TABLE 1.
Classification of membrane-anchored actinobacterial 1CSs
| Group identifier | No. of proteins | Lengtha | Protein domain architectureb | Taxonomical spanc | Conserved genomic context |
|---|---|---|---|---|---|
| Kinases | |||||
| 1CS_1.1 | 633 | 560 ± 136 | TMHn-Pkinase | Widespread | None |
| Pkinase-TMHn | |||||
| TMHn-Pkinase-TMHn | |||||
| 1CS_1.2 | 163 | 640 ± 61 | Pkinase-TMH1–2-PASTA1–5 | At, B, Cf, F | Transpeptidase, FtsW |
| 1CS_1.3 | 15 | 735 ± 106 | Pkinase-NHL1–4 | At, Cf, Dt, F, Pr | None |
| 1CS_1.4 | 12 | 852 ± 82 | Pkinase-TMH-WD402–7 | At, Cf, Cy, Dt, Pl, V | None |
| 1CS_1.5 | 9 | 609 ± 32 | Pkinase-TMH_PknH_C | At | None |
| 1CS_1.6 | 8 | 761 ± 37 | Pkinase-TMH-PQQ_22 | At, Cf, Cy, Dt | None |
| 1CS_1.7 | 5 | 789 ± 13 | TMH2-PAP2-Pkinase-UPF0104 | At | None |
| 1CS_1.8 | 5 | 587 ± 83 | Pkinase-TMH-DUF4352 | At, Cf | None |
| 1CS_1.9 | 5 | 619 ± 26 | Pkinase-TMH-Lipoprotein_21 | At | None |
| 1CS_1.unclassified | 47 | NA | Various | NA | NA |
| Phosphatases | |||||
| 1CS_2.1 | 117 | 392 ± 44 | SpoIIE-TMH | Widespread | None |
| TMH-SpoIIE1–4/16 | |||||
| TMH-PP2C_2 | |||||
| 1CS_2.2 | 35 | 527 ± 153 | TMH2–8-HD | Widespread | None |
| TMH1–10-GGDEF-HD | |||||
| TMH-(7TMR-HDED)-7TM_7MR_HD-HD | |||||
| 1CS_2.3 | 7 | 609 ± 52 | (TMH)-CHASE-TMH-HAMP-SpoIIE1–2 | At, Cy | None |
| 1CS_2.4 | 5 | 680 ± 36 | MASE1-(PAS/GAF)-SpoIIE | At, Cy, Pt, Sp | None |
| 1CS_2.unclassified | 6 | NA | Various | NA | NA |
| Guanylate cyclases | |||||
| 1CS_3.1 | 192 | 419 ± 92 | TMH1–10-GGDEF | Widespread | None |
| 1CS_3.2 | 130 | 783 ± 131 | TMH1–10-GGDEF-EAL | Widespread | None |
| TMH2/5-GGDEF2-EAL | |||||
| TMH2-GGDEF-EAL-TMH | |||||
| TMH10-GGDEF-TMH9-GGDEF-EAL | |||||
| 1CS_3.3 | 118 | 548 ± 67 | TMH2–7-HAMP-Guanylate_cyc | Widespread | None |
| 1CS_3.4 | 43 | 931 ± 110 | TMH1–2/5–6/8–9-PAS1–2/4-GGDEF-EAL | Widespread | None |
| TMH5–7-GAF-GGDEF-EAL | |||||
| TMH5-GGDEF-EAL-GAF1–2 | |||||
| 1CS_3.5 | 9 | 757 ± 133 | MASE1-(PAS2–3)-(GAF)-GGDEF-(EAL) | Ac, At, Cy, F, Pr | None |
| 1CS_3.6 | 6 | 725 ± 27 | TMH1–3-HAMP-GAF-GGDEF | At, Cf, Cy, Dt, F, Nt, Pr | None |
| 1CS_3.7 | 6 | 641 ± 177 | TMH6–9-GAF/PAS1–3-GGDEF | Widespread | None |
| 1CS_3.8 | 6 | 543 ± 156 | TMH2–7/PTS_EIIC-(PAS)-EAL | Widespread | None |
| 1CS_3.9 | 5 | 1,362 ± 48 | TMH2-PAS-GGDEF-(TMH1–3)-(PAS)-GGDEF1–2 | At | Acyl-CoA dehydrogenase |
| 1CS_3.unclassified | 12 | NA | Various | NA | NA |
| DNA-binding proteins | |||||
| 1CS_4.1 | 188 | 469 ± 88 | TMH1–13-GerE | Widespread | None |
| TMH8-GerE-TMH12 | |||||
| 1CS_4.2 | 62 | 372 ± 409 | HTH1–2-TMH1–8 | Widespread | None |
| TMH1–4-HTH | |||||
| 1CS_4.3 | 34 | 232 ± 49 | TetR_N-TMH1–2-(TetR_C) | Widespread | None |
| TMH4-TetR_N | |||||
| 1CS_4.4 | 19 | 282 ± 22 | HTH_25-TMH-DUF4115 | Widespread | FtsK, 2-methylthioadenine synthetase, CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase |
| 1CS_4.5 | 7 | 371 ± 75 | HTH_31-TMH-DUF2690 | At | None |
| 1CS_4.6 | 6 | 279 ± 97 | DUF2637-HTH | At | None |
| 1CS_4.7 | 6 | 368 ± 55 | TMH-DUF4066-HTH_18 | Ac, At, B, Cf, Cy, Df, F, Gm, Pl, Pr, Sp, V | None |
| 1CS_4.unclassified | 35 | NA | Various | NA | NA |
| RNA-binding proteins | |||||
| 1CS_5.1 | 1 | 200 | TMH2-ANTAR | At, B, F, Fu, Nt, Pr, Sp, Sy, T | None |
Amino acids (mean ± standard deviation).
Protein domain designations as in the Pfam database. Note that when TMHs are not explicitly mentioned in the domain architecture, they are part of one of the assigned domains.
Ac, Acidobacteria; Aq, Aquificae; Ar, Armatimonadetes; At, Actinobacteria; B, Bacteroidetes; Ca, Caldiserica; Cf, Chloroflexi; Ch, Chlorobi; Cl, Chlamydiae; Cr, Chrysiogenetes; Cy, Cyanobacteria; Df, Deferribacteres; Dg, Dictyoglomi; Dt, Deinococcus-Thermus; E, Elusimicrobia; Fb, Fibrobacteres; Fu, Fusobacteria; Gm, Gemmatimonadetes; I, Ignaeribacteriae; L, Lentisphaerae; M, Marinimicrobia; Nn, Nitrospinae; Nt, Nitrospirales; Pl, Plantomycetes; Pr, Proteobacteria; Sp, Spirochaetes; Sy, Synergistetes; T, Tenericutes; Td, Thermodesulfobacteria; Tt, Thermotogae; V, Verrucomicrobia. NA, not applicable. In this context, “widespread” refers to 19 to 31 bacterial phyla.