive JCVI_PEP_metagenomic.orf.21444910.1 1113211797758 36 105 49 43 31 19 60 33 72 69 74 51 62 47 93 49 95 118 95 54 52 58 80 1445 glycosyl transferase, group 1 || Starch (bacterial glycogen) synthase Glycolysis glk ROK family protein || Glucokinase RoseRS_2512 0 – weak day JCVI_PEP_metagenomic.orf.21401443.1 1113211797781 3 1 3 0 2 2 0 1 5 6 14 9 9 10 8 7 8 10 10 5 2 1 1 117 glk ROK family protein || Glucokinase RoseRS_0099 4 – weak night JCVI_PEP_metagenomic.orf.21577714.1 1113211797807 29 65 16 31 13 11 23 5 11 20 22 11 33 14 30 12 18 32 20 18 27 34 49 544 glk ROK family protein || N-acylmannosamine kinase RoseRS_3170 0 – weak day JCVI_PEP_metagenomic.orf.21368981.1 1113211796612 8 76 12 4 17 5 28 10 31 22 57 37 38 20 57 29 36 30 29 43 41 15 6 651 ROK family protein || Glucokinase RoseRS_2311 0 – weak day JCVI_PEP_metagenomic.orf.21158541.1 1113211797592 10 33 11 12 14 8 10 10 21 15 49 23 35 22 40 31 37 45 30 16 22 3 11 508 pgi Aldose 1-epimerase || Aldose 1-epimerase RoseRS_4356 2 – constitutive JCVI_PEP_metagenomic.orf.21436898.1 1113211797605 42 140 49 78 30 37 57 36 48 60 118 63 76 63 109 86 141 167 126 146 103 71 92 1938 pfk glucose-6-phosphate || Glucose-6-phosphateRoseRS_0693 isomerase 2 – constitutive JCVI_PEP_metagenomic.orf.21315454.1 1113211797399 4 6 2 5 3 1 0 6 2 1 17 11 7 0 13 1 7 18 7 6 5 2 6 130 pfk 1-phosphofructokinase || 1-phosphofructokinase RoseRS_1829 3 – strong night JCVI_PEP_metagenomic.orf.21542270.1 1113211797745 189 174 131 195 160 99 79 61 31 53 88 28 76 32 63 41 102 316 419 458 435 302 268 3800 pfk phosphofructokinase || 6-phosphofructokinase RoseRS_1831 4 – weak night JCVI_PEP_metagenomic.orf.21542214.1 1113211797745 1530 2591 2155 2091 1338 1466 2324 928 930 1102 1010 1129 939 817 1855 814 3764 8047 7067 5544 4598 2534 2272 56845 pfk Phosphofructokinase || 6-phosphofructokinase RoseRS_2734 0 – weak day JCVI_PEP_metagenomic.orf.21406539.1 1113211797422 16 29 10 12 5 13 18 13 19 26 81 32 41 25 48 16 49 55 19 20 28 10 36 621 6-phosphofructokinase || 6-phosphofructokinase RoseRS_2049 3 – strong night JCVI_PEP_metagenomic.orf.20845497.1 1113211797229 121 187 221 130 151 148 137 115 49 86 102 60 69 27 63 24 149 298 258 329 267 213 156 3360 tpiA protein of unknown function RoseRS_3813 2 – constitutive JCVI_PEP_metagenomic.orf.20897539.1 1113211796899 51 111 73 106 78 85 81 47 109 98 127 98 122 89 212 93 168 173 172 126 113 89 85 2506 gapA triose-phosphate isomerase || Triosephosphate isomeraseRoseRS_0387 4 – weak night JCVI_PEP_metagenomic.orf.21094861.1 1113211797081 1154 1384 1043 1379 825 912 886 651 433 444 630 720 875 534 1110 404 1539 3839 3537 2866 2493 1634 1121 30413 pgk Glyceraldehyde 3-phosphate dehydrogenase, NADRoseRS_1473 binding domain || Glyceraldehyde4 – weak night 3-phosphateJCVI_PEP_metagenomic.orf.21289224.1 dehydrogenase (phosphorylating) 1113211796995 161 180 206 157 156 168 165 89 123 124 229 170 247 126 269 111 272 267 184 207 188 270 187 4256 gpm phosphoglycerate kinase || Phosphoglycerate kinaseRoseRS_0245 2 – constitutive JCVI_PEP_metagenomic.orf.21370189.1 1113211797586 12 43 26 37 36 35 29 15 49 42 77 42 71 33 81 36 53 68 34 27 33 32 12 923 phosphoglycerate mutase || Phosphoglycerate mutaseRoseRS_0822 2 – constitutive JCVI_PEP_metagenomic.orf.21520132.1 1113211797755 89 153 112 144 95 99 100 82 162 132 204 148 203 143 234 237 218 203 148 174 125 73 128 3406 2,3-bisphosphoglycerate-independent phosphoglycerateRoseRS_1012 mutase || Phosphoglycerate2 – constitutive mutaseJCVI_PEP_metagenomic.orf.21368105.1 1113211797668 4 6 13 12 7 7 9 2 8 11 13 17 12 10 26 11 15 18 8 8 16 2 15 250 phosphoglycerate mutase family protein RoseRS_1599 4 – weak night JCVI_PEP_metagenomic.orf.21142060.1 1113211796952 27 48 110 134 34 38 25 9 22 30 54 27 40 28 47 17 62 64 53 15 16 71 70 1041 phosphoglycerate mutase || Phosphoglycerate mutaseRoseRS_1699 4 – weak night JCVI_PEP_metagenomic.orf.21381872.1 1113211797781 23 45 34 89 22 36 39 11 21 24 35 13 28 13 46 17 36 39 18 31 29 32 36 717 phosphoglycerate mutase || Phosphoglycerate mutaseRoseRS_4586 0 – weak day JCVI_PEP_metagenomic.orf.21532634.1 1113211797768 8 43 10 39 19 12 16 13 33 33 71 45 46 39 77 27 55 71 79 35 43 10 25 849 eno phosphoglycerate mutase || Phosphoglycerate mutaseRoseRS_4532 4 – weak night JCVI_PEP_metagenomic.orf.21195286.1 1113211797094 513 673 600 828 468 493 482 339 433 447 524 460 489 382 640 502 784 881 613 789 697 598 872 13507 pyk phosphopyruvate hydratase || Phosphopyruvate hydrataseRoseRS_1428 4 – weak night JCVI_PEP_metagenomic.orf.21111556.1 1113211796034 39 100 23 40 21 22 34 10 30 42 46 20 32 20 62 28 22 44 46 38 42 47 57 865 pyruvate kinase || Pyruvate kinase Gluconeogenesis glpX RoseRS_4187 4 – weak night JCVI_PEP_metagenomic.orf.21528842.1 1113211797823 5 22 24 5 11 16 12 9 13 17 30 11 34 6 21 4 20 30 15 30 14 25 41 415 glpX fructose-1,6-bisphosphatase, class II RoseRS_4129 4 – weak night JCVI_PEP_metagenomic.orf.21524149.1 1113211797790 76 132 104 106 74 87 79 83 85 79 112 105 110 88 100 58 88 110 77 115 78 78 90 2114 fructose-1,6-bisphosphatase, class II RoseRS_2049 3 – strong night JCVI_PEP_metagenomic.orf.20845497.1 1113211797229 121 187 221 130 151 148 137 115 49 86 102 60 69 27 63 24 149 298 258 329 267 213 156 3360 protein of unknown function oxidative pentose phosphate pathway ( Entner-Doudoroff) zwf RoseRS_2562 0 – weak day JCVI_PEP_metagenomic.orf.21206975.1 1113211797330 5 8 1 1 0 5 7 6 7 7 18 21 11 12 16 8 23 18 17 2 10 3 0 206 gnd glucose-6-phosphate dehydrogenase || Glucose-6-phosphateRoseRS_4286 1-dehydrogenase2 – constitutive JCVI_PEP_metagenomic.orf.21238889.1 1113211796700 14 34 18 21 6 18 19 10 17 24 53 22 38 40 64 29 51 65 34 24 38 19 39 697 6-phosphogluconate dehydrogenase (decarboxylating) || Phosphogluconate dehydrogenase (decarboxylating) non-oxidative pentose phosphate pathway rpiA ribose-5-phosphate isomerase RoseRS_2910 2 – constitutive JCVI_PEP_metagenomic.orf.21312388.1 1113211797731 16 75 28 17 18 20 21 12 36 38 60 44 52 37 79 72 119 156 151 102 104 38 72 1367 tktA transketolase RoseRS_4614 2 – constitutive JCVI_PEP_metagenomic.orf.21531348.1 1113211797768 295 700 395 521 226 252 453 233 307 399 587 520 424 466 961 489 943 749 614 601 638 352 418 11543 talA (putative) transaldolase RoseRS_4615 2 – constitutive JCVI_PEP_metagenomic.orf.21531291.1 1113211797768 36 55 41 71 31 57 48 30 45 37 70 43 70 42 90 71 70 56 35 51 64 51 67 1231 rbsK ribokinase RoseRS_3280 0 – weak day JCVI_PEP_metagenomic.orf.21379816.1 1113211796406 2 15 16 14 7 7 19 8 16 21 39 20 21 18 31 16 20 22 29 29 22 7 6 405 ribose-phosphate pyrophosphokinase RoseRS_0965 2 – constitutive JCVI_PEP_metagenomic.orf.21367513.1 1113211797668 41 77 26 42 26 37 29 23 27 35 78 51 67 46 82 56 87 79 58 62 53 23 40 1145 RoseRS_4394 2 – constitutive JCVI_PEP_metagenomic.orf.21540916.1 1113211797761 100 266 123 208 160 137 168 90 139 139 195 141 168 118 308 189 276 270 265 190 176 176 162 4164 RoseRS_4537 0 – weak day JCVI_PEP_metagenomic.orf.21182834.1 1113211797094 15 60 20 32 21 8 21 16 45 33 70 54 66 30 78 48 61 60 33 23 40 38 17 889 anapleurotic reactions ppc PEP carboxylase RoseRS_2753 2 – constitutive JCVI_PEP_metagenomic.orf.21412605.1 1113211797422 73 278 126 113 65 59 116 88 73 94 150 108 106 72 229 148 275 238 200 179 168 106 148 3212 - pyruvate carboxyltransferase, RoseRS_1061 2 – constitutive JCVI_PEP_metagenomic.orf.21444985.1 1113211797758 32 76 40 32 54 32 34 19 58 74 104 52 71 46 69 38 92 76 24 75 70 68 24 1260 pckA PEP carboxykinase RoseRS_2496 3 – strong night JCVI_PEP_metagenomic.orf.21397285.1 1113211797781 2262 3065 2769 2564 1567 1924 1974 1421 768 1010 1243 1045 1433 963 1700 1175 4006 16970 11712 10199 6101 4207 3254 83332 malic (tme) (malate + NAD+ → pyruvate + CO2 + NADH) RoseRS_2286 2 – constitutive JCVI_PEP_metagenomic.orf.21197625.1 1113211797592 39 125 101 171 52 75 103 46 96 109 178 129 121 75 130 125 211 185 141 110 107 114 104 2647 oxidative tricarboxylic acid cycle pyruvate dehydrogenase E2 subunit (2.3.1.12) pyruvate dehydrogenase RoseRS_1726 2 – constitutive JCVI_PEP_metagenomic.orf.21451764.1 1113211797617 25 33 30 40 23 12 25 8 19 32 58 32 50 34 97 101 147 124 76 67 42 42 64 1181 pyruvate dehydrogenase E1 subunit (1.2.4.1) RoseRS_1727 0 – weak day JCVI_PEP_metagenomic.orf.21451547.1 1113211797617 20 37 28 58 16 16 15 16 31 17 44 46 73 57 101 112 161 100 45 43 27 30 16 1109 pyruvate dehydrogenase E1 subunit (1.2.4.1) RoseRS_1728 2 – constitutive JCVI_PEP_metagenomic.orf.21451375.1 1113211797617 41 96 71 43 27 14 50 12 36 37 94 56 93 99 269 172 341 232 129 95 130 83 81 2301 pyruvate dehydrogenase E1 subunit (1.2.4.1) RoseRS_2952 0 – weak day JCVI_PEP_metagenomic.orf.21462964.1 1113211797824 22 49 53 56 51 34 36 32 45 66 161 119 130 87 159 69 132 103 102 61 47 55 62 1731 pyruvate:ferredoxin (1.2.7.1) porA RoseRS_1213 3 – strong night JCVI_PEP_metagenomic.orf.21465853.1 1113211797794 702 928 1071 847 544 532 577 350 103 217 107 52 47 27 66 35 1551 8050 5065 4089 2287 1521 1077 29845 gltA citrate synthase RoseRS_3488 JCVI_PEP_metagenomic.orf.21373771.1 1113211797117 9 21 34 20 45 24 29 18 22 19 31 33 51 31 53 38 85 87 23 18 14 7 10 722 acnA RoseRS_0235 2 – constitutive JCVI_PEP_metagenomic.orf.21547364.1 1113211797774 194 257 255 282 198 193 177 141 279 291 522 479 578 322 672 501 566 489 286 373 310 256 325 7946 icd isocitrate dehydrogenase RoseRS_0785 2 – constitutive JCVI_PEP_metagenomic.orf.21240518.1 1113211796856 226 720 380 475 220 241 372 226 493 350 604 673 456 481 1032 849 957 738 591 570 560 302 474 11990 korG 2-oxoglutarate ferredoxin oxidoreductase, gammaRoseRS_1368 subunit 4 – weak night JCVI_PEP_metagenomic.orf.21206676.1 1113211796325 26 43 58 49 29 20 18 14 18 14 46 15 12 12 36 15 27 58 78 74 67 32 14 775 korA 2-oxoglutarate ferredoxin oxidoreductase, alpha subunitRoseRS_1551 1 – strong day JCVI_PEP_metagenomic.orf.21475489.1 1113211797697 52 105 75 153 71 50 58 41 102 166 355 443 592 492 852 591 1155 1263 277 162 126 91 76 7348 korB 2-oxoglutarate ferredoxin oxidoreductase, beta subunitRoseRS_1552 1 – strong day JCVI_PEP_metagenomic.orf.21475562.1 1113211797697 63 118 95 96 42 53 46 30 86 154 355 479 460 458 873 630 954 832 272 177 139 53 108 6573 sucB 2-OGDH, E2 subunit RoseRS_1675 0 – weak day JCVI_PEP_metagenomic.orf.21315295.1 1113211796836 3 26 8 42 7 12 12 11 19 21 77 31 52 37 52 48 50 59 25 27 19 13 3 654 sucA 2-OGDH, E2 subunit RoseRS_3396 1 – strong day JCVI_PEP_metagenomic.orf.21408599.1 1113211795955 35 82 41 47 50 54 35 39 129 143 342 253 275 201 363 232 360 403 134 95 88 44 63 3508 2-OGDH, E2 subunit RoseRS_3397 0 – weak day JCVI_PEP_metagenomic.orf.21408781.1 1113211795955 10 38 28 21 6 19 25 18 45 62 112 104 110 78 147 100 173 198 89 73 58 31 43 1588 sucD succinyl-CoA synthetase, alpha subunit RoseRS_3250 2 – constitutive JCVI_PEP_metagenomic.orf.21400372.1 1113211796869 82 133 88 169 113 69 123 59 144 152 202 184 217 140 284 181 215 196 188 172 201 92 136 3540 sucC succinyl-CoA synthetase, beta subunit RoseRS_3930 2 – constitutive JCVI_PEP_metagenomic.orf.21390869.1 1113211797444 163 242 188 342 234 137 225 112 284 299 449 435 383 211 486 217 393 335 257 269 234 144 221 6260 sdhA succinate dehydrogenase, flavoprotein subunit RoseRS_2399 0 – weak day JCVI_PEP_metagenomic.orf.21579710.1 1113211797738 254 279 601 527 396 555 509 339 1063 855 1580 1356 1443 940 1496 725 1515 1071 565 471 369 328 378 17615 succinate dehydrogenase, cytochrome b subunit RoseRS_2400 2 – constitutive JCVI_PEP_metagenomic.orf.21579686.1 1113211797738 121 81 211 189 186 219 134 115 268 214 379 291 384 242 350 136 372 288 173 90 96 106 129 4774 fumC RoseRS_3341 2 – constitutive JCVI_PEP_metagenomic.orf.21258870.1 1113211796263 304 427 441 609 248 332 508 224 416 461 866 506 596 371 753 389 704 624 353 439 425 358 489 10843 mdh malate dehydrogenase RoseRS_0253 4 – weak night JCVI_PEP_metagenomic.orf.21236220.1 1113211798670 37 30 56 54 45 52 46 28 25 38 40 39 37 24 45 26 63 78 96 69 69 52 51 1100

PHB synthesis/degradation

PHB ↔ 3-hydroxybutanoyl-CoA alpha/beta fold RoseRS_4553 4 – weak night JCVI_PEP_metagenomic.orf.21533702.1 1113211797768 1465 1251 2502 3219 2772 3858 2462 1564 1882 1382 1496 971 1105 532 552 287 279 298 443 746 873 1434 1355 32728

3-hydroxybutanoyl-CoA ↔ acetoacyl-CoA oxidoreductase, short chain dehydrogenase/reductaseRoseRS_4347 family || 3-oxoacyl-[acyl-carrier3 – strong night protein]JCVI_PEP_metagenomic.orf.21437532.1 reductase 1113211797605 1080 1864 1489 1098 524 568 697 347 351 356 486 604 571 588 1174 772 2786 5320 5725 6017 3877 2543 1728 40565 Acetoacyl-CoA ↔ acetyl-CoA hypothetical protein RoseRS_0429 0 – weak day JCVI_PEP_metagenomic.orf.21553164.1 1113211797732 19 152 35 59 21 37 95 34 167 97 150 72 107 43 91 47 98 255 184 56 83 17 47 1966 acetyl-CoA acetyltransferases || Acetyl-CoA C-acyltransferaseRoseRS_2969 1 – strong day JCVI_PEP_metagenomic.orf.21457639.1 1113211797824 40 63 57 47 24 48 65 36 358 289 2068 1084 879 377 794 424 289 150 71 69 55 34 55 7376 acetyl-CoA acetyltransferases || Acetyl-CoA C-acetyltransferaseRoseRS_3911 2 – constitutive JCVI_PEP_metagenomic.orf.21391156.1 1113211797444 8 34 21 45 8 17 22 12 27 17 57 41 51 21 34 35 67 91 40 38 46 24 18 774 acetyl-CoA acetyltransferases || Acetyl-CoA C-acetyltransferaseRoseRS_4348 4 – weak night JCVI_PEP_metagenomic.orf.21437414.1 1113211797605 1645 1380 1514 1893 1232 982 802 442 354 443 582 581 718 542 924 699 2234 4185 4187 4018 2739 2747 2137 36980 Acetoacyl-CoA ↔ acetoacetate acetoacetate-CoA || Acetoacetate--CoA ligaseRoseRS_1953 2 – constitutive JCVI_PEP_metagenomic.orf.21500266.1 1113211797752 83 234 152 95 70 63 95 86 110 143 257 232 259 172 374 161 301 338 301 239 170 120 136 4191

Branched-chain amino acid biosynthesis Acetolactate synthase small subunit (ilvB) Thiamine pyrophosphate enzyme, central domain RoseRS_0954|| Acetolactate synthase2 – constitutive JCVI_PEP_metagenomic.orf.21346864.1 1113211797061 33 35 15 38 30 25 26 10 16 41 60 47 49 24 38 23 42 57 36 35 36 32 20 768 Acetolactate synthase large subunit (ilvH) acetolactate synthase, small subunit || AcetolactateRoseRS_1967 synthase 2 – constitutive JCVI_PEP_metagenomic.orf.21294566.1 1113211797266 227 323 236 231 223 217 227 168 527 276 348 515 337 303 786 325 616 449 390 452 431 355 300 8262 Acetolactate synthase small subunit (ilvB) acetolactate synthase, large subunit, biosynthetic RoseRS_1968type || Acetolactate 2synthase – constitutive JCVI_PEP_metagenomic.orf.21294521.1 1113211797266 581 605 737 558 596 541 659 381 1306 745 940 1142 922 857 1815 674 1755 940 884 1027 1112 930 512 20219 Ketol-acid reductoisomerase ketol-acid reductoisomerase || Ketol-acid reductoisomeraseRoseRS_1966 0 – weak day JCVI_PEP_metagenomic.orf.21294966.1 1113211797266 96 224 112 102 85 93 85 81 293 208 279 264 220 215 353 242 313 181 182 153 197 121 82 4181 dihydroxyacid dihydroxy-acid dehydratase || Dihydroxy-acid dehydrataseRoseRS_3155 2 – constitutive JCVI_PEP_metagenomic.orf.21349906.1 1113211796612 98 103 135 130 79 105 109 69 106 108 167 182 170 92 229 115 154 192 131 168 160 133 121 3056 branched-chain amino acid transferase branched-chain amino acid aminotransferase || Branched-chainRoseRS_1962 amino2 acid– constitutive transaminaseJCVI_PEP_metagenomic.orf.21296904.1 1113211797266 48 91 80 126 49 86 51 50 88 106 127 121 135 86 145 103 228 154 117 134 137 83 53 2398 branched-chain amino acid transferase branched-chain amino acid aminotransferase || Branched-chainRoseRS_2544 amino0 acid– weak transaminase day JCVI_PEP_metagenomic.orf.21179865.1 1113211800320 3 8 10 14 4 1 5 0 15 8 17 7 11 8 19 14 11 20 3 5 7 2 5 197 2-isopropylmalate synthase 2-isopropylmalate synthase || 2-isopropylmalate synthaseRoseRS_1965 2 – constitutive JCVI_PEP_metagenomic.orf.21295850.1 1113211797266 143 123 201 153 137 139 104 56 248 223 261 201 222 140 260 174 282 219 155 264 189 209 129 4232 2-isopropylmalate synthase 2-isopropylmalate synthase/homocitrate synthase RoseRS_1963family protein || 2-isopropylmalate2 – constitutive synthaseJCVI_PEP_metagenomic.orf.21296484.1 1113211797266 111 150 107 98 79 101 100 74 199 217 255 226 203 159 255 180 350 207 197 211 262 133 99 3973 3-isopropylmalate dehydratase large subunit Aconitase family (aconitate hydratase) || 3-isopropylmalateRoseRS_1053 dehydratase2 – constitutive JCVI_PEP_metagenomic.orf.20932068.1 1113211796561 84 344 56 109 72 50 148 70 154 88 214 154 109 111 330 89 299 169 190 197 193 113 136 3479 3-isopropylmalate dehydratase small subunit 3-isopropylmalate dehydratase, small subunit || HomoaconitateRoseRS_1056 hydratase4 – weak night JCVI_PEP_metagenomic.orf.20937838.1 1113211796561 50 47 36 48 52 29 31 8 36 37 59 29 25 19 42 19 39 25 24 48 61 53 38 855 isopropylmalate isomerase small subunit (leuD) 3-isopropylmalate dehydratase, small subunit || 3-isopropylmalateRoseRS_1960 dehydratase0 – weak day JCVI_PEP_metagenomic.orf.21297858.1 1113211797266 43 151 44 102 45 31 72 58 144 130 137 174 130 80 208 161 388 215 171 181 203 60 62 2990 isopropylmalate isomerase large subunit 3-isopropylmalate dehydratase, large subunit || 3-isopropylmalateRoseRS_1961 dehydratase2 – constitutive JCVI_PEP_metagenomic.orf.21297409.1 1113211797266 133 294 150 189 125 103 154 85 212 234 313 260 238 241 359 234 515 407 243 196 271 198 164 5318 3-isopropylmalate dehydrogenase dehydrogenase, isocitrate/isopropylmalate family ||RoseRS_1057 3-isopropylmalate 4dehydrogenase – weak night JCVI_PEP_metagenomic.orf.20940733.1 1113211796561 81 280 124 144 60 70 59 48 100 85 164 91 114 95 142 97 135 136 116 177 137 139 183 2777 Valyl-tRNA synthetase valyl-tRNA synthetase || Valine--tRNA ligase RoseRS_0129 0 – weak day JCVI_PEP_metagenomic.orf.21159482.1 1113211797147 165 333 227 262 156 149 222 128 240 274 572 447 577 395 957 353 608 641 523 296 281 209 211 8226 Isoleucyl-tRNA synthetase isoleucyl-tRNA synthetase || Isoleucine--tRNA ligaseRoseRS_0727 4 – weak night JCVI_PEP_metagenomic.orf.21331018.1 1113211797399 211 330 317 332 195 204 261 174 128 206 312 211 180 121 284 126 379 456 356 421 297 295 325 6121 Leucyl-tRNA synthetase (leuS) tRNA synthetases class I (I, L, M and V) || Leucine--tRNARoseRS_4535 ligase 2 – constitutive JCVI_PEP_metagenomic.orf.21189519.1 1113211797094 167 208 173 235 171 145 204 96 241 287 529 426 495 264 640 293 589 427 257 255 181 207 217 6707

3-Hydroxypropionate pathway Acetyl-CoA carboxylase accB acetyl-CoA carboxylase, biotin carboxyl carrier proteinRoseRS_3172 2 – constitutive JCVI_PEP_metagenomic.orf.21354538.1 1113211796612 85 175 108 120 111 118 157 108 198 211 219 221 206 197 238 194 264 285 284 180 209 71 107 4066 accD acetyl-CoA carboxylase, carboxyl transferase, betaRoseRS_3199 subunit || Propionyl-CoA1 – strong carboxylase day JCVI_PEP_metagenomic.orf.21360881.1 1113211796612 8 32 7 6 13 23 25 12 735 444 2177 1277 1382 769 1413 425 712 134 24 13 27 9 2 9669 accD acetyl-CoA carboxylase, carboxyl transferase, alphaRoseRS_0393 subunit || Acetyl-CoA2 – constitutive carboxylase JCVI_PEP_metagenomic.orf.20995989.1 1113211800964 0 1 0 0 0 0 2 0 3 0 9 2 4 4 7 0 4 4 5 3 0 0 0 48 accA acetyl-CoA carboxylase, carboxyl transferase, alphaRoseRS_3200 subunit || Acetyl-CoA1 – strong carboxylase day JCVI_PEP_metagenomic.orf.21361072.1 1113211796612 6 29 21 17 24 32 23 14 775 432 1931 1394 1152 630 973 445 547 82 15 6 13 11 7 8579 accA RoseRS_0392 No orf accC acetyl-CoA carboxylase, biotin carboxylase || BiotinRoseRS_3203 carboxylase 0 – weak day JCVI_PEP_metagenomic.orf.21363077.1 1113211796612 117 234 215 222 147 166 229 150 378 345 1325 926 810 502 776 542 424 375 223 207 200 102 155 8770 Propionyl-CoA carboxylase pcc ATP-grasp domain || Biotin carboxylase RoseRS_0434 0 – weak day JCVI_PEP_metagenomic.orf.21553310.1 1113211797732 13 40 34 21 15 6 29 12 25 40 66 40 62 41 66 88 77 57 50 51 37 16 9 895 propionyl-CoA carboxylase || Propionyl-CoA carboxylaseRoseRS_2907 2 – constitutive JCVI_PEP_metagenomic.orf.21311038.1 1113211797731 312 726 439 461 191 162 249 94 129 185 405 493 610 709 1352 1036 3640 3711 3992 3395 2482 977 908 26658 carboxyl transferase || Propionyl-CoA carboxylaseRoseRS_3291 4 – weak night JCVI_PEP_metagenomic.orf.21348955.1 1113211795939 170 329 283 440 381 431 702 450 420 381 419 322 339 191 265 84 200 344 215 220 353 216 176 7331 Malonyl-CoA reductase mcr oxidoreductase, short chain dehydrogenase/reductaseRoseRS_3201 family || 3-oxoacyl-[acyl-carrier1 – strong day protein]JCVI_PEP_metagenomic.orf.21361823.1 reductase 1113211796612 144 288 327 336 265 401 580 277 1690 971 3975 2484 2213 1151 2106 620 1040 409 125 156 166 164 145 20033 Propionyl-CoA synthase pcs AMP-dependent synthetase and ligase || Acetate--CoARoseRS_3202 ligase 1 – strong day JCVI_PEP_metagenomic.orf.21362308.1 1113211796612 289 388 617 699 456 805 823 488 2286 1423 6483 3798 3381 2000 3047 1142 1577 825 370 291 315 322 273 32098 Methylmalonyl-CoA epimerase methylmalonyl-CoA epimerase || Methylmalonyl-CoARoseRS_0480 epimerase 2 – constitutive JCVI_PEP_metagenomic.orf.21523327.1 1113211797790 100 137 136 130 98 79 75 55 88 81 158 114 181 94 178 122 208 212 137 129 119 125 92 2848 Methylmalonyl-CoA mutase methylmalonyl-CoA mutase N-terminal domain || Methylmalonyl-CoARoseRS_0544 mutase4 – weak night JCVI_PEP_metagenomic.orf.21344843.1 1113211797795 412 1222 423 692 431 489 691 419 396 379 529 378 398 301 472 368 718 3910 3359 2350 1555 777 915 21584 methylmalonyl-CoA mutase N-terminal domain || Methylmalonyl-CoARoseRS_0545 mutase4 – weak night JCVI_PEP_metagenomic.orf.21345573.1 1113211797795 388 575 492 687 412 529 639 350 536 513 626 580 660 383 875 373 1132 3222 2854 1894 1223 710 661 20314 methylmalonyl-CoA mutase C-terminal domain || 2-methyleneglutarateRoseRS_2024 2 mutase– constitutive JCVI_PEP_metagenomic.orf.20798168.1 1113211797229 71 99 66 64 44 56 86 34 55 64 127 92 116 87 173 86 171 164 103 111 96 66 75 2106 succinyl-CoA-malate-CoA transferase smtA L-carnitine dehydratase/bile acid-inducible proteinRoseRS_4176 F || Formyl-CoA transferase2 – constitutive JCVI_PEP_metagenomic.orf.21516914.1 1113211797791 54 55 54 111 78 76 57 23 109 74 127 54 103 56 107 46 158 126 93 61 52 98 77 1849 smtB L-carnitine dehydratase/bile acid-inducible proteinRoseRS_4175 F || Formyl-CoA transferase0 – weak day JCVI_PEP_metagenomic.orf.21516935.1 1113211797791 124 311 216 289 159 202 276 125 538 439 654 474 392 362 404 334 671 371 311 161 212 178 189 7392 Mesaconyl-CoA C1-C4 CoA transferase mct hypothetical protein RoseRS_4174 2 – constitutive JCVI_PEP_metagenomic.orf.21516982.1 1113211797791 104 302 210 232 145 181 321 146 302 280 327 251 230 174 286 231 462 420 281 195 193 133 196 5602 malyl-CoA mcl HpcH/HpaI aldolase/citrate lyase family || Citrate lyaseRoseRS_4173 4 – weak night JCVI_PEP_metagenomic.orf.21517014.1 1113211797791 171 255 290 439 270 378 339 181 409 370 513 284 311 221 415 196 331 332 232 194 211 275 351 6968 mesaconyl-C1-CoA hydratase mch MaoC domain protein dehydratase RoseRS_4172 2 – constitutive JCVI_PEP_metagenomic.orf.21517066.1 1113211797791 159 303 233 350 228 308 419 218 461 402 521 444 267 249 497 287 634 548 335 323 253 264 280 7983 mesaconyl-C4-CoA hydratase meh hypothetical protein RoseRS_4177 2 – constitutive JCVI_PEP_metagenomic.orf.21519604.1 1113211797791 31 75 44 36 41 28 59 41 57 62 100 50 50 51 72 33 108 169 123 100 65 54 67 1516

Glycolate metabolism glycolate dehydrogenase glcD D-lactate dehydrogenase (cytochrome) || D-lactateRoseRS_3360 dehydrogenase (cytochrome)2 – constitutive JCVI_PEP_metagenomic.orf.21263197.1 1113211796263 109 143 104 138 80 91 95 58 116 134 216 183 241 114 233 150 255 234 157 148 159 93 93 3344 glycolate dehydrogenase glcD FAD linked oxidase domain protein || D-lactate dehydrogenaseRoseRS_3362 (cytochrome)0 – weak day JCVI_PEP_metagenomic.orf.21263810.1 1113211796263 56 112 29 39 38 29 56 27 38 71 101 93 111 91 202 133 202 141 105 91 113 47 72 1997 glyoxylate reductase glyoxylate reductase || Glyoxylate reductase RoseRS_0216 0 – weak day JCVI_PEP_metagenomic.orf.21547646.1 1113211797774 20 38 26 13 20 14 25 17 32 60 77 73 50 73 120 74 107 67 42 44 56 20 33 1101 glyoxylate shunt isocitrate lyase isocitrate lyase || Isocitrate lyase RoseRS_4164 1 – strong day JCVI_PEP_metagenomic.orf.21517400.1 1113211797791 67 172 153 176 116 154 280 168 1044 1171 2238 1407 1101 802 775 457 466 453 231 209 169 88 122 12019 malate synthase malate synthase A || Malate synthase RoseRS_4165 1 – strong day JCVI_PEP_metagenomic.orf.21517344.1 1113211797791 86 149 134 191 145 238 246 161 851 928 1749 1168 1001 712 862 333 480 386 191 201 156 110 97 10575

Acetate metabolism acetate/glycolate transport Na+/solute symporter RoseRS_1628 0 – weak day JCVI_PEP_metagenomic.orf.21220879.1 1113211796818 1189 5102 1516 1267 718 662 1420 667 1558 1148 4480 5331 4643 4780 7567 8594 6853 4176 2260 3513 4943 1840 1982 acetate/glycolate transport Na+/solute symporter RoseRS_0112 2 – constitutive JCVI_PEP_metagenomic.orf.21471143.1 1113211797719 39 82 48 26 40 26 43 20 46 69 128 61 55 51 116 39 92 105 73 61 44 50 17 Acetyl-CoA synthetase acetate--CoA ligase || Acetate--CoA ligase RoseRS_2003 2 – constitutive JCVI_PEP_metagenomic.orf.21479863.1 1113211797614 1056 1109 1170 1028 694 854 648 337 756 848 1909 1702 2007 1693 2545 1689 3066 3259 2473 2115 1385 1487 1308 35138 Acetaldehyde dehydrogenase aldehyde dehydrogenase (NAD) family protein || AldehydeRoseRS_0265 dehydrogenase4 – weak (NAD+) night JCVI_PEP_metagenomic.orf.21222599.1 1113211797606 208 316 238 416 295 360 359 220 303 303 515 308 344 145 332 122 275 255 238 238 196 169 250 6405 aldehyde dehydrogenase (NAD) family protein || AldehydeRoseRS_0829 dehydrogenase2 – constitutive (NAD+) JCVI_PEP_metagenomic.orf.21265177.1 1113211797304 73 111 87 157 57 61 69 49 78 64 125 113 138 92 193 92 257 225 155 158 133 135 147 2769 Alcohol dehydrogenase oxidoreductase, zinc-binding dehydrogenase familyRoseRS_3921 || L-iditol 2-dehydrogenase2 – constitutive JCVI_PEP_metagenomic.orf.21393159.1 1113211797444 82 121 80 137 53 69 107 63 85 118 176 133 224 113 248 154 180 248 178 145 189 114 98 3115

Fatty Acid Metabolism biosynthesis fabD hypothetical protein RoseRS_3469 4 – weak night JCVI_PEP_metagenomic.orf.21409832.1 1113211795955 159 244 259 285 198 187 248 91 170 179 273 195 209 127 312 188 424 295 242 264 266 283 323 5421 fabF 3-oxoacyl-[acyl-carrier-protein] synthase 2 || 3-oxoacyl-[acyl-carrierRoseRS_3468 protein]2 – constitutive synthase JCVI_PEP_metagenomic.orf.21410046.1 1113211795955 87 437 128 153 87 126 167 68 182 161 261 208 219 128 314 186 265 275 208 209 219 148 220 4456 3-oxoacyl-[acyl-carrier-protein] synthase 2 || 3-oxoacyl-[acyl-carrierRoseRS_3590 protein]0 – weak synthase day JCVI_PEP_metagenomic.orf.21275898.1 1113211795871 24 52 57 55 31 29 57 19 62 73 156 107 131 75 175 114 127 117 66 53 44 48 46 1718 fabH 3-oxoacyl-[acyl-carrier-protein] synthase III || 3-oxoacyl-[acyl-carrierRoseRS_2614 protein]0 – weak synthase day JCVI_PEP_metagenomic.orf.21546020.1 1113211797799 51 386 141 159 91 62 201 107 156 198 294 309 258 249 454 324 410 361 235 215 248 77 109 5095 fabG oxidoreductase, short chain dehydrogenase/reductaseRoseRS_0479 family || 3-oxoacyl-[acyl-carrier0 – weak day protein]JCVI_PEP_metagenomic.orf.21523310.1 reductase 1113211797790 0 5 4 1 6 1 5 6 14 8 37 25 28 9 29 19 30 20 9 9 16 13 14 308 3-oxoacyl-[acyl-carrier-protein] reductase || 3-oxoacyl-[acyl-carrierRoseRS_0987 protein]2 – constitutive reductase JCVI_PEP_metagenomic.orf.21374643.1 1113211797668 28 79 74 79 51 50 49 32 55 69 115 105 120 56 166 86 123 166 89 77 77 63 33 1842 oxidoreductase, short chain dehydrogenase/reductaseRoseRS_1126 family || 3-oxoacyl-[acyl-carrier2 – constitutive protein]JCVI_PEP_metagenomic.orf.21522808.1 reductase 1113211797805 89 129 88 116 71 91 58 45 81 54 166 124 95 83 162 86 157 171 175 246 149 124 81 2641 hypothetical protein RoseRS_2282 2 – constitutive JCVI_PEP_metagenomic.orf.21139070.1 1113211797592 11 23 12 19 15 20 3 9 9 14 35 43 34 35 39 34 80 42 19 20 25 9 24 574 oxidoreductase, short chain dehydrogenase/reductaseRoseRS_4347 family || 3-oxoacyl-[acyl-carrier3 – strong night protein]JCVI_PEP_metagenomic.orf.21437532.1 reductase 1113211797605 1080 1864 1489 1098 524 568 697 347 351 356 486 604 571 588 1174 772 2786 5320 5725 6017 3877 2543 1728 40565 oxidoreductase, short chain dehydrogenase/reductaseRoseRS_4552 family || 3-oxoacyl-[acyl-carrier4 – weak night protein]JCVI_PEP_metagenomic.orf.21533736.1 reductase 1113211797768 504 995 1103 1234 884 1188 1504 892 1153 809 1083 683 450 346 394 150 233 144 291 416 620 573 615 16264 fabZ beta-hydroxyacyl-(acyl-carrier-protein) dehydrataseRoseRS_3122 FabZ 0 – weak day JCVI_PEP_metagenomic.orf.21273485.1 1113211797249 3 13 0 5 2 1 3 1 4 4 14 9 10 8 7 5 11 6 4 4 9 1 1 125 fabI hypothetical protein RoseRS_1555 2 – constitutive JCVI_PEP_metagenomic.orf.21475931.1 1113211797697 24 58 43 29 27 20 26 19 23 30 65 38 48 31 68 52 91 62 45 39 37 27 72 974 β-oxidation Acyl-CoA synthetase AMP-dependent synthetase and ligase || Long-chain-fatty-acid--CoARoseRS_0623 ligase0 – weak day JCVI_PEP_metagenomic.orf.21256748.1 1113211797092 82 107 80 147 81 59 96 40 114 141 301 264 278 217 417 175 317 197 135 125 120 112 107 3712 Acyl-CoA synthetase AMP-dependent synthetase and ligase || O-succinylbenzoate--CoARoseRS_1007 ligase0 – weak day JCVI_PEP_metagenomic.orf.21369463.1 1113211797668 411 619 515 607 293 460 622 396 715 900 2113 1762 1335 1284 2181 957 1911 1250 643 612 498 604 526 21214 Acyl-CoA synthetase AMP-dependent synthetase and ligase || Long-chain-fatty-acid--CoARoseRS_2084 ligase0 – weak day JCVI_PEP_metagenomic.orf.21239206.1 1113211797102 1016 1710 1330 2013 1274 1195 1621 683 1500 1629 3783 3566 3158 2703 6024 2419 4489 2915 1442 1090 1199 1211 1558 49528 Acyl-CoA synthetase AMP-dependent synthetase and ligase || Long-chain-fatty-acid--CoARoseRS_2094 ligase0 – weak day JCVI_PEP_metagenomic.orf.21338233.1 1113211797080 3 3 0 2 0 0 0 1 0 1 10 5 11 3 8 15 6 6 3 1 1 5 2 86 Acyl-CoA dehydrogenase Acyl-CoA dehydrogenase, C-terminal domain || Long-chainRoseRS_2850 acyl-CoA dehydrogenase0 – weak day JCVI_PEP_metagenomic.orf.21550302.1 1113211797772 4 12 2 0 7 5 5 6 11 13 15 17 11 8 25 13 16 18 7 6 5 0 15 221 Acyl-CoA dehydrogenase Acyl-CoA dehydrogenase, C-terminal domain || Acyl-CoARoseRS_2971 dehydrogenase1 – strong day JCVI_PEP_metagenomic.orf.21456968.1 1113211797824 59 88 68 98 83 61 72 39 674 418 2498 1474 1319 620 858 657 377 292 137 88 122 71 84 10257 3-hydroxyacyl-CoA hydrolase enoyl-CoA hydratase/isomerase || Enoyl-CoA hydrataseRoseRS_3825 0 – weak day JCVI_PEP_metagenomic.orf.20836766.1 1113211796899 6 7 10 6 0 14 7 2 18 19 25 25 12 8 22 29 26 19 14 14 19 3 2 307 3-hydroxyacyl-CoA hydrolase enoyl-CoA hydratase/isomerase || Enoyl-CoA hydrataseRoseRS_4259 2 – constitutive JCVI_PEP_metagenomic.orf.21314490.1 1113211796935 36 47 66 38 44 23 28 22 35 47 87 73 94 47 93 58 92 99 60 62 33 37 79 1300 3-hydroxyacyl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase, NAD-binding RoseRS_2970|| 3-hydroxyacyl-CoA1 –dehydrogenase strong day JCVI_PEP_metagenomic.orf.21457405.1 1113211797824 76 130 172 184 102 120 118 67 889 654 5064 2828 1742 1017 1677 1248 672 323 132 128 143 129 248 17863 Beta-ketoacyl thiolase acetyl-CoA acetyltransferases || Acetyl-CoA C-acyltransferaseRoseRS_2969 1 – strong day JCVI_PEP_metagenomic.orf.21457639.1 1113211797824 40 63 57 47 24 48 65 36 358 289 2068 1084 879 377 794 424 289 150 71 69 55 34 55 7376

Wax Ester Biosynthesis/degradation wax ester synthase/acyl-CoA/diacylglycerol synthase wax ester synthase/acyl-CoA/diacylglycerol synthaseRoseRS_2761 2 – constitutive JCVI_PEP_metagenomic.orf.21408019.1 1113211797422 198 542 260 267 199 221 234 141 308 345 583 445 551 485 965 720 824 841 480 474 449 291 424 10247 wax ester synthase/acyl-CoA/diacylglycerol synthase acyltransferase, WS/DGAT/MGAT RoseRS_2456 3 – strong night JCVI_PEP_metagenomic.orf.21403104.1 1113211797781 400 672 468 386 274 317 326 238 83 120 53 16 21 20 32 12 634 3315 2394 1843 1230 767 601 14222 Hydrogenase hypE hydrogenase accessory protein HypB RoseRS_0972 0 – weak day JCVI_PEP_metagenomic.orf.21369156.1 1113211797668 8 23 18 18 14 13 16 7 31 38 67 37 60 49 59 45 165 232 136 62 54 18 19 1189 hypD hydrogenase assembly chaperone HypC/HupF RoseRS_0973 0 – weak day JCVI_PEP_metagenomic.orf.21369953.1 1113211797668 7 9 6 11 8 4 4 5 6 7 12 23 9 8 28 13 28 32 21 15 20 2 6 284 hypB hydrogenase expression/formation protein HypE ||RoseRS_0975 Thiamine-phosphate0 –kinase weak day JCVI_PEP_metagenomic.orf.21370491.1 1113211797668 2 12 7 6 10 4 0 1 11 4 30 14 22 15 31 16 24 32 22 18 11 12 23 327 hypA hydrogenase nickel insertion protein HypA RoseRS_0967 3 – strong night JCVI_PEP_metagenomic.orf.21367928.1 1113211797668 188 197 230 138 124 95 103 29 55 74 9 4 8 4 18 16 101 268 339 342 269 271 246 3128 hydA hydrogenase (NiFe) small subunit (hydA) || HydrogenaseRoseRS_2319 (acceptor) 3 – strong night JCVI_PEP_metagenomic.orf.21206005.1 1113211797592 78 126 93 55 45 42 36 21 4 15 14 3 6 4 2 1 107 350 278 321 268 198 132 2199 hydB Nickel-dependent hydrogenase || Hydrogen:quinoneRoseRS_2320 oxidoreductase 3 – strong night JCVI_PEP_metagenomic.orf.21207658.1 1113211797592 281 352 339 235 164 107 150 80 27 46 38 11 22 11 30 11 445 1151 943 829 672 758 479 7181 hydC – bcyt Ni/Fe-hydrogenase, b-type cytochrome subunit RoseRS_2321 3 – strong night JCVI_PEP_metagenomic.orf.21208155.1 1113211797592 94 189 141 94 65 39 76 56 16 28 38 21 18 13 25 5 160 389 475 422 414 241 128 3147 hydD? RoseRS_2322 3 – strong night JCVI_PEP_metagenomic.orf.21208918.1 1113211797592 28 144 58 51 39 31 34 22 9 22 12 11 3 3 11 10 124 336 323 321 318 132 53 2095

Nitrogenase hydrogenase expression/formation protein nifH nitrogenase iron protein || Nitrogenase RoseRS_1201 3 – strong night JCVI_PEP_metagenomic.orf.21465397.1 1113211797794 568 1205 482 184 394 184 238 273 113 40 67 24 38 8 46 34 125 342 1098 869 840 495 704 8371 nifB radical SAM domain protein RoseRS_1200 3 – strong night JCVI_PEP_metagenomic.orf.21465479.1 1113211797794 297 520 261 80 171 85 126 140 116 23 33 11 35 18 30 37 63 182 439 543 473 251 293 4227 nifD nitrogenase component I, alpha chain || NitrogenaseRoseRS_1199 3 – strong night JCVI_PEP_metagenomic.orf.21465649.1 1113211797794 1123 1950 1067 339 666 370 391 398 241 89 113 36 60 30 105 69 214 405 1880 1548 1258 1140 999 14491 nifK , nitrogenase component 1 and otherRoseRS_1198 families || Nitrogenase3 – strong night JCVI_PEP_metagenomic.orf.21465742.1 1113211797794 411 646 303 78 251 120 99 152 92 22 22 7 21 6 35 44 65 134 581 515 496 295 376 4771

Phototrophy pufLM Photosynthetic reaction center protein RoseRS_3268 3 – strong night JCVI_PEP_metagenomic.orf.21379875.1 1113211796406 7644 11891 9490 11110 6738 8124 8897 5814 5672 4157 1546 661 825 347 635 360 2380 3588 6347 11735 9729 10595 9983 138268 pufC cytoChrome c-554 (Cytochrome c554). RoseRS_3267 3 – strong night JCVI_PEP_metagenomic.orf.21380061.1 1113211796406 6660 18269 7724 9467 5574 6320 10207 5496 6719 4835 2185 932 827 411 1147 558 2967 4762 7625 10907 11151 7280 9952 141975 bchN light-iNdependent protochlorophyllide reductase subunitRoseRS_1910 n (li-por subunit3 – n) strong (dpor night subunitJCVI_PEP_metagenomic.orf.21554312.1 n). 1113211797749 332 841 580 375 333 270 422 289 229 142 38 9 35 8 20 9 140 331 523 641 550 458 290 6865 bchB light-independent protochlorophyllide reductase, BRoseRS_1909 subunit || Nitrogenase3 – strong night JCVI_PEP_metagenomic.orf.21554348.1 1113211797749 781 1672 1152 1114 940 530 851 552 641 399 91 28 49 36 81 43 413 598 1162 1317 1158 1165 955 15728 bchL light-independent protochlorophyllide reductase, iron-sulfurRoseRS_1908 ATP-binding3 – protein strong ||night NitrogenaseJCVI_PEP_metagenomic.orf.21554368.1 1113211797749 456 1169 754 498 473 358 927 450 493 319 71 23 35 24 69 24 324 633 948 1107 1147 706 695 11703 bchM magnesium protoporphyrin O-methyltransferase ||RoseRS_1907 Magnesium protoporphyrin3 – strong IX nightmethyltransferaseJCVI_PEP_metagenomic.orf.21554380.1 1113211797749 62 188 105 56 104 59 97 56 72 52 22 8 8 5 8 4 80 68 100 133 121 97 77 1582 bchH magnesium chelatase, H subunit || CobaltochelataseRoseRS_1904 3 – strong night JCVI_PEP_metagenomic.orf.21554414.1 1113211797749 540 1508 945 804 592 500 645 410 499 269 107 56 88 48 67 48 328 501 787 1060 1022 774 603 12201 bchH magnesium chelatase, H subunit || CobaltochelataseRoseRS_2525 3 – strong night JCVI_PEP_metagenomic.orf.21387404.1 1113211797781 351 787 619 373 301 324 451 262 246 248 267 161 209 128 266 120 1036 2362 1963 1452 1036 657 612 14231 bchI BchI || Magnesium chelatase RoseRS_1902 4 – weak night JCVI_PEP_metagenomic.orf.21554468.1 1113211797749 171 301 235 249 210 152 162 137 181 113 83 61 79 47 97 49 160 154 250 363 255 191 181 3881 bchI BchI || Magnesium chelatase RoseRS_0883 2 – constitutive JCVI_PEP_metagenomic.orf.21363975.1 1113211797061 24 76 71 53 27 38 45 21 70 73 105 91 82 48 120 97 123 134 48 67 59 45 82 1599 bchJ bacteriochlorophyll 4-vinyl reductase RoseRS_0940 3 – strong night JCVI_PEP_metagenomic.orf.21367082.1 1113211797061 323 878 548 408 332 247 266 162 66 92 31 8 16 3 15 3 129 508 537 821 795 641 631 7460 bchE BchE RoseRS_0942 3 – strong night JCVI_PEP_metagenomic.orf.21367614.1 1113211797061 679 1567 1136 879 581 495 733 340 214 240 37 14 29 4 34 7 458 1031 1431 1245 1215 936 922 14227 bchD BchD || Magnesium chelatase RoseRS_2823 4 – weak night JCVI_PEP_metagenomic.orf.21550396.1 1113211797772 76 147 58 87 64 39 101 68 65 81 161 85 76 59 147 48 146 113 124 121 132 77 94 2169 bchG geranylgeranyl reductase RoseRS_3266 3 – strong night JCVI_PEP_metagenomic.orf.21380358.1 1113211796406 575 992 723 969 586 825 626 410 732 511 212 112 136 74 120 65 299 323 516 778 788 806 767 11945 bchP geranylgeranyl reductase RoseRS_3265 3 – strong night JCVI_PEP_metagenomic.orf.21380654.1 1113211796406 341 472 472 442 354 430 350 260 293 230 152 66 88 30 64 44 120 204 261 557 335 596 462 6623 bchF 2-vinyl bacteriochlorophyllide hydratase RoseRS_3262 4 – weak night JCVI_PEP_metagenomic.orf.21381327.1 1113211796406 133 660 260 196 150 165 198 171 112 150 158 76 51 75 87 58 286 234 320 251 298 196 224 4509 bchC oxidoreductase, zinc-binding dehydrogenase familyRoseRS_3261 || L-iditol 2-dehydrogenase4 – weak night JCVI_PEP_metagenomic.orf.21381543.1 1113211796406 430 1643 716 605 432 602 795 365 473 464 331 185 186 113 276 117 496 644 815 779 801 745 712 12725 bchX chlorophyllide reductase iron protein subunit X RoseRS_3260 3 – strong night JCVI_PEP_metagenomic.orf.21381819.1 1113211796406 801 1464 1290 1167 1024 923 1018 490 512 604 292 173 175 98 201 109 320 440 786 785 881 1219 1182 15954 bchY chlorophyllide reductase subunit Y RoseRS_3257 0 – weak day JCVI_PEP_metagenomic.orf.21382390.1 1113211796406 8 22 15 13 15 9 26 17 34 33 51 22 26 15 34 18 41 44 27 26 15 8 8 527 bchZ chlorophyllide reductase subunit Z RoseRS_3256 2 – constitutive JCVI_PEP_metagenomic.orf.21382762.1 1113211796406 24 38 70 47 24 32 40 12 88 79 122 40 76 19 77 33 80 82 82 52 55 34 72 1278

Electron transport NADH menaquinone oxidoreductase nuoA RoseRS_2089 4 – weak night JCVI_PEP_metagenomic.orf.21337196.1 1113211797080 23 44 28 14 37 26 16 24 12 16 29 32 29 17 49 13 30 148 90 146 106 38 30 997 nuoC RoseRS_2091 1 – strong day JCVI_PEP_metagenomic.orf.21337539.1 1113211797080 0 10 5 0 0 1 0 2 3 10 22 51 45 59 56 101 82 63 10 9 5 19 0 553 nuoE RoseRS_3543 3 – strong night JCVI_PEP_metagenomic.orf.21484586.1 1113211796757 70 221 138 89 30 45 76 76 18 30 22 4 9 19 12 11 120 474 353 325 345 145 83 2715 nuoD RoseRS_2992 4 – weak night JCVI_PEP_metagenomic.orf.21453555.1 1113211797824 244 278 253 428 202 177 273 108 125 181 237 239 260 164 324 145 481 1214 946 616 528 302 313 8038 nuoI RoseRS_2993 4 – weak night JCVI_PEP_metagenomic.orf.21453727.1 1113211797824 172 317 300 324 259 203 275 133 204 235 299 263 268 203 422 181 478 862 1063 471 429 370 326 8057 nuoH RoseRS_2994 2 – constitutive JCVI_PEP_metagenomic.orf.21453994.1 1113211797824 43 128 97 59 63 61 63 50 67 81 127 107 118 91 122 82 159 294 318 179 207 98 77 2691 nuoJ RoseRS_2995 0 – weak day JCVI_PEP_metagenomic.orf.21454137.1 1113211797824 58 126 92 48 46 44 68 36 118 159 170 176 165 130 322 149 241 277 433 304 226 82 82 3552 nuoK RoseRS_2996 2 – constitutive JCVI_PEP_metagenomic.orf.21454158.1 1113211797824 27 99 27 49 24 27 38 34 27 45 79 43 46 46 52 47 134 183 198 137 109 39 43 1553 nuoL RoseRS_2997 2 – constitutive JCVI_PEP_metagenomic.orf.21454619.1 1113211797824 11 39 17 22 14 19 18 11 19 20 43 24 36 26 34 29 54 59 70 61 46 9 16 697 nuoM RoseRS_2998 2 – constitutive JCVI_PEP_metagenomic.orf.21454905.1 1113211797824 40 83 64 39 72 49 72 68 68 66 157 126 117 65 129 78 158 174 167 139 112 78 48 2169 nuoA RoseRS_3678 1 – strong day JCVI_PEP_metagenomic.orf.21579072.1 1113211797744 23 55 43 53 29 24 24 12 58 78 195 230 125 143 289 218 325 169 62 27 32 21 47 2282 nuoB RoseRS_3677 1 – strong day JCVI_PEP_metagenomic.orf.21579078.1 1113211797744 13 10 18 25 8 12 11 5 24 32 78 67 59 40 81 65 93 92 30 13 14 15 21 826 nuoC RoseRS_3676 1 – strong day JCVI_PEP_metagenomic.orf.21579082.1 1113211797744 26 60 30 15 39 26 40 14 59 80 166 144 176 134 184 92 212 213 59 42 25 21 15 1872 nuoD RoseRS_3675 1 – strong day JCVI_PEP_metagenomic.orf.21579096.1 1113211797744 54 63 64 85 48 64 69 36 169 213 358 323 344 191 523 206 551 452 154 108 86 63 42 4266 nuoE RoseRS_2238 1 – strong day JCVI_PEP_metagenomic.orf.21285545.1 1113211797096 41 91 43 44 34 29 55 19 113 167 401 457 427 296 658 379 728 722 195 100 81 37 37 5154 nuoF RoseRS_2237 1 – strong day JCVI_PEP_metagenomic.orf.21286499.1 1113211797096 31 61 33 55 24 39 22 17 59 117 257 204 318 139 332 162 432 400 116 58 62 40 62 3040 nuoG RoseRS_2236 1 – strong day JCVI_PEP_metagenomic.orf.21287001.1 1113211797096 20 50 18 27 17 12 12 9 35 45 146 107 181 118 244 99 259 222 74 49 38 15 38 1835 nuoH RoseRS_2235 1 – strong day JCVI_PEP_metagenomic.orf.21287201.1 1113211797096 5 15 9 14 11 10 16 6 17 34 55 55 65 49 93 43 75 59 21 11 12 14 2 691 nuoI RoseRS_2234 2 – constitutive JCVI_PEP_metagenomic.orf.21287480.1 1113211797096 1 9 12 0 4 5 4 1 3 6 9 8 13 6 16 11 12 22 2 3 3 6 5 161 nuoJ RoseRS_2233 0 – weak day JCVI_PEP_metagenomic.orf.21287661.1 1113211797096 3 30 0 0 1 7 1 0 5 26 37 37 30 18 27 13 48 43 20 10 7 3 14 380 nuoK RoseRS_2232 1 – strong day JCVI_PEP_metagenomic.orf.21288299.1 1113211797096 13 48 21 18 22 13 15 33 49 91 194 137 168 138 222 144 231 216 89 54 70 24 11 2021 nuoL RoseRS_2231 1 – strong day JCVI_PEP_metagenomic.orf.21288755.1 1113211797096 8 24 17 13 8 7 9 13 14 42 99 55 70 58 86 52 113 71 39 17 14 31 12 872 nuoM RoseRS_2230 0 – weak day JCVI_PEP_metagenomic.orf.21289398.1 1113211797096 19 44 31 16 10 19 18 31 35 57 102 56 82 75 151 104 177 149 61 51 44 25 77 1434 alternative complex III quinone oxidoreductase actA (Cp) RoseRS_4139 4 – weak night JCVI_PEP_metagenomic.orf.21518227.1 1113211797791 319 468 419 544 361 348 382 231 407 355 246 150 173 77 226 102 348 439 497 378 423 290 466 7649 actB (Cp) RoseRS_4140 4 – weak night JCVI_PEP_metagenomic.orf.21518159.1 1113211797791 117 263 230 240 144 130 205 110 161 132 110 54 79 53 59 79 198 170 290 278 216 122 211 3651 actC (Cp) RoseRS_4141 4 – weak night JCVI_PEP_metagenomic.orf.21518067.1 1113211797791 1161 1719 1484 2251 1377 1511 1362 780 1192 923 596 311 423 217 554 378 1148 1524 1564 1492 1497 1460 2041 26965 actD (Cp) RoseRS_4142 4 – weak night JCVI_PEP_metagenomic.orf.21517970.1 1113211797791 487 898 775 895 508 585 679 352 381 319 266 152 170 127 175 174 488 778 734 686 679 612 764 11684 actE (Cp) RoseRS_4143 4 – weak night JCVI_PEP_metagenomic.orf.21518134.1 1113211797791 571 1128 771 1048 539 606 814 537 631 402 342 184 169 170 212 197 759 824 945 980 849 751 1084 14513 actF (Cp) RoseRS_4144 4 – weak night JCVI_PEP_metagenomic.orf.21518170.1 1113211797791 172 350 332 320 217 250 190 113 176 155 99 65 71 54 104 65 159 195 273 294 276 270 337 4537 auracyanin RoseRS_2366 0 – weak day JCVI_PEP_metagenomic.orf.21579704.1 1113211797738 49 70 84 60 45 56 79 35 81 114 240 205 261 137 241 62 190 241 90 95 79 43 87 2644 cytochrome c oxidase – Complex IV cyoE protoheme IX farnesyltransferase RoseRS_0224 0 – weak day JCVI_PEP_metagenomic.orf.21547864.1 1113211797774 6 26 1 8 0 1 5 9 13 24 39 30 22 6 23 11 76 494 87 25 13 2 1 922 ctaC Cytochrome c RoseRS_2263 0 – weak day JCVI_PEP_metagenomic.orf.21466287.1 1113211797741 6 4 1 0 2 0 0 3 8 13 37 25 12 7 20 15 45 70 12 4 4 0 0 288 ctaD cytochrome c oxidase, subunit I || Cytochrome-c oxidaseRoseRS_2264 1 – strong day JCVI_PEP_metagenomic.orf.21466511.1 1113211797741 25 52 28 31 7 24 34 16 117 240 368 211 167 150 293 118 557 1087 193 55 42 24 36 3875 ctaE Cytochrome c oxidase subunit III || Cytochrome-c RoseRS_2265oxidase JCVI_PEP_metagenomic.orf.20810199.1 1041023785840 2 10 6 19 5 7 10 3 9 60 57 21 18 35 54 18 169 245 45 9 11 4 8 825 ctaF caa(3)-type oxidase, subunit IV RoseRS_2266 2 – constitutive JCVI_PEP_metagenomic.orf.21466602.1 1113211797741 41 102 40 41 46 32 53 27 38 76 111 63 53 47 100 44 295 409 95 51 57 36 53 1910 cbaA Cytochrome C and Quinol oxidase polypeptide I || RoseRS_0934Cytochrome-c oxidase3 – strong night JCVI_PEP_metagenomic.orf.21365133.1 1113211797061 28 82 48 79 15 24 34 40 56 103 59 26 42 27 30 19 874 2128 806 133 109 62 94 4918 cbaB Copper binding proteins, plastocyanin/azurin familyRoseRS_0933 || Cytochrome-c oxidase3 – strong night JCVI_PEP_metagenomic.orf.21364773.1 1113211797061 4 29 10 20 6 14 4 14 12 32 14 6 9 12 6 5 248 784 228 27 45 23 7 1559 CO dehydrogenase, molybdopterin-dependent coxS hypothetical protein RoseRS_0340 2 – constitutive JCVI_PEP_metagenomic.orf.21240198.1 1113211796958 690 491 1005 945 543 718 336 160 419 489 1016 970 891 910 1403 937 1398 944 697 677 508 1542 999 18688 coxL aldehyde oxidase and xanthine dehydrogenase, molybdopterinRoseRS_0341 binding2 || – Carbon-monoxide constitutive JCVI_PEP_metagenomic.orf.21241037.1 dehydrogenase (acceptor) 1113211796958 1408 1180 1508 1864 907 1233 825 403 1237 1306 2334 2537 3382 2421 4579 2539 4128 2666 1638 2312 1624 2394 1957 46382 coxM molybdopterin dehydrogenase, FAD-binding || Carbon-monoxideRoseRS_0342 dehydrogenase2 – constitutive (acceptor)JCVI_PEP_metagenomic.orf.21241626.1 1113211796958 293 230 311 402 204 225 174 122 232 225 462 643 544 540 894 565 985 661 363 432 367 419 352 9645

Nitrogen metabolism amtB ammonium transporter RoseRS_2984 0 – weak day JCVI_PEP_metagenomic.orf.21450994.1 1113211797824 531 1204 770 614 412 312 397 389 1338 645 1874 1107 1866 847 2171 1549 1783 667 515 264 520 424 726 20925 Cobalamin biosynthesis cobyric acid synthase CobQ RoseRS_0577 0 – weak day JCVI_PEP_metagenomic.orf.21318241.1 1113211796113 5 16 10 19 6 12 2 13 20 11 36 16 15 9 24 26 24 33 12 13 10 6 3 341 aminotransferase, classes I and II || Histidinol-phosphateRoseRS_0576 transaminase0 – weak day JCVI_PEP_metagenomic.orf.21317796.1 1113211796113 2 16 8 12 12 5 8 5 22 17 28 22 22 15 35 14 28 45 15 17 11 5 12 376 adenosylcobinamide-phosphate guanylyltransferaseRoseRS_0575 || Adenosylcobinamide-phosphate0 – weak day guanylyltransferaseJCVI_PEP_metagenomic.orf.21317553.1 1113211796113 6 32 14 4 13 4 22 7 12 17 70 28 37 15 52 42 76 76 22 18 16 14 25 622 cobyrinic acid a,c-diamide synthase RoseRS_0574 0 – weak day JCVI_PEP_metagenomic.orf.21317299.1 1113211796113 2 15 12 13 3 5 14 10 18 8 44 26 27 11 39 22 42 37 13 23 13 6 7 410 uroporphyrin-III C-methyltransferase || Uroporphyrin-IIIRoseRS_0573 C-methyltransferase0 – weak day JCVI_PEP_metagenomic.orf.21316970.1 1113211796113 4 12 9 10 3 10 12 1 11 11 24 23 27 19 18 29 28 39 12 14 8 3 2 329 precorrin-3B C17-methyltransferase || Precorrin-2 RoseRS_0572dehydrogenase 0 – weak day JCVI_PEP_metagenomic.orf.21316806.1 1113211796113 10 69 33 17 12 24 47 32 46 67 101 54 85 50 91 75 118 149 55 57 47 23 52 1314 precorrin-4 C11-methyltransferase || Precorrin-4 C(11)-methyltransferaseRoseRS_0571 0 – weak day JCVI_PEP_metagenomic.orf.21316220.1 1113211796113 4 21 5 8 2 2 16 6 7 31 31 33 30 10 22 33 35 23 23 17 11 6 11 387 precorrin-2 C20-methyltransferase || Cobalt-factor RoseRS_0570II C(20)-methyltransferase2 – constitutive JCVI_PEP_metagenomic.orf.21316064.1 1113211796113 19 21 27 26 13 8 13 8 26 25 50 35 39 23 44 34 52 61 44 50 26 11 24 679 precorrin-6y C5,15-methyltransferase (decarboxylating),RoseRS_0569 CbiE subunit 0|| –Precorrin-6Y weak day C(5,15)-methyltransferaseJCVI_PEP_metagenomic.orf.21315876.1 (decarboxylating) 1113211796113 4 27 9 6 7 6 11 4 34 41 53 31 49 36 66 48 57 55 50 27 25 10 14 670 cobalamin biosynthesis protein CbiD RoseRS_0568 2 – constitutive JCVI_PEP_metagenomic.orf.21315452.1 1113211796113 63 179 128 106 79 72 92 37 127 148 249 165 235 161 463 239 375 246 150 152 133 119 154 3872 precorrin-8X methylmutase || Precorrin-8X methylmutaseRoseRS_0567 2 – constitutive JCVI_PEP_metagenomic.orf.21315156.1 1113211796113 96 152 155 155 90 101 129 74 113 132 226 140 198 133 209 149 375 275 184 177 131 102 146 3642 hypothetical protein RoseRS_0566 4 – weak night JCVI_PEP_metagenomic.orf.21315028.1 1113211796113 3 0 6 0 2 0 0 0 0 0 0 2 0 0 2 0 2 1 0 0 0 3 0 21 anaerobic cobalt chelatase (cbiK) cobalamin (vitamin B12) biosynthesis CbiX proteinRoseRS_0565 || Sirohydrochlorin ferrochelatase2 – constitutive JCVI_PEP_metagenomic.orf.21314898.1 1113211796113 124 267 197 272 153 149 174 100 207 239 381 278 330 232 505 297 669 571 352 246 243 161 327 6474 cobalt ABC transporter, ATP-binding protein || Fe(3+)-transportingRoseRS_0563 ATPase2 – constitutive JCVI_PEP_metagenomic.orf.21314192.1 1113211796113 37 99 71 34 39 30 57 46 39 55 91 52 77 58 72 44 81 118 110 77 68 38 35 1428 cobalt ABC transporter, permease protein CbiQ RoseRS_0562 2 – constitutive JCVI_PEP_metagenomic.orf.21314028.1 1113211796113 71 101 81 94 57 73 101 34 68 83 110 89 91 91 130 58 140 207 143 107 112 63 102 2206 cobalt transport protein RoseRS_0561 2 – constitutive JCVI_PEP_metagenomic.orf.21313836.1 1113211796113 19 47 35 59 34 28 40 23 37 37 55 46 53 43 67 49 76 64 42 44 32 41 64 1035 cobalamin biosynthesis protein CbiM RoseRS_0560 2 – constitutive JCVI_PEP_metagenomic.orf.21313803.1 1113211796113 58 94 107 129 78 67 79 53 55 87 103 91 142 80 147 46 175 168 92 108 81 42 114 2196 aerobic cobalt chelatase subunit (cobT) nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferaseRoseRS_0559 0 – || weak Nicotinate-nucleotide-dimethylbenzimidazole day JCVI_PEP_metagenomic.orf.21256374.1 phosphoribosyltransferase1113211798672 39 107 78 77 49 54 48 39 85 103 214 122 210 131 233 187 133 182 69 113 96 54 44 2467 aerobic cobalt chelatase subunit (cobN) cobaltochelatase, CobN subunit || CobaltochelataseRoseRS_0558 2 – constitutive JCVI_PEP_metagenomic.orf.21313223.1 1113211796113 304 702 492 622 403 397 559 277 526 636 930 769 847 582 1169 611 1091 1092 785 703 598 372 492 14959 aerobic cobalt chelatase subunit (cobS) cobalamin 5'-phosphate synthase RoseRS_4584 0 – weak day JCVI_PEP_metagenomic.orf.21532664.1 1113211797768 11 39 9 19 7 5 14 12 22 23 43 32 26 16 43 28 32 52 27 22 27 9 4 522

Nucleic Acid Metabolism aerobic ribonucleoside-diphosphate reductase (1.17.4.1, ribonucleotide reductase RoseRS_1973 4 – weak night JCVI_PEP_metagenomic.orf.21292697.1 1113211797266 320 816 417 412 274 266 546 247 199 208 245 178 210 132 195 161 388 672 764 825 887 449 474 9285 anaerobic ribonucleoside-diphosphate reductase (1.17.4.2,ribonucleoside-triphosphate reductase || Ribonucleoside-triphosphateRoseRS_4577 reductase2 – constitutive JCVI_PEP_metagenomic.orf.21532950.1 1113211797768 377 678 473 696 359 433 448 262 529 361 758 517 585 531 872 618 766 669 519 586 850 648 563 13098 aerobic dihydroorotate oxidase (1.3.3.1) dihydroorotate dehydrogenase || Dihydroorotate oxidaseRoseRS_1785 3 – strong night JCVI_PEP_metagenomic.orf.21263423.1 1113211797323 253 731 256 224 145 179 278 229 54 98 19 13 11 2 18 1 344 1558 1173 1302 1047 380 292 8607 aerobic dihydroorotate oxidase (1.3.3.1) dihydroorotate oxidase || Dihydroorotate oxidase RoseRS_2860 0 – weak day JCVI_PEP_metagenomic.orf.21482640.1 1113211797698 4 19 5 7 9 1 8 4 6 12 26 17 16 17 37 15 20 29 6 16 9 11 8 302 anaerobic dihydroorotate oxidase (1.3.99.11) dihydroorotate dehydrogenase family protein || DihydroorotateRoseRS_0764 oxidase0 – weak day JCVI_PEP_metagenomic.orf.21254429.1 1113211796856 9 31 14 15 7 3 25 7 23 26 31 32 22 9 42 25 35 39 28 34 28 9 16 510

Sulfur metabolism ATPsulfurylase: sulfate adenylylsulfate kinase/transferasesulfate (sulfate->APS) adenylyltransferase || Adenylylsulfate kinaseRoseRS_3336 2 – constitutive JCVI_PEP_metagenomic.orf.21261717.1 1113211796263 33 48 46 68 24 41 23 23 61 79 75 55 81 47 115 69 145 138 79 94 60 42 60 1506 inorganic diphosphatase inorganic diphosphatase || Inorganic diphosphataseRoseRS_3220 4 – weak night JCVI_PEP_metagenomic.orf.21355754.1 1113211796612 94 101 123 98 137 96 108 75 82 88 98 104 127 95 176 76 162 212 120 107 121 144 152 2696 PAPS reductase (PAPS → sulfite + PAP) phosophoadenylyl-sulfate reductase || Phosphoadenylyl-sulfateRoseRS_0739 reductase2 – constitutive(thioredoxin) JCVI_PEP_metagenomic.orf.21305403.1 1113211797399 14 32 25 11 4 2 9 4 12 14 10 18 11 8 17 18 59 43 27 16 18 18 12 402 cysteine synthase (cysK) cysteine synthase A || Cysteine synthase RoseRS_1506 1 – strong day JCVI_PEP_metagenomic.orf.21334002.1 1113211796039 1 13 8 19 5 8 9 10 39 22 162 137 167 96 192 79 111 48 19 9 10 16 0 1180 cysteine synthase (cysM) cysteine synthases || Cysteine synthase RoseRS_0720 1 – strong day JCVI_PEP_metagenomic.orf.21329177.1 1113211797399 18 33 21 21 14 23 20 22 34 62 287 501 567 364 845 366 422 98 58 24 46 17 28 3891

Oxidative stress glutathione peroxidase glutathione peroxidase || Glutathione peroxidase RoseRS_3106 1 – strong day JCVI_PEP_metagenomic.orf.21442863.1 1113211797699 28 53 30 41 31 23 30 23 95 117 376 298 323 265 414 156 197 153 82 22 49 28 24 2858 superoxide dismutase superoxide dismutase (Mn/Fe family), C-terminal domainRoseRS_3237 || Superoxide2 dismutase– constitutive JCVI_PEP_metagenomic.orf.21351952.1 1113211796612 614 639 831 634 596 519 422 249 302 337 1084 1185 1150 778 1817 798 1725 966 690 816 717 813 836 18518 GroEL chaperonin GroL I RoseRS_1077 2 – constitutive JCVI_PEP_metagenomic.orf.21376699.1 1113211797060 657 514 518 208 178 247 134 130 142 194 1489 698 539 762 2625 48 146 138 80 179 179 959 328 chaperonin GroEL I RoseRS_1077 2 – constitutive JCVI_PEP_metagenomic.orf.21244211.1 1113211797102 20 25 20 6 13 13 6 7 7 17 88 23 31 59 144 1 12 15 7 13 11 47 8 chaperonin GroL II RoseRS_4131 1 – strong day JCVI_PEP_metagenomic.orf.21528106.1 1113211797790 507 960 724 390 386 581 494 173 778 842 5660 4069 3093 3645 8824 294 2054 1021 425 369 451 710 463 Chloroflexus spp. Number of uniquely mapped transcripts homolog on Chloroflexus metagenome aurantiacus J-10-fl transcription metagenome gene annotation genome category metagenome ORF scaffold 12AM 1AM 2AM 3AM 4AM 5AM 6AM 7AM 8AM 9AM 10AM 12PM 1PM 2PM 3PM 4PM 5PM 6PM 7PM 8PM 9PM 10PM 11PM TOTAL Polyglucose biosynthesis (and degradation?) Glycosyl hydrolase family 1 || Beta-glucosidase Caur_1548 JCVI_PEP_metagenomic.orf.21287388.1 1113211797382 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 0 2 2 1 0 0 2 0 14 Glycogen synthesis/degradation alpha-glucan phosphorylases || Phosphorylase Caur_0735 0 – day JCVI_PEP_metagenomic.orf.20806045.1 1113211797649 0 1 4 0 0 0 5 2 3 6 9 10 23 14 12 32 21 20 4 5 2 6 0 179 glycosyl transferase group 1 Caur_1245 2 – 4PM spike JCVI_PEP_metagenomic.orf.21138689.1 1113211797213 0 2 0 2 0 0 0 1 3 1 8 2 7 3 11 12 2 2 0 0 2 0 0 58 glycosyl transferase, group 1 || Phosphatidylinositol Caur_1522alpha-mannosyltransferase5 – day JCVI_PEP_metagenomic.orf.21232887.1 1113211797293 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 3 glycosyl transferase group 1 Caur_0642 3 – constitutive JCVI_PEP_metagenomic.orf.20956588.1 1113211796557 0 6 8 0 2 1 2 0 9 5 1 3 10 2 4 9 15 2 1 7 3 6 0 96 glycosyl transferase, group 1 || Starch (bacterial glycogen)Caur_2520 synthase 2 – 4PM spike JCVI_PEP_metagenomic.orf.21218775.1 1113211796702 1 0 1 0 0 0 0 0 4 2 5 4 4 4 4 6 8 2 0 0 6 5 0 56

Glycolysis ROK family protein || N-acylmannosamine kinase Caur_2345 0 – day JCVI_PEP_metagenomic.orf.21322762.1 1113211797072 1 0 4 5 8 4 8 0 9 10 13 26 28 5 25 16 36 72 18 3 1 6 1 299 glucokinase || Glucokinase Caur_3196 5 – day JCVI_PEP_metagenomic.orf.21100309.1 1113211797484 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 4 pfk 6-phosphofructokinase || 6-phosphofructokinase Caur_0258 1 – night JCVI_PEP_metagenomic.orf.21091681.1 1113211797470 1 8 5 11 3 0 1 1 2 2 0 2 3 0 1 3 1 40 23 10 6 19 0 142 pfk Phosphofructokinase || 6-phosphofructokinase Caur_0869 2 – 4PM spike JCVI_PEP_metagenomic.orf.21255733.1 1113211797140 0 0 3 0 0 0 2 0 2 2 7 4 2 2 3 10 13 10 1 3 0 0 0 64 6-phosphofructokinase || 6-phosphofructokinase 2 – 4PM spike JCVI_PEP_metagenomic.orf.21256013.1 1113211797140 0 0 0 0 0 0 0 0 0 2 0 1 3 0 0 5 0 0 0 0 0 0 0 11 pgk phosphoglycerate kinase || Phosphoglycerate kinaseCaur_2821 3 – constitutive JCVI_PEP_metagenomic.orf.21360339.1 1113211795997 6 13 20 1 5 9 7 4 9 11 12 16 13 9 14 27 21 20 7 3 5 7 28 267 gpm phosphoglycerate mutase || Phosphoglycerate mutaseCaur_3351 5 – day JCVI_PEP_metagenomic.orf.21328339.1 1113211797268 0 0 0 0 0 0 0 0 2 0 4 1 4 0 5 0 4 4 0 0 0 0 0 24 2,3-bisphosphoglycerate-independent phosphoglycerateCaur_1142 mutase || Phosphoglycerate0 – day mutaseJCVI_PEP_metagenomic.orf.21464537.1 1113211797531 3 3 7 4 14 4 5 4 11 3 12 14 30 13 19 9 26 34 11 11 4 2 2 245 phosphoglycerate mutase Caur_2937 4 – constitutive JCVI_PEP_metagenomic.orf.20831712.1 1113211800771 0 1 3 0 0 0 1 2 2 2 4 2 7 1 4 0 1 0 1 0 0 0 1 32 phosphoglycerate mutase || Phosphoglycerate mutaseCaur_0633 3 – constitutive JCVI_PEP_metagenomic.orf.20994481.1 1113211796557 0 0 1 1 1 2 0 1 3 1 0 3 3 2 5 6 5 4 10 3 1 0 4 56 gluconeogenesis fructose-1,6-bisphosphatase, class II Caur_3319 0 – day JCVI_PEP_metagenomic.orf.21337664.1 1113211796835 8 8 11 14 6 9 10 0 22 8 19 27 30 11 25 36 57 44 6 4 4 5 0 364 fructose-1,6-bisphosphatase, class II Caur_1234 2 – 4PM spike JCVI_PEP_metagenomic.orf.21349528.1 1113211797516 0 0 0 0 1 0 0 0 0 0 0 0 1 1 1 2 0 0 0 0 0 0 0 6 oxidative pentose phosphate pathway ( Entner-Doudoroff) zwf glucose-6-phosphate dehydrogenase || Glucose-6-phosphateCaur_0501 1-dehydrogenase3 – constitutive JCVI_PEP_metagenomic.orf.21270728.1 1113211797005 3 0 1 10 10 1 4 1 2 4 7 3 10 5 13 2 11 10 6 2 0 1 11 117 gnd 6-phosphogluconate dehydrogenase (decarboxylating)Caur_0500 || Phosphogluconate2 – 4PM dehydrogenase spike JCVI_PEP_metagenomic.orf.21270469.1 (decarboxylating) 1113211797005 1 0 0 0 4 0 0 0 0 1 0 0 4 5 0 12 3 7 3 2 0 0 0 42 non-oxidative pentose phosphate pathway tktA transketolase || Transketolase Caur_1827 5 – day JCVI_PEP_metagenomic.orf.20942255.1 1113211797252 0 0 0 0 0 0 0 0 2 1 2 3 3 0 1 0 3 1 0 0 0 0 0 16 transketolase || Transketolase 2 – 4PM spike JCVI_PEP_metagenomic.orf.20943406.1 1113211797252 0 0 0 0 0 0 2 0 0 0 4 1 8 5 6 5 6 7 0 2 1 3 0 50 talA putative transaldolase || Transaldolase Caur_2803 3 – constitutive JCVI_PEP_metagenomic.orf.21340784.1 1113211797191 1 3 2 4 4 5 3 1 2 1 2 6 10 0 6 1 6 4 0 3 2 2 0 68 ribose-phosphate diphosphokinase || Ribose-phosphateCaur_3604 diphosphokinase0 – day JCVI_PEP_metagenomic.orf.21355291.1 1113211797515 0 5 1 7 0 0 0 3 2 4 10 10 12 7 13 11 9 2 1 2 1 1 0 101 anapleurotic reactions PEP carboxylase (ppc) (oxaloacetate + PO4 → PEP + CO2)phosphoenolpyruvate carboxylase || PhosphoenolpyruvateCaur_3161 carboxylase0 – day JCVI_PEP_metagenomic.orf.20896409.1 1113211797666 2 1 9 2 8 3 4 5 23 10 23 23 29 21 22 15 47 14 6 1 6 5 0 279 PEP carboxykinase (pckA) (oxaloacetate + GTP → PEP +phosphoenolpyruvate GDP + CO2) carboxykinase (GTP) || PhosphoenolpyruvateCaur_2331 carboxykinase1 – night (GTP)JCVI_PEP_metagenomic.orf.21325208.1 1113211797072 336 794 772 554 263 237 301 86 138 135 27 19 45 30 30 63 815 3824 1993 998 588 827 810 13685 malic enzyme (tme) (malate + NAD+ → pyruvate + CO2 +Malic NADH) enzyme, NAD binding domain || Malate dehydrogenaseCaur_1614 (oxaloacetate5 – day decarboxylating)JCVI_PEP_metagenomic.orf.21259144.1 1113211797383 1 0 0 0 0 0 0 0 5 0 5 1 5 5 6 2 6 0 0 0 0 1 0 37 oxidative tricarboxylic acid cycle pyruvate dehydrogenase E2 subunit (2.3.1.12) catalytic domain of components of various dehydrogenaseCaur_1974 complexes 2|| –Dihydrolipoyllysine-residue 4PM spike JCVI_PEP_metagenomic.orf.21261224.1 succinyltransferase 1113211801082 2 3 0 0 0 0 0 0 0 2 4 4 3 2 7 7 15 10 1 2 2 0 0 64 pyruvate dehydrogenase E1 subunit (1.2.4.1) transketolase, central region || Pyruvate dehydrogenaseCaur_1973 (acetyl-transferring)0 – day JCVI_PEP_metagenomic.orf.21261103.1 1113211801082 1 2 3 2 0 0 1 0 3 5 11 8 6 6 11 15 23 17 5 1 4 1 11 136 pyruvate dehydrogenase E1 subunit (1.2.4.1) pyruvate dehydrogenase (acetyl-transferring) E1 component,Caur_1972 alpha subunit4 – constitutive || Pyruvate dehydrogenaseJCVI_PEP_metagenomic.orf.21028914.1 (acetyl-transferring) 1113211800054 0 0 2 3 0 0 0 0 1 1 4 1 0 3 3 5 14 5 1 5 0 6 0 54 pyruvate dehydrogenase E1 subunit (1.2.4.1) pyruvate dehydrogenase (lipoamide) || Pyruvate dehydrogenaseCaur_3672 (acetyl-transferring)2 – 4PM spike JCVI_PEP_metagenomic.orf.21510975.1 1113211796800 0 0 0 0 0 0 0 0 1 2 9 15 11 14 21 21 21 7 0 2 0 0 0 124 pyruvate dehydrogenase E1 subunit (1.2.4.1) transketolase, central region || Pyruvate dehydrogenaseCaur_2805 (acetyl-transferring)2 – 4PM spike JCVI_PEP_metagenomic.orf.21258720.1 1113211796512 2 0 1 0 4 1 2 1 0 3 6 5 7 3 0 6 5 3 2 0 2 0 0 53 pyruvate dehydrogenase E3 subunit (1.8.1.4) dihydrolipoyl dehydrogenase || Dihydrolipoyl dehydrogenanseCaur_2840 0 – day JCVI_PEP_metagenomic.orf.21330150.1 1113211797179 2 5 8 0 2 9 9 3 7 12 9 21 24 13 24 50 71 18 14 10 7 10 9 337 pyruvate:ferredoxin oxidoreductase (1.2.7.1) porA pyruvate flavodoxin/ferredoxin oxidoreductase domainCaur_2080 protein || Pyruvate1 – dehydrogenasenight JCVI_PEP_metagenomic.orf.21406517.1 (NADP+) 1113211796694 17 20 27 30 7 11 13 14 9 18 0 0 0 0 0 2 43 110 81 78 40 48 24 592 gltA citrate (Si)-synthase || Citrate (Si)-synthase Caur_3809 3 – constitutive JCVI_PEP_metagenomic.orf.21373771.1 1113211797117 9 21 34 20 45 24 29 18 22 19 31 33 51 31 53 38 85 87 23 18 14 7 10 722 acnA aconitate hydratase 1 || Aconitate hydratase Caur_3150 0 – day JCVI_PEP_metagenomic.orf.21345114.1 1113211796680 6 5 1 13 9 3 11 2 11 15 12 10 29 9 18 35 53 46 5 12 12 13 1 331 icd isocitrate dehydrogenase, NADP-dependent || IsocitrateCaur_2895 dehydrogenase0 –(NADP+) day JCVI_PEP_metagenomic.orf.21220427.1 1113211797481 4 11 3 4 14 3 9 5 16 16 16 21 34 13 34 31 30 21 7 1 5 5 0 303 2-oxoglutarate synthase (FOR, 1.2.7.3 korA) pyruvate flavodoxin/ferredoxin oxidoreductase domainCaur_0249 protein || 2-oxoglutarate0 – day synthaseJCVI_PEP_metagenomic.orf.20952291.1 1113211796457 0 1 3 0 0 1 0 1 4 2 2 9 10 5 8 4 18 11 2 5 1 1 2 90 pyridoxamine 5'-phosphate oxidase || Pyridoxamine-phosphate oxidase3 – constitutive JCVI_PEP_metagenomic.orf.21247135.1 1113211797160 3 1 5 0 0 0 0 0 0 2 2 6 5 3 8 1 5 1 1 1 0 3 0 47 2-oxoglutarate dehydrogenase subunit E2 (sucB) catalytic domain of components of various dehydrogenaseCaur_1691 complexes 0|| –Dihydrolipoyllysine-residue day JCVI_PEP_metagenomic.orf.21460781.1 succinyltransferase 1113211797547 3 1 1 1 8 2 0 1 0 8 9 12 16 6 9 5 8 18 4 1 0 4 0 117 dihydrolipoyl dehydrogenase || Dihydrolipoyl dehydrogenanseCaur_2840 0 – day JCVI_PEP_metagenomic.orf.21330150.1 1113211797179 2 5 8 0 2 9 9 3 7 12 9 21 24 13 24 50 71 18 14 10 7 10 9 337 sucC succinate-CoA ligase, beta subunit || Succinate--CoACaur_1121 ligase (ADP-forming)0 – day JCVI_PEP_metagenomic.orf.21038359.1 1113211801391 0 3 5 6 3 2 1 0 7 5 6 22 16 6 16 24 25 7 0 0 1 2 0 157 succinate dehydrogenase (or fumarate reductase) cytochromeCaur_1882 b subunit,0 – b558day family JCVI_PEP_metagenomic.orf.21039395.1 1113211799073 0 3 0 0 5 5 3 0 11 11 28 19 38 14 31 11 46 26 14 4 1 4 31 305 mdh chain C, Large Improvement In The Thermal StabilityCaur_0900 Of A Tetrameric 3Malate – constitutive DehydrogenaseJCVI_PEP_metagenomic.orf.21337934.1 By Single s At The Dimer-Dimer Interface.1113211797173 || L-lactate dehydrogenase 4 7 4 0 6 2 9 3 5 4 0 12 2 5 7 3 1 6 3 6 1 4 0 94

PHB synthesis/degradation Acetoacyl-CoA ↔ acetyl-CoA hypothetical protein Caur_0234 4 – constitutive JCVI_PEP_metagenomic.orf.21184884.1 1113211800678 0 1 1 0 0 0 0 2 0 0 0 0 1 2 0 1 2 1 0 0 0 0 0 11 acetyl-CoA acetyltransferases || Acetyl-CoA C-acyltransferaseCaur_3220 0 – day JCVI_PEP_metagenomic.orf.21343301.1 1113211797461 3 5 13 14 4 1 3 1 5 9 18 14 11 7 12 20 28 14 2 2 4 10 15 215 acetyl-CoA acetyltransferases || Acetyl-CoA C-acetyltransferaseCaur_1540 3 – constitutive JCVI_PEP_metagenomic.orf.20855243.1 1113211801530 4 4 6 0 3 3 2 3 5 7 6 8 16 8 8 12 9 4 8 4 2 3 8 133

Branched-chain amino acid biosynthesis Acetolactate synthase large subunit (ilvH) acetolactate synthase, small subunit || Acetolactate Caur_0164synthase 0 – day JCVI_PEP_metagenomic.orf.21200198.1 1113211797301 2 2 0 1 2 4 1 4 6 14 21 13 6 3 24 17 34 3 5 3 3 4 0 172 Acetolactate synthase small subunit (ilvB) Thiamine pyrophosphate enzyme, central domain || AcetolactateCaur_0163 synthase0 – day JCVI_PEP_metagenomic.orf.21199197.1 1113211797301 3 7 5 6 9 3 5 8 11 12 33 21 21 15 17 6 30 14 14 1 1 13 13 268 acetolactate synthase, large subunit, biosynthetic type || Acetolactate synthase0 – day JCVI_PEP_metagenomic.orf.21200052.1 1113211797301 1 3 2 1 4 1 2 5 3 5 17 8 6 0 7 13 17 1 5 1 0 1 5 108 Ketol-acid reductoisomerase ketol-acid reductoisomerase || Ketol-acid reductoisomeraseCaur_0165 0 – day JCVI_PEP_metagenomic.orf.21200772.1 1113211797301 2 6 2 0 0 1 1 0 9 7 25 16 18 9 10 12 15 4 2 0 3 2 0 144 dihydroxyacid dehydratase dihydroxy-acid dehydratase (DAD). || Dihydroxy-acidCaur_2851 dehydratase 2 – 4PM spike JCVI_PEP_metagenomic.orf.21420874.1 1113211797505 1 1 0 0 0 0 0 0 3 2 12 4 7 7 4 9 12 10 0 0 0 3 0 75 Dehydratase family || Dihydroxy-acid dehydratase 0 – day JCVI_PEP_metagenomic.orf.21420908.1 1113211797505 1 7 1 10 2 3 7 2 6 7 12 7 20 3 14 14 16 9 4 7 2 3 0 157 3-isopropylmalate dehydratase large subunit homoaconitate hydratase family protein || 3-isopropylmalateCaur_0329 dehydratase5 – day JCVI_PEP_metagenomic.orf.20946622.1 1113211796889 0 0 1 0 0 0 0 0 1 0 0 0 1 0 1 0 5 0 0 0 0 0 0 9 3-isopropylmalate dehydratase small subunit 3-isopropylmalate dehydratase, small subunit || HomoaconitateCaur_0330 hydratase5 – day JCVI_PEP_metagenomic.orf.20947790.1 1113211796889 0 0 0 0 0 0 0 0 7 0 2 2 9 0 8 2 5 0 0 0 0 2 0 37 isopropylmalate isomerase large subunit Aconitase family (aconitate hydratase) || 3-isopropylmalateCaur_0168 dehydratase5 – day JCVI_PEP_metagenomic.orf.21201758.1 1113211797301 1 2 0 0 0 0 0 0 3 0 4 7 4 6 4 3 7 0 0 0 0 3 0 44 fumC biosynthesis protein LysW Caur_0332 4 – constitutive JCVI_PEP_metagenomic.orf.20949892.1 1113211796889 0 0 0 0 5 0 0 0 0 1 0 0 0 1 2 0 3 1 0 0 0 2 0 15 lysine biosynthesis protein LysW 3 – constitutive JCVI_PEP_metagenomic.orf.20950479.1 1113211796889 0 0 3 3 0 0 2 0 1 3 0 0 0 1 4 3 2 4 1 0 0 8 0 35 3-isopropylmalate dehydrogenase dehydrogenase, isocitrate/isopropylmalate family || 3-isopropylmalateCaur_0331 dehydrogenase3 – constitutive JCVI_PEP_metagenomic.orf.20949598.1 1113211796889 3 2 2 0 0 1 0 0 9 1 7 2 7 6 2 2 12 4 2 5 6 2 0 75 Valyl-tRNA synthetase tRNA synthetases class I (I, L, M and V) || Valine--tRNACaur_2648 ligase 3 – constitutive JCVI_PEP_metagenomic.orf.21316093.1 1113211797113 2 0 6 2 5 5 11 5 6 8 3 5 18 11 21 11 19 9 8 0 0 0 3 158 tRNA synthetases class I (I, L, M and V) || Valine--tRNA ligase 0 – day JCVI_PEP_metagenomic.orf.21316333.1 1113211797113 9 6 8 13 14 5 11 5 27 19 45 32 57 24 67 45 54 44 8 13 4 9 12 531 Isoleucyl-tRNA synthetase isoleucyl-tRNA synthetase || Isoleucine--tRNA ligaseCaur_2692 4 – constitutive JCVI_PEP_metagenomic.orf.21198913.1 1113211797301 2 3 0 0 0 0 0 0 6 5 6 4 14 4 3 2 10 12 1 1 2 0 0 75 Leucyl-tRNA synthetase (leuS) leucyl-tRNA synthetase || Leucine--tRNA ligase Caur_2759 0 – day JCVI_PEP_metagenomic.orf.20985933.1 1113211796912 1 12 2 6 0 14 9 5 5 13 21 28 38 20 41 26 51 63 13 19 8 7 0 402

Glycolate metabolism glycolate dehydrogenase glcD D-lactate dehydrogenase (cytochrome) || D-lactate dehydrogenaseCaur_2132 (cytochrome)3 – constitutive JCVI_PEP_metagenomic.orf.21317521.1 1113211797435 2 1 8 0 5 6 0 1 6 2 11 19 15 4 4 9 8 4 0 3 0 0 0 108 glycolate dehydrogenase glcD FAD linked oxidase domain protein || D-lactate dehydrogenaseCaur_2133 (cytochrome)0 – day JCVI_PEP_metagenomic.orf.20818441.1 1113211796848 0 4 5 0 0 2 3 2 2 7 11 21 22 5 15 17 22 8 2 3 0 1 0 152 other subunits/homologs protein of unknown function cysteine-rich region domainCaur_2135 protein || CoB--CoM0 – day heterodisulfideJCVI_PEP_metagenomic.orf.21317770.1 reductase 1113211797435 1 5 2 0 5 0 0 0 5 11 27 32 40 14 42 27 37 24 0 2 3 5 4 286 glyoxylate reductase glyoxylate reductase || Gluconate 2-dehydrogenase Caur_0825 5 – day JCVI_PEP_metagenomic.orf.21141232.1 1113211796099 0 0 0 0 0 0 0 0 1 0 0 1 2 0 0 0 0 0 0 0 0 0 0 4

Glyoxylate bypass isocitrate lyase isocitrate lyase || Isocitrate lyase Caur_3889 3 – constitutive JCVI_PEP_metagenomic.orf.21321019.1 1113211797113 31 46 91 89 87 75 58 53 58 43 50 105 118 40 71 68 161 142 60 79 46 76 103 1750 acetate metabolism Acetaldehyde dehydrogenase aldehyde dehydrogenase (NAD(+)) || Betaine-aldehydeCaur_3336 dehydrogenase4 – constitutive JCVI_PEP_metagenomic.orf.21334442.1 1113211796835 0 1 0 0 0 1 0 0 3 1 2 3 7 3 1 1 3 8 0 0 0 2 0 36 Acetaldehyde dehydrogenase aldehyde dehydrogenase (NAD) family protein || AldehydeCaur_1767 dehydrogenase3 – constitutive (NAD+) JCVI_PEP_metagenomic.orf.21046067.1 1113211797291 3 0 2 0 6 1 1 4 6 2 4 12 17 1 8 1 14 13 0 8 1 4 1 109

Fatty Acid Metabolism biosynthesis fabD hypothetical protein Caur_2407 3 – constitutive JCVI_PEP_metagenomic.orf.21025425.1 1113211797291 1 0 2 4 2 1 5 0 3 3 10 9 13 4 5 1 11 14 7 1 0 1 12 109 Beta-ketoacyl synthase, C-terminal domain || 3-oxoacyl-[acyl-carrierCaur_1931 protein]4 – constitutive synthase JCVI_PEP_metagenomic.orf.21135123.1 1113211796012 0 0 0 0 1 1 0 2 3 4 3 1 8 1 1 4 12 4 2 1 0 0 0 48 acetyl-CoA carboxylase, biotin carboxylase || PyruvateCaur_1378 carboxylase 1 – night JCVI_PEP_metagenomic.orf.21400738.1 1113211796654 9 18 33 46 31 32 16 9 19 9 6 7 11 2 16 14 13 14 15 24 11 11 25 391 3-oxoacyl-[acyl-carrier-protein] reductase || 3-oxoacyl-[acyl-carrierCaur_3422 protein]0 – day reductase JCVI_PEP_metagenomic.orf.21313168.1 1113211797113 2 1 4 1 4 2 2 1 7 6 14 16 11 5 16 8 8 12 5 0 0 0 0 125 fabI oxidoreductase, short chain dehydrogenase/reductaseCaur_2911 family || Enoyl-[acyl-carrier3 – constitutive protein]JCVI_PEP_metagenomic.orf.21209322.1 reductase (NADH) 1113211797481 0 0 0 0 1 0 0 0 3 0 3 3 6 1 6 1 9 2 0 0 3 0 8 46 β-oxidation Acyl-CoA synthetase AMP-dependent synthetase and ligase Caur_1085 5 – day JCVI_PEP_metagenomic.orf.21199274.1 1113211800494 0 0 2 0 1 0 0 0 1 2 2 6 5 1 0 0 3 1 0 0 0 0 0 24 Acyl-CoA synthetase AMP-dependent synthetase and ligase || Long-chain-fatty-acid--CoACaur_1072 ligase0 – day JCVI_PEP_metagenomic.orf.21235551.1 1113211797293 19 12 29 19 23 8 12 6 29 31 61 63 89 33 88 72 126 118 27 16 5 19 22 927 3-hydroxyacyl-CoA hydrolase enoyl-CoA hydratase/isomerase || Enoyl-CoA hydrataseCaur_1565 5 – day JCVI_PEP_metagenomic.orf.21397975.1 1113211797159 0 0 0 0 0 0 0 0 0 1 0 3 3 1 1 0 0 0 0 0 0 0 0 9 3-hydroxyacyl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase NAD-binding Caur_3221 3 – constitutive JCVI_PEP_metagenomic.orf.21343104.1 1113211797461 4 0 5 1 0 0 0 1 2 3 5 1 8 1 0 5 10 5 0 1 3 5 0 60 Beta-ketoacyl thiolase acetyl-CoA acetyltransferases || Acetyl-CoA C-acyltransferaseCaur_3220 0 – day JCVI_PEP_metagenomic.orf.21343301.1 1113211797461 3 5 13 14 4 1 3 1 5 9 18 14 11 7 12 20 28 14 2 2 4 10 15 215 Hydrogenase hypE hydrogenase accessory protein HypB Caur_2773 1 – night JCVI_PEP_metagenomic.orf.21266967.1 1113211797005 0 1 0 4 3 1 0 2 0 3 4 2 2 0 8 5 83 84 6 4 5 3 8 228 hypC hydrogenase expression/formation protein HypD Caur_2762 4 – constitutive JCVI_PEP_metagenomic.orf.21269280.1 1113211797005 2 4 0 0 0 0 0 2 1 4 3 7 11 5 8 9 38 23 4 0 0 2 0 123 hypB hydrogenase expression/formation protein HypE || Thiamine-phosphateCaur_2761 4 kinase– constitutive JCVI_PEP_metagenomic.orf.21269519.1 1113211797005 0 3 0 0 0 0 0 2 1 0 2 4 1 0 0 3 3 4 0 0 0 0 0 23 hydrogenase expression/formation protein HypE. 4 – constitutive JCVI_PEP_metagenomic.orf.21269613.1 1113211797005 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 7 1 0 0 0 0 0 10 hypA hydrogenase nickel insertion protein HypA Caur_2774 0 – day JCVI_PEP_metagenomic.orf.21266809.1 1113211797005 0 1 1 0 2 1 6 0 1 1 0 2 4 5 4 0 59 41 4 4 0 1 0 137 hydA NADH ubiquinone oxidoreductase 20 kda subunit || HydrogenaseCaur_2771 (acceptor)1 – night JCVI_PEP_metagenomic.orf.21267278.1 1113211797005 1 3 3 0 3 2 5 1 1 6 3 10 4 10 11 10 129 134 13 8 7 5 20 389 hydB hydrogenase nickel insertion protein HypA Caur_2770 0 – day JCVI_PEP_metagenomic.orf.21266809.1 1113211797005 0 1 1 0 2 1 6 0 1 1 0 2 4 5 4 0 59 41 4 4 0 1 0 137

Nitrogen metabolism nitrate reductase (narG) formate dehydrogenase || Formate dehydrogenase Caur_3201 1 – night JCVI_PEP_metagenomic.orf.20873559.1 1113211797666 0 5 3 0 10 0 1 2 1 1 7 4 7 7 8 7 9 76 1 16 4 4 14 187 Ammonium transporter amtB Ammonium Transporter Family Caur_1002 0 – day JCVI_PEP_metagenomic.orf.21231306.1 1113211797494 2 10 7 8 8 5 11 4 49 8 19 15 55 7 33 49 12 5 17 4 6 5 4 343 Ammonium transporter amtB ammonium transporter 0 – day JCVI_PEP_metagenomic.orf.21230906.1 1113211797494 3 15 10 13 9 11 2 11 88 31 46 30 65 44 130 70 59 25 25 3 3 8 12 713

Phototrophy pufM Photosynthetic reaction center protein Caur_1051 1 – night JCVI_PEP_metagenomic.orf.21005934.1 1113211796884 34 38 36 44 17 18 14 15 23 26 24 17 17 6 12 18 31 67 37 42 32 55 33 656 pufC cytoChrome c-554 (Cytochrome c554). Caur_2089 1 – night JCVI_PEP_metagenomic.orf.21408788.1 1113211796694 5 7 10 0 6 7 10 1 11 0 12 5 9 2 1 5 10 21 22 21 8 19 6 198 bchN light-iNdependent protochlorophyllide reductase subunitCaur_2557 n (li-por subunit1 –n) night (dpor subunit JCVI_PEP_metagenomic.orf.20992898.1n). 1113211797414 16 8 27 37 17 11 7 5 31 25 14 18 21 7 2 16 44 26 17 23 16 16 28 432 bchB light-independent protochlorophyllide reductase, B subunitCaur_2556 || Nitrogenase3 – constitutive JCVI_PEP_metagenomic.orf.20994004.1 1113211797414 18 22 64 44 19 23 20 15 66 37 52 33 49 11 12 22 94 88 18 36 21 24 29 817 bchL light-independent protochlorophyllide reductase, iron-sulfurCaur_2554 ATP-binding3 –protein constitutive || NitrogenaseJCVI_PEP_metagenomic.orf.20997892.1 1113211797414 14 10 26 10 11 11 16 3 30 18 17 13 10 6 18 30 33 33 15 12 4 16 15 371 bchM magnesium protoporphyrin O-methyltransferase || MagnesiumCaur_2588 protoporphyrin IX methyltransferaseJCVI_PEP_metagenomic.orf.20986494.1 1113211796617 14 8 15 0 6 1 7 1 11 5 1 0 1 0 0 5 1 5 11 0 2 7 0 101 acsF magnesium-protoporphyrin IX monomethyl ester aerobicCaur_2590 oxidative cyclase1 – night || Magnesium-protoporphyrinJCVI_PEP_metagenomic.orf.20989773.1 IX monomethyl ester (oxidative)1113211796617 cyclase 12 11 43 26 41 14 14 9 48 36 6 5 5 2 0 11 34 18 24 6 12 24 4 405 bchH BchH || Cobaltochelatase Caur_3151 1 – night JCVI_PEP_metagenomic.orf.21345407.1 1113211796680 290 457 435 457 283 309 410 172 199 233 80 71 111 59 103 79 555 838 522 453 239 564 474 7393 BchH || Cobaltochelatase 1 – night JCVI_PEP_metagenomic.orf.21345589.1 1113211796680 108 163 102 217 109 69 147 62 50 60 20 30 19 10 24 36 143 292 179 137 64 223 115 2379 bchH magnesium chelatase, H subunit Caur_2591 4 – constitutive JCVI_PEP_metagenomic.orf.20990598.1 1113211796617 0 0 0 6 0 0 1 0 3 2 0 0 1 0 0 0 1 4 0 0 0 0 0 18 magnesium chelatase, H subunit || Cobaltochelatase 3 – constitutive JCVI_PEP_metagenomic.orf.20993616.1 1113211796617 2 9 15 2 6 5 4 1 18 13 3 0 7 0 0 3 16 15 3 5 1 9 10 147 magnesium chelatase, H subunit || Cobaltochelatase 3 – constitutive JCVI_PEP_metagenomic.orf.20993889.1 1113211796617 0 0 3 9 1 1 9 1 12 3 1 0 2 1 0 2 4 0 1 0 0 0 0 50 bchH magnesium chelatase, H subunit || CobaltochelataseCaur_3371 1 – night JCVI_PEP_metagenomic.orf.20910567.1 1113211796457 16 22 22 26 8 13 18 9 17 12 11 16 15 12 13 13 71 50 23 17 12 36 6 458 bchI BchI || Magnesium chelatase Caur_0419 1 – night JCVI_PEP_metagenomic.orf.21420078.1 1113211796546 10 6 10 6 14 8 14 8 3 5 2 0 4 0 4 0 11 27 7 12 17 22 4 194 BchI || Magnesium chelatase 1 – night JCVI_PEP_metagenomic.orf.21420123.1 1113211796546 3 1 5 0 7 8 1 1 5 5 3 3 3 2 0 1 4 5 6 3 8 7 0 81 bchI magnesium chelatase || Magnesium chelatase Caur_1255 4 – constitutive JCVI_PEP_metagenomic.orf.21144555.1 1113211797213 2 0 0 4 1 0 0 3 2 3 4 10 7 9 3 5 9 8 0 1 1 5 0 77 bchJ bacteriochlorophyll 4-vinyl reductase Caur_3677 1 – night JCVI_PEP_metagenomic.orf.21439308.1 1113211796181 3 16 15 15 4 12 2 13 17 19 0 0 0 2 0 1 14 23 10 7 16 20 1 210 bchE BchE Caur_3676 1 – night JCVI_PEP_metagenomic.orf.20838211.1 1113211796981 12 7 18 6 16 6 10 6 15 15 0 1 3 1 0 2 21 11 14 4 7 17 2 194 BchE 3 – constitutive JCVI_PEP_metagenomic.orf.21439337.1 1113211796181 1 2 9 17 6 1 5 6 9 6 0 0 0 0 0 0 13 14 3 5 5 6 6 114 bchD BchD || Magnesium chelatase Caur_0420 1 – night JCVI_PEP_metagenomic.orf.21420158.1 1113211796546 15 31 37 15 20 26 24 14 12 14 8 8 15 4 11 2 8 31 26 36 32 50 24 463 bchP geranylgeranyl reductase Caur_2087 1 – night JCVI_PEP_metagenomic.orf.21409078.1 1113211796694 9 35 43 33 20 17 23 13 24 16 21 31 27 13 34 24 65 107 49 64 38 24 61 791 bchF 2-vinyl bacteriochlorophyllide hydratase Caur_0415 1 – night JCVI_PEP_metagenomic.orf.21419849.1 1113211796546 15 11 21 5 4 7 4 1 11 6 1 2 7 3 3 1 11 23 14 12 14 21 12 209 bchC oxidoreductase, zinc-binding dehydrogenase family Caur_0416|| L-iditol 2-dehydrogenase1 – night JCVI_PEP_metagenomic.orf.21419938.1 1113211796546 11 79 96 71 25 24 25 19 170 100 20 29 27 8 23 65 273 232 166 252 125 73 58 1971 bchX chlorophyllide reductase iron protein subunit X Caur_0417 1 – night JCVI_PEP_metagenomic.orf.21419970.1 1113211796546 5 4 16 13 9 7 4 2 13 7 3 1 12 1 4 4 13 22 7 17 9 17 10 200 bchY chlorophyllide reductase subunit Y Caur_3805 0 – day JCVI_PEP_metagenomic.orf.21272354.1 1113211797285 8 1 3 4 2 4 3 2 13 3 36 27 41 8 39 37 47 16 12 3 7 4 4 324 bchK BchGc Caur_0138 1 – night JCVI_PEP_metagenomic.orf.21148454.1 1113211799203 8 14 5 20 2 4 8 4 10 7 7 5 7 4 3 3 18 28 11 5 11 23 18 225 bchS magnesium chelatase, H subunit || CobaltochelataseCaur_3371 1 – night JCVI_PEP_metagenomic.orf.20910567.1 1113211796457 16 22 22 26 8 13 18 9 17 12 11 16 15 12 13 13 71 50 23 17 12 36 6 458 csmA BaCteriochlorophyll c-binding protein (BChl c-binding)(ChlorosomeCaur_0126 protein1 – night A) (Light-harvestingJCVI_PEP_metagenomic.orf.21429221.1 protein B-740) (5.7 kDachlorosomal protein).1113211797122 10 2 11 6 8 6 0 8 12 3 15 7 12 1 2 1 15 29 12 18 9 10 2 199 csmM CsmM Caur_0139 1 – night JCVI_PEP_metagenomic.orf.21149279.1 1113211799203 59 84 143 208 135 105 106 43 94 95 62 71 54 10 58 26 175 221 100 85 89 84 50 2157 csmN 18 kDa protein Caur_0140 1 – night JCVI_PEP_metagenomic.orf.21149899.1 1113211799203 55 54 100 61 88 57 49 17 53 78 53 54 42 15 31 27 105 136 52 82 47 77 74 1407 csmP hypothetical protein Caur_0142 3 – constitutive JCVI_PEP_metagenomic.orf.21356762.1 1113211795997 8 4 0 0 3 3 7 2 14 2 4 4 10 5 7 0 7 7 4 1 3 12 3 110

3-Hydroxypropionate pathway accD acetyl-CoA carboxylase, carboxyl transferase, beta Caur_1648subunit || Propionyl-CoA3 – constitutive carboxylaseJCVI_PEP_metagenomic.orf.20984922.1 1113211797209 5 10 12 33 12 8 12 10 20 16 22 32 31 11 22 9 53 48 10 4 10 19 4 413 accA acetyl-CoA carboxylase, carboxyl transferase, alphaCaur_1647 subunit || Acetyl-CoA3 – constitutive carboxylase JCVI_PEP_metagenomic.orf.20985197.1 1113211797209 0 1 4 1 1 1 1 1 1 1 6 3 8 2 4 5 1 3 1 0 0 2 0 47 accC acetyl-CoA carboxylase, biotin carboxylase || Biotin Caur_3421carboxylase 0 – day JCVI_PEP_metagenomic.orf.21313246.1 1113211797113 1 11 1 0 11 6 4 3 8 25 21 25 50 16 30 33 23 37 6 2 2 6 6 327 pcc carbamoyl-phosphate synthase L chain ATP-bindingCaur_2832 || Biotin carboxylase5 – day JCVI_PEP_metagenomic.orf.21044982.1 1113211801443 0 0 1 0 1 0 0 1 0 3 5 2 7 1 4 5 10 3 0 0 0 0 0 43 carboxyl transferase || Propionyl-CoA carboxylase Caur_2360 3 – constitutive JCVI_PEP_metagenomic.orf.21163593.1 1113211797400 0 3 10 3 6 9 3 4 5 7 7 12 14 3 14 8 14 16 9 2 9 2 0 160 acetyl-CoA carboxylase, biotin carboxylase || PyruvateCaur_1378 carboxylase 1 – night JCVI_PEP_metagenomic.orf.21400738.1 1113211796654 9 18 33 46 31 32 16 9 19 9 6 7 11 2 16 14 13 14 15 24 11 11 25 391 mcr malonyl-CoA reductase Caur_2614 1 – night JCVI_PEP_metagenomic.orf.21361591.1 1113211797486 4 1 4 14 1 5 1 0 10 0 2 2 5 4 0 1 5 10 7 3 2 3 0 84 pcs propionyl-CoA synthase || Acetate--CoA ligase Caur_0613 3 – constitutive JCVI_PEP_metagenomic.orf.20994761.1 1113211796557 21 6 21 8 14 13 33 6 32 51 26 32 29 5 27 10 57 61 10 18 3 21 3 507 Methylmalonyl-CoA epimerase propionyl-CoA synthase || NADPH:quinone reductase 1 – night JCVI_PEP_metagenomic.orf.20996131.1 1113211796557 19 20 50 57 28 28 46 25 54 86 49 67 63 17 36 11 120 167 57 87 21 50 57 1215 hypothetical protein Caur_2509 3 – constitutive JCVI_PEP_metagenomic.orf.21343591.1 1113211797461 5 0 0 1 1 1 1 1 7 3 3 11 6 3 4 1 11 6 5 1 0 0 0 71 methylmalonyl-CoA mutase, large subunit || Methylmalonyl-CoA mutase0 – day JCVI_PEP_metagenomic.orf.21343698.1 1113211797461 17 21 24 25 25 19 41 23 33 36 28 56 78 54 117 75 150 140 45 28 29 10 20 1094 methylmalonyl-CoA mutase N-terminal domain || Methylmalonyl-CoACaur_2508 mutase4 – constitutive JCVI_PEP_metagenomic.orf.21343876.1 1113211797461 31 50 35 46 48 33 32 29 63 30 34 101 114 54 97 110 243 213 67 54 43 45 17 1589 methylmalonyl-CoA mutase C-terminal domain || 2-methyleneglutarateCaur_0042 2 mutase – 4PM spike JCVI_PEP_metagenomic.orf.21300701.1 1113211797380 0 0 1 0 2 0 1 3 1 3 6 2 5 2 9 12 11 10 1 4 0 0 0 73 ccl pyruvate carboxyltransferase || Hydroxymethylglutaryl-CoACaur_2265 lyase 2 – 4PM spike JCVI_PEP_metagenomic.orf.21370707.1 1113211797127 0 0 7 0 0 0 0 0 3 2 4 5 10 3 1 10 5 0 0 0 1 0 0 51

Β-oxidation of fatty acids Acyl-CoA synthetase AMP-dependent synthetase and ligase Caur_1085 5 – day JCVI_PEP_metagenomic.orf.21199274.1 1113211800494 0 0 2 0 1 0 0 0 1 2 2 6 5 1 0 0 3 1 0 0 0 0 0 24 Acyl-CoA synthetase AMP-dependent synthetase and ligase || Long-chain-fatty-acid--CoACaur_1072 ligase0 – day JCVI_PEP_metagenomic.orf.21235551.1 1113211797293 19 12 29 19 23 8 12 6 29 31 61 63 89 33 88 72 126 118 27 16 5 19 22 927 3-hydroxyacyl-CoA hydrolase enoyl-CoA hydratase/isomerase || Enoyl-CoA hydrataseCaur_1565 5 – day JCVI_PEP_metagenomic.orf.21397975.1 1113211797159 0 0 0 0 0 0 0 0 0 1 0 3 3 1 1 0 0 0 0 0 0 0 0 9 3-hydroxyacyl-CoA dehydrogenase 3-hydroxyacyl-CoA dehydrogenase NAD-binding Caur_3221 3 – constitutive JCVI_PEP_metagenomic.orf.21343104.1 1113211797461 4 0 5 1 0 0 0 1 2 3 5 1 8 1 0 5 10 5 0 1 3 5 0 60 Beta-ketoacyl thiolase acetyl-CoA acetyltransferases || Acetyl-CoA C-acyltransferaseCaur_3220 0 – day JCVI_PEP_metagenomic.orf.21343301.1 1113211797461 3 5 13 14 4 1 3 1 5 9 18 14 11 7 12 20 28 14 2 2 4 10 15 215

Electron transport nuoF NADH dehydrogenase (quinone) || NADH dehydrogenaseCaur_1185 (quinone) 1 – night JCVI_PEP_metagenomic.orf.21070739.1 1113211797376 1 7 2 6 1 5 1 1 3 6 0 1 1 0 1 2 25 109 33 11 11 11 12 250 nuoA NADH-ubiquinone/plastoquinone oxidoreductase chainCaur_1987 3 || NADH dehydrogenase4 – constitutive (quinone)JCVI_PEP_metagenomic.orf.21302938.1 1113211797398 0 3 1 0 0 0 1 1 1 0 3 2 5 0 1 2 7 33 2 2 1 0 1 66 nuoB NADH-quinone oxidoreductase, B subunit || NADH dehydrogenaseCaur_1986 (quinone)1 – night JCVI_PEP_metagenomic.orf.21302974.1 1113211797398 2 2 6 6 3 2 8 6 8 6 6 7 7 2 3 3 19 50 16 9 5 5 18 199 nuoC hypothetical protein Caur_1985 1 – night JCVI_PEP_metagenomic.orf.21303040.1 1113211797398 8 2 2 4 0 0 2 5 4 1 2 2 2 3 6 0 8 20 6 3 2 1 3 86 nuoD NADH dehydrogenase (quinone), D subunit || NADHCaur_1984 dehydrogenase (quinone)3 – constitutive JCVI_PEP_metagenomic.orf.21303171.1 1113211797398 0 7 7 8 4 2 7 2 2 9 8 5 12 2 8 5 16 27 3 6 11 10 0 161 nuoH NADH dehydrogenase || NADH dehydrogenase (quinone)Caur_1982 4 – constitutive JCVI_PEP_metagenomic.orf.20948554.1 1113211801500 0 6 4 18 1 0 0 1 1 0 5 4 7 3 2 7 26 16 3 4 0 6 0 114 nuoJ NADH-ubiquinone/plastoquinone oxidoreductase, chainCaur_1981 6 || NADH dehydrogenase3 – constitutive (quinone)JCVI_PEP_metagenomic.orf.21303311.1 1113211797398 2 1 0 7 5 0 9 0 5 1 5 5 4 1 6 2 9 10 4 2 0 1 0 79 nuoK NADH-ubiquinone oxidoreductase, chain 4l || NADHCaur_1980 dehydrogenase (quinone)4 – constitutive JCVI_PEP_metagenomic.orf.21303443.1 1113211797398 0 2 2 1 1 0 0 0 1 0 1 2 0 0 1 0 3 2 0 1 1 2 0 20 nuoL proton-translocating NADH-quinone oxidoreductase,Caur_1979 chain L || NADH dehydrogenase0 – day (quinone)JCVI_PEP_metagenomic.orf.21303957.1 1113211797398 5 5 2 3 5 3 7 5 15 7 8 16 21 9 23 11 53 45 5 9 2 4 7 270 nuoM proton-translocating NADH-quinone oxidoreductase,Caur_1978 chain M || NADH 1dehydrogenase – night (quinone)JCVI_PEP_metagenomic.orf.21304313.1 1113211797398 11 3 6 6 2 14 1 1 4 8 8 6 12 1 2 5 28 18 13 4 3 4 4 164 nuoM proton-translocating NADH-quinone oxidoreductase,Caur_1977 chain m 4 – constitutive JCVI_PEP_metagenomic.orf.20969487.1 1113211801454 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 2 3 0 0 0 0 8 16 proton-translocating NADH-quinone oxidoreductase, chain M || NADH 3dehydrogenase – constitutive (quinone)JCVI_PEP_metagenomic.orf.21304535.1 1113211797398 0 1 1 13 2 0 2 2 1 0 5 4 1 2 0 0 6 8 0 4 1 1 0 54 nuoN proton-translocating NADH-quinone oxidoreductase,Caur_1976 chain n || NADH dehydrogenase2 – 4PM spike (quinone)JCVI_PEP_metagenomic.orf.20971456.1 1113211801454 0 2 0 0 0 0 0 0 0 0 1 3 0 0 3 2 6 2 0 0 1 0 0 20 nuoA NADH-ubiquinone/plastoquinone oxidoreductase chainCaur_2896 3 || NADH dehydrogenase0 – day (quinone)JCVI_PEP_metagenomic.orf.21206653.1 1113211797481 0 4 2 0 0 0 1 0 7 3 5 5 13 8 25 16 25 8 3 1 0 3 0 129 nuoB NADH-quinone oxidoreductase, B subunit || NADH dehydrogenaseCaur_2897 (quinone)5 – day JCVI_PEP_metagenomic.orf.21207403.1 1113211797481 0 0 0 0 0 0 0 1 0 4 3 9 5 1 12 4 11 16 0 1 0 0 0 67 nuoC NADH (or F420H2) dehydrogenase, subunit C || NADHCaur_2898 dehydrogenase3 (quinone)– constitutive JCVI_PEP_metagenomic.orf.21207783.1 1113211797481 3 2 13 11 1 0 0 1 0 2 0 9 19 3 11 1 39 16 2 0 2 1 0 136 nuoD NADH dehydrogenase (quinone), D subunit || NADHCaur_2899 dehydrogenase (quinone)0 – day JCVI_PEP_metagenomic.orf.21208160.1 1113211797481 0 2 0 0 0 0 1 1 6 3 8 17 19 8 8 20 26 18 5 4 3 1 0 150 nuoE NADH oxidoreductase (quinone), F subunit || NADH Caur_2900dehydrogenase (quinone)0 – day JCVI_PEP_metagenomic.orf.21209193.1 1113211797481 1 1 0 0 0 0 1 1 2 5 12 8 11 8 22 24 40 32 3 3 0 1 0 175 nuoF NADH dehydrogenase (quinone), G subunit || NADHCaur_2901 dehydrogenase 0 – day JCVI_PEP_metagenomic.orf.21210555.1 1113211797481 1 8 8 5 2 2 3 2 8 6 19 22 36 8 42 35 101 73 14 3 7 7 18 430 nuoG NADH dehydrogenase || NADH dehydrogenase (quinone)Caur_2902 2 – 4PM spike JCVI_PEP_metagenomic.orf.21211290.1 1113211797481 0 4 13 0 1 0 0 1 2 0 8 5 13 17 13 14 28 10 6 0 2 0 0 137 nuoH NADH-quinone oxidoreductase, chain i || NADH dehydrogenaseCaur_2904 (quinone)2 – 4PM spike JCVI_PEP_metagenomic.orf.21211410.1 1113211797481 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 6 1 1 0 0 0 0 0 11 nuoI NADH-ubiquinone/plastoquinone oxidoreductase chainCaur_2905 6 || NADH dehydrogenase2 – 4PM spike (quinone)JCVI_PEP_metagenomic.orf.21212647.1 1113211797481 0 0 1 0 0 0 0 0 0 0 0 4 2 2 3 3 15 5 0 2 0 0 0 37 nuoJ NADH-ubiquinone oxidoreductase, chain 4l || NADHCaur_2906 dehydrogenase (quinone)2 – 4PM spike JCVI_PEP_metagenomic.orf.21212888.1 1113211797481 0 1 0 0 1 0 0 0 0 0 9 4 1 3 1 4 5 5 0 0 1 1 0 36 nuoK proton-translocating NADH-quinone oxidoreductase,Caur_2907 chain L || NADH dehydrogenase2 – 4PM spike (quinone)JCVI_PEP_metagenomic.orf.21213493.1 1113211797481 0 0 0 0 0 0 2 0 0 0 4 0 5 2 11 8 7 11 1 1 0 2 0 54 nuoL proton-translocating NADH-quinone oxidoreductase,Caur_2908 chain M || NADH 5dehydrogenase – day (quinone)JCVI_PEP_metagenomic.orf.21214359.1 1113211797481 0 0 0 1 2 0 0 0 0 2 3 0 4 5 5 2 14 5 1 2 3 0 0 49 nuoM proton-translocating NADH-quinone oxidoreductase,Caur_2909 chain N || NADH dehydrogenase5 – day (quinone)JCVI_PEP_metagenomic.orf.21215921.1 1113211797481 0 0 0 0 0 0 1 0 0 1 1 1 4 1 5 0 8 3 4 0 1 0 0 30 actA (Cp) hypothetical protein Caur_0621 3 – constitutive JCVI_PEP_metagenomic.orf.20980827.1 1113211796557 6 6 11 10 14 10 4 8 5 4 12 27 33 5 14 6 18 22 7 4 4 3 6 239 actB (Cp) 4Fe-4S ferredoxin, iron-sulfur binding domain proteinCaur_0622 3 – constitutive JCVI_PEP_metagenomic.orf.20983345.1 1113211796557 5 0 2 0 5 1 0 1 11 5 2 8 9 3 4 1 1 4 0 1 3 0 0 66 hypothetical protein 3 – constitutive JCVI_PEP_metagenomic.orf.20983067.1 1113211796557 17 11 51 58 40 25 26 12 68 45 86 79 114 49 92 41 91 59 24 18 23 52 26 1107 actC (Cp) polysulphide reductase NrfD Caur_0623 3 – constitutive JCVI_PEP_metagenomic.orf.20983620.1 1113211796557 4 3 12 0 11 8 7 8 21 19 28 28 18 17 15 7 47 13 12 9 1 16 7 311 actE (Cp) hypothetical protein Caur_0625 3 – constitutive JCVI_PEP_metagenomic.orf.20985830.1 1113211796557 12 18 28 28 27 11 11 4 27 14 27 22 48 29 59 40 83 26 23 21 7 11 22 598 actF (Cp) hypothetical protein Caur_0626 0 – day JCVI_PEP_metagenomic.orf.20987765.1 1113211796557 5 12 28 63 18 18 22 11 28 18 54 36 63 36 61 54 82 44 16 11 8 20 12 720 actB (Cr) hypothetical protein Caur_2136 0 – day JCVI_PEP_metagenomic.orf.21317963.1 1113211797435 1 4 8 6 0 1 2 0 10 5 20 17 19 20 35 22 72 94 14 8 3 5 0 366 actE (Cr) hypothetical protein Caur_2137 2 – 4PM spike JCVI_PEP_metagenomic.orf.21318038.1 1113211797435 2 0 3 0 0 1 1 0 0 2 4 2 1 4 6 9 22 11 2 0 1 0 0 71 actA (Cr) hypothetical protein Caur_2138 3 – constitutive JCVI_PEP_metagenomic.orf.21318148.1 1113211797435 5 14 9 15 10 5 11 9 13 4 7 13 36 31 31 17 40 72 9 14 14 6 21 406 actG (Cr) hypothetical protein Caur_2139 4 – constitutive JCVI_PEP_metagenomic.orf.21318218.1 1113211797435 1 0 0 1 1 0 0 0 2 1 2 1 5 1 5 6 26 16 0 2 0 1 0 71 SC01/SenC e-transport? electron transport protein SCO1/SenC Caur_2140 0 – day JCVI_PEP_metagenomic.orf.21318409.1 1113211797435 0 6 0 0 4 0 6 0 4 0 8 16 19 11 20 21 28 26 12 2 2 1 12 198 auracyanin a Copper binding proteins, plastocyanin/azurin family Caur_3248 3 – constitutive JCVI_PEP_metagenomic.orf.21250072.1 1113211797160 1 3 6 2 4 3 4 0 9 8 5 12 12 6 26 5 21 8 10 2 7 0 0 154 auracyanin b Copper binding proteins, plastocyanin/azurin family Caur_1950 3 – constitutive JCVI_PEP_metagenomic.orf.21116124.1 1113211796012 0 4 8 2 0 4 2 2 8 2 12 8 8 1 4 6 19 10 1 0 1 3 3 108 COX II Cytochrome C and Quinol oxidase polypeptide I || Cytochrome-cCaur_2142 oxidase0 – day JCVI_PEP_metagenomic.orf.21318697.1 1113211797435 3 3 22 6 4 5 20 7 8 13 21 19 38 25 42 35 61 51 3 1 2 7 31 427 COX III Cytochrome c oxidase subunit III Caur_2143 0 – day JCVI_PEP_metagenomic.orf.21318773.1 1113211797435 10 5 12 9 2 4 1 6 15 4 10 7 24 13 18 43 47 36 10 2 2 7 1 288 oxidative stress glutathione peroxidase glutathione peroxidase || Glutathione peroxidase Caur_3684 2 – 4PM spike JCVI_PEP_metagenomic.orf.21439329.1 1113211796181 0 1 0 0 1 0 0 0 0 0 3 0 4 0 1 3 1 6 0 1 0 0 0 21 superoxide dismutase Caur_1176

CO dehydrogenase, molybdopterin-dependent coxSLM hypothetical protein Caur_3469 0 – day JCVI_PEP_metagenomic.orf.21410707.1 1113211796539 0 3 11 7 4 1 2 2 10 9 11 32 64 35 42 33 76 31 2 5 1 1 0 382 aldehyde oxidase and xanthine dehydrogenase molybdopterinCaur_3468 binding 0|| –Carbon-monoxide day JCVI_PEP_metagenomic.orf.21410856.1 dehydrogenase (acceptor) 1113211796539 1 3 6 6 3 10 9 4 15 26 94 95 138 64 134 102 215 136 22 10 13 3 15 1124 aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding0 || – Carbon-monoxide day JCVI_PEP_metagenomic.orf.21410881.1 dehydrogenase (acceptor) 1113211796539 0 0 7 1 1 0 3 0 5 13 21 67 99 36 71 64 130 68 4 2 4 4 7 607 molybdopterin dehydrogenase FAD-binding || Carbon-monoxideCaur_3467 dehydrogenase0 – day (acceptor)JCVI_PEP_metagenomic.orf.21410905.1 1113211796539 3 2 5 0 7 5 4 2 13 20 43 75 100 55 97 95 134 72 11 7 1 3 6 760

Cobalamin biosynthesis anaerobic cobalt chelatase (cbiK) cobalamin (vitamin B12) biosynthesis CbiX protein ||Caur_2572 Sirohydrochlorin ferrochelatase4 – constitutive JCVI_PEP_metagenomic.orf.21176861.1 1113211796056 0 7 3 0 5 0 0 2 0 4 6 5 14 4 7 5 18 8 2 1 0 3 0 94 aerobic cobalt chelatase subunit (cobT) nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferaseCaur_2578 3 – || constitutive Nicotinate-nucleotide-dimethylbenzimidazoleJCVI_PEP_metagenomic.orf.21172626.1 phosphoribosyltransferase1113211796056 4 2 17 2 10 8 3 2 13 6 8 20 19 6 14 12 25 16 11 4 5 10 7 224 aerobic cobalt chelatase subunit (cobN) cobaltochelatase, CobN subunit || CobaltochelataseCaur_2579 0 – day JCVI_PEP_metagenomic.orf.21168486.1 1113211796056 0 12 12 17 1 0 0 2 13 16 14 21 28 7 19 18 39 10 7 4 1 3 7 251 cob(I)yrinic acid a,c-diamide adenosyltransferase || Cob(I)yrinicCaur_2580 acid a,c-diamide3 – constitutive adenosyltransferaseJCVI_PEP_metagenomic.orf.21166754.1 1113211796056 2 0 1 6 0 2 0 0 2 0 5 7 2 5 10 5 3 1 0 2 0 0 0 53

Sulfur metabolism ATPsulfurylase: sulfate adenylylsulfate kinase/transferasesulfate (sulfate->APS) adenylyltransferase || Sulfate adenylyltransferaseCaur_2113 4 – constitutive JCVI_PEP_metagenomic.orf.21355091.1 1113211796660 0 0 4 0 0 1 0 0 0 0 0 0 4 0 0 1 0 0 0 0 0 0 0 10 sqr Pyridoxal-phosphate dependent enzyme || Cysteine Caur_3894synthase 2 – 4PM spike JCVI_PEP_metagenomic.orf.21441960.1 1113211796790 0 0 0 0 0 0 0 0 0 1 0 2 4 2 1 10 7 0 0 0 0 1 0 28