| Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.n1) | Fphi_1459 | B0TYT8 | 1 |
| Cytokinin riboside 5'-monophosphate phosphoribohydrolase (EC 3.2.2.n1) | FTN_1229 | A0Q795 | 1 |
| Cytoplasmic membrane protein | lemA spr1163 | Q8DPH4 | 1 |
| Cytosine deaminase | codA PA0437 | Q9I680 | 1 |
| Cytosine deaminase (EC 3.5.4.1) | VSAK1_17107 | A6CUY2 | 1 |
| Cytosine-specific methyltransferase (EC 2.1.1.37) | SPCG_1339 | B2IQG7 | 1 |
| Cytosine-specific methyltransferase (EC 2.1.1.37) | SP70585_1071 | C1C707 | 1 |
| Cytosol aminopeptidase | pepB FTN_0780 | A0Q606 | 1 |
| Cytosol non-specific dipeptidase (EC 3.4.13.18) (Aminoacyl-histidine dipeptidase) (Beta-alanyl-histidine dipeptidase) (Carnosinase) (Cysteinylglycinase) (Peptidase D) (Xaa-His dipeptidase) (X-His dipeptidase) | pepD pepH b0237 JW0227 | P15288 | 1 |
| Cytotoxicity-associated immunodominant antigen (120 kDa protein) | cagA cai | P80200 | 1 |
| Cytotoxicity-associated immunodominant antigen (120 kDa protein) (CAG pathogenicity island protein 26) | cagA cag26 cai jhp_0495 | Q9ZLT1 | 1 |
| D-3-phosphoglycerate dehydrogenase | Fphi_1431 | B0TYI0 | 1 |
| D-3-phosphoglycerate dehydrogenase | B195_00135 | M5QQG7 | 1 |
| D-3-phosphoglycerate dehydrogenase (PGDH) (EC 1.1.1.95) (2-oxoglutarate reductase) (EC 1.1.1.399) | serA BSU23070 | P35136 | 1 |
| D-3-phosphoglycerate dehydrogenase (PGDH) (EC 1.1.1.95) (2-oxoglutarate reductase) (EC 1.1.1.399) | serA Rv2996c MTV012.10 | P9WNX3 | 1 |
| D-3-phosphoglycerate dehydrogenase / alpha-ketoglutarate reductase (EC 1.1.1.95) (EC 1.1.99.2) | serA PP_5155 | Q88CM5 | 1 |
| D-alanine aminotransferase (EC 2.6.1.21) | SAOUHSC_01867 | Q2FXI0 | 1 |
| D-alanine--D-alanine ligase (EC 6.3.2.4) (D-Ala-D-Ala ligase) (D-alanylalanine synthetase) | ddl FTN_0161 | A0Q4A6 | 1 |
| D-alanine--D-alanine ligase (EC 6.3.2.4) (D-Ala-D-Ala ligase) (D-alanylalanine synthetase) | ddl ddlA SPy_1421 M5005_Spy1158 | Q99Z34 | 1 |
| D-alanine--D-alanine ligase B (EC 6.3.2.4) (D-Ala-D-Ala ligase B) (D-alanylalanine synthetase B) | ddlB PA4410 | Q9LCT6 | 1 |
| D-alanine--poly(phosphoribitol) ligase subunit 1 (EC 6.1.1.13) (D-alanine-D-alanyl carrier protein ligase) (DCL) (D-alanine-activating enzyme) (DAE) | dltA SPy_1312 M5005_Spy1073 | Q99ZA6 | 1 |
| D-alanine--poly(phosphoribitol) ligase subunit 2 (EC 6.1.1.13) (D-alanyl carrier protein) (DCP) | dltC SPy_1310 M5005_Spy1071 | P63959 | 1 |
| D-alanine--poly(Phosphoribitol) ligase, subunit 1 (EC 6.1.1.13) (Peptide synthetase-like protein) | dltA BTH_I2418 DR63_3356 | Q2SVW0 | 1 |
| D-alanyl-D-alanine carboxypeptidase | dacB PP_2098 | Q88L37 | 1 |
| D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | dacA spr0776 | Q8DQ99 | 1 |
| D-alanyl-D-alanine carboxypeptidase (Penicillin binding protein) family protein (EC 3.4.16.4) | dacD FTT_1029 | Q5NG28 | 1 |
| D-alanyl-D-alanine carboxypeptidase (Penicillin binding protein) family protein (EC 3.4.16.4) | dacB1 FTT_1039 | Q5NG20 | 1 |
| D-alanyl-D-alanine carboxypeptidase (Putative sporulation-specific penicillin-binding protein) (EC 3.4.16.4) | dacF1 CD630_24980 | Q182I4 | 1 |
| D-alanyl-D-alanine carboxypeptidase dacA (EC 3.4.16.4) | dacA HPSD74_1374 | U4SHN6 | 1 |
| D-alanyl-D-alanine carboxypeptidase DacF (DD-carboxypeptidase) (DD-peptidase) (EC 3.4.16.4) (Penicillin-binding protein DacF) (PBP) | dacF BSU23480 | P38422 | 1 |
| D-alanyl-D-alanine carboxypeptidase family protein | AC1_2465 | B1R359 | 1 |
| D-alanyl-D-alanine carboxypeptidase penicillin-binding protein 6a | dacC SCH_0857 | Q57R98 | 1 |
| D-alanyl-D-alanine carboxypeptidase, penicillin-binding protein 5 | dacA SCH_0666 | Q57RT9 | 1 |
| D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase | B195_07190 | M5QMJ3 | 1 |
| D-alanyl-D-alanine dipeptidase (D-Ala-D-Ala dipeptidase) (EC 3.4.13.22) | pdgL ddpX STM1599 | H9L442 | 1 |
| D-amino acid dehydrogenase (EC 1.4.99.-) | dadA B195_00590 | M5R1A7 | 1 |
| D-LACTATE DEHYDROGENASE | dld jhp_1143 | Q9ZK04 | 1 |
| D-lactate dehydrogenase | VSAK1_17237 | A6CV08 | 1 |
| D-lactate dehydrogenase (EC 1.1.1.28) | NMBB_1621 | E3D641 | 1 |
| D-lactate dehydrogenase (EC 1.1.1.28) | dld NMB0997 | Q9JZL7 | 1 |
| D-lactate dehydrogenase (EC 1.1.1.28) | hslI YPO2329 | Q0WEJ2 | 1 |
| D-lactate dehydrogenase (EC 1.1.1.28) | NGK_0915 | B4RLA5 | 1 |
| D-lactate dehydrogenase (EC 1.1.1.28) | HPSD74_1847 | U4SCR4 | 1 |
| D-lactate dehydrogenase, putative (EC 1.1.1.28) | SAOUHSC_02875 | Q2FV62 | 1 |
| D-methionine binding transport protein, ABC transporter, membrane and periplasmic protein | metIQ FTT_1125 | Q5NFU4 | 1 |
| D-methionine transport system permease | LMRG_02588 | A0A0H3G902 | 1 |
| D-methionine-binding lipoprotein MetQ | metQ STM0245 | Q8ZRN1 | 1 |
| D-methionine-binding lipoprotein MetQ | metQ YPO1071 y3106 YP_2778 | Q8ZH40 | 1 |
| D-proline reductase proprotein prdA (EC 1.21.4.1) | prdA CD630_32440 | Q17ZY9 | 1 |
| D-proline reductase subunit gamma (EC 1.21.4.1) (Proline reductase) | prdB_1 prdB_2 CDFC105_63473 IM33_17710 SAMEA3374973_02406 SAMEA3374989_01450 SAMEA3375004_02699 | A0A0D6FQX8 | 1 |
| D-proline reductase subunit gamma (EC 1.21.4.1) (Proline reductase) | prdB_1 prdB_2 BN1095_540013 BN1096_740070 BN1097_500026 IM33_17715 SAMEA3374973_02405 SAMEA3374989_01451 SAMEA3375004_02698 SAMEA3375059_02268 | A0A031WLJ6 | 1 |
| D-ribose pyranase (EC 5.4.99.62) | rbsD BSU35930 | P36946 | 1 |
| D-ribose-binding periplasmic domain protein (Fragment) | HPSD74_1712 | U4SCR7 | 1 |
| D-serine transporter DsdX | dsdX orf445 yfdA yfdD b2365 JW2362 | P08555 | 1 |
| D-tagatose-1,6-bisphosphate aldolase subunit GatY (TBPA) (TagBP aldolase) (EC 4.1.2.40) (D-tagatose-bisphosphate aldolase class II) (Tagatose-bisphosphate aldolase) | gatY yegF b2096 JW5343 | P0C8J6 | 1 |
| D-tagatose-1,6-bisphosphate aldolase subunit GatZ | gatZ b2095 JW2082 | P0C8J8 | 1 |
| D12 class N6 adenine-specific DNA methyltransferase | VSAK1_09108 | A6D7G6 | 1 |
| DamX-related protein | VC_A0573 | Q9KM16 | 1 |
| DcrH | dcrH | Q46583 | 1 |
| dCTP deaminase (EC 3.5.4.13) (Deoxycytidine triphosphate deaminase) | dcd B195_11116 | M5QYA7 | 1 |
| dCTP deaminase (EC 3.5.4.13) (Deoxycytidine triphosphate deaminase) | dcd Rv0321 MTCY63.26 | P9WP17 | 1 |
| DEAD-box ATP-dependent RNA helicase CshA (EC 3.6.4.13) | cshA MW2004 | Q7A0D2 | 1 |
| DEAD-box ATP-dependent RNA helicase CshA (EC 3.6.4.13) | cshA SAOUHSC_02316 | Q2FWH5 | 1 |
| DEAD-box ATP-dependent RNA helicase CshA (EC 3.6.4.13) | cshA LMRG_02289 | A0A0H3GAJ1 | 1 |
| DEAD-box ATP-dependent RNA helicase CshA (EC 3.6.4.13) (Exported protein 9) | cshA exp9 spr1440 | P0A4D8 | 1 |
| DEAD-box ATP-dependent RNA helicase CshB (EC 3.6.4.13) | rheB cshB spr0670 | Q8DQH1 | 1 |
| DEAD-box ATP-dependent RNA helicase CshB (EC 3.6.4.13) | cshB SPy_1659 | Q99YK3 | 1 |
| DEAD-box ATP-dependent RNA helicase CshB (EC 3.6.4.13) | cshB SAOUHSC_01659 | Q2FY15 | 1 |
| DEAD-box ATP-dependent RNA helicase CshB (EC 3.6.4.13) | cshB LMRG_00902 | A0A0H3GGC0 | 1 |
| DedA family protein | MXAN_0324 | Q1DFH4 | 1 |
| DedA family protein | dedA1 FTT_1223 | Q5NFL1 | 1 |
| Deferrochelatase/peroxidase EfeB (EC 1.11.1.-) | efeB YPO1856 y2450 YP_1537 | Q7CI09 | 1 |
| Degenerate transposase | SPCG_1219 | B2IQ47 | 1 |
| Degenerate transposase | SPCG_1859 | B2ISY4 | 1 |
| Degenerate transposase (Fusion of orf1 and orf2) | spr1721 | Q8CWP0 | 1 |
| Degenerate transposase (Orf1) | spr0019 | Q8DRP4 | 1 |
| Degenerate transposase (Orf1) | spr0029 | Q8DRN8 | 1 |
| Degenerate transposase (Orf1) | spr0886 | Q8DQ22 | 1 |
| Degenerate transposase (Orf2) | spr0017 | Q8DRP6 | 1 |
| Degenerate transposase (Orf2) | spr0986 | Q8DPV7 | 1 |
| Degenerate transposase (Orf2) | spr1008 spr1676 | Q8CM31 | 1 |
| Degenerate transposase (Orf2) | spr1702 | Q8DNI3 | 1 |
| DegV domain-containing protein spr0652 | spr0652 | Q8DQI6 | 1 |
| DegV domain-containing protein SPy_0865/M5005_Spy0672 | SPy_0865 M5005_Spy0672 | Q9A0A6 | 1 |
| DegV domain-containing protein SPy_1493/M5005_Spy1226 | SPy_1493 M5005_Spy1226 | P67372 | 1 |
| DegV domain-containing protein SPy_1698/M5005_Spy1391 | SPy_1698 M5005_Spy1391 | Q99YH7 | 1 |
| DegV domain-containing protein SPy_1936/M5005_Spy1650 | SPy_1936 M5005_Spy1650 | P67374 | 1 |
| DegV family protein | CPC_0331 | B1BJW1 | 1 |
| DegV family protein | CJD_3151 | B1UZY2 | 1 |
| DegV family protein | CPC_0025 | B1BHY9 | 1 |
| Dehydrogenase | FTN_0964 | A0Q6I7 | 1 |
| Deleted. | 0 | A3M886 | 1 |
| Deleted. | 0 | A3M505 | 1 |
| Deleted. | 0 | A3M9X2 | 1 |
| Deleted. | 0 | A3M9D7 | 1 |
| Deleted. | 0 | A3M908 | 1 |
| Deleted. | 0 | A3M879 | 1 |
| Deleted. | 0 | A3M9X3 | 1 |
| Deleted. | 0 | A3M885 | 1 |
| Deleted. | 0 | A3M884 | 1 |