TABLE 2.
Domain-based classification of actinobacterial HKs
| Group identifier | No. of proteins | Lengtha | Protein domain architectureb | Taxonomical spanc | Predicted sensing | Notesd |
|---|---|---|---|---|---|---|
| HK_01 | 42 | 547 ± 36 | TMH-CHASE3-TMH-HAMP-HisKA-HATPase_c | At, Pr, Cy, B, Dt, F, Pl, V, Df | Extracytoplasmic | CHASE-CHASE6 sensor-like |
| GenCon: in operon with RRs | ||||||
| HK_02 | 68 | 547 ± 32 | TMH-(PAS)-TMH-PAS-HATPase_c | Pr, F, At, Sy, Sp, Df | Extracytoplasmic | CitA/DcuS-like |
| GenCon: RR-HK-transporter | ||||||
| HK_03 | 730 | 507 ± 106 | TMH-[50–300 aa]-TMH-HAMP-HisKA-HATPase_c | ND | Extracytoplasmic | Prototypical sensors |
| HK_04 | 30 | 409 ± 24 | TMH-[60 aa]-TMH-HAMP-HisKA-HATPase_c | ND | Extracytoplasmic | NarX/Q-like |
| HK_05 | 68 | 382 ± 26 | TMH-[30–40 aa]-TMH-HAMP-HisKA-HATPase_c | ND | Extracytoplasmic | PrmB-like |
| HK_06 | 26 | 374 ± 28 | TMH-[25–30 aa]-TMH-HAMP-HisKA-HATPase_c | ND | Extracytoplasmic | VanS-like |
| HK_07 | 384 | 461 ± 108 | TMH-HAMP-HisKA-HATPase_c | ND | Membrane? | |
| HK_08 | 244 | 419 ± 60 | TMH3-(HAMP)-HisKA-HATPase_c | ND | Membrane? | |
| HK_09 | 5 | 404 ± 117 | TMH0–5-HisKA-GerE | F, At, Ap, Pr | Membrane? | Overrepresented in Firmicutes |
| HK_10 | 35 | 724 ± 141 | TMH2–6-(HisKA)-HATPase-TMH1–6 | At | Membrane | |
| HK_11 | 71 | 435 ± 33 | PspC-TMH4–6-HATPase_c | At | Membrane | GenCon: downstream of pspC |
| HK_12 | 26 | 722 ± 234 | TMH9-HisKA-HATPase_c | ND | Membrane | |
| HK_13 | 6 | 735 ± 70 | TMH2–5-HisKA_3-(HATPAse_c)-TMH3–5-HisKA-HATPase_c | ND | Membrane? | Restricted to Actinomycetales |
| HK_14 | 11 | 541 ± 52 | TMH4-HisKA-HATPase_c-TMH | ND | Membrane | Restricted to Actinomycetales |
| HK_15 | 4 | 701 ± 138 | TMH2-HAMP-HisKA-HATPase_c-TMH11–14 | ND | Extracytoplasmic or membrane | |
| HK_16 | 139 | 421 ± 108 | TMH-[5–25 aa]-TMH-(HAMP)-HisKA-HATPase_c | ND | Membrane | LiaS-like |
| HK_17 | 937 | 416 ± 43 | TMH4/5-HisKA-HATPase_c-(TMH) | ND | Membrane | DesK-like |
| HK_18 | 162 | 441 ± 59 | TMH6/7-HATPase_c | ND | Membrane | ComD/ArgC fit descriptor |
| HK_19 | 1 | 664 | TMH-7TMR_DISM_7TM-HisKA-HATPase_c | F, Pr, Sp, B, At | Membrane | |
| HK_20 | 5 | 841 ± 204 | TMH11/12-HisKA-HATPase_c-(TMH) | ND | Membrane | PutP-like |
| HK_21 | 41 | 606 ± 74 | TMH8/10-HisKA-HATPase_c | ND | Membrane | ComP-like |
| HK_22 | 2 | 680 ± 3 | TMH8/10-PAS-HisKA-HATPase_c | ND | Membrane | Restricted to Propinibacterineae |
| HK_23 | 2 | 795 ± 177 | MASE1-(PAS3)-HisKA-HATPase | At | Membrane/cytoplasm | |
| HK_24 | 11 | 567 ± 58 | TMH3–10-GAF-HisKA-HATPase_c | ND | Membrane/cytoplasm | |
| HK_25 | 2 | 721 ± 6 | TMH2/3-PAS-GAF-HisKA-HATPase_c | ND | Membrane/cytoplasm | Restricted to Mycobacterium |
| HK_26 | 12 | 881 ± 67 | TMH2-PAS-GAF-SpoIIE-HATPase_c | ND | Membrane/cytoplasm | Restricted to Streptomyces |
| HK_27 | 71 | 858 ± 30 | KdpD-Usp-TMH3-HisKA-HATPase_c | Pr, At, F, B, T | Cytoplasm | KdpD-like GenCon: part of kdp operon |
| HK_28 | 40 | 415 ± 73 | PAS-(HisKA)-HATPase_c | ND | Cytoplasm | NtrB-like |
| HK_29 | 9 | 554 ± 106 | PAS2/3-(HisKA)-HATPase_c | ND | Cytoplasm | KinA-like |
| HK_30 | 3 | 798 ± 32 | PAS-GAF-PHY-HisKA-HATPase_c | Pr, Cy, B, At, Pl, V | Cytoplasm | |
| HK_31 | 100 | 499 ± 12 | H_kinase_N-PAS-HisKA-HATPase_c | At, F | Cytoplasm | |
| HK_32 | 5 | 1598 ± 5 | Pkinase-AAA_16-(TRP_2/GAF_2)-HisKA-HATPase_c | F, At, Cy | Cytoplasm | |
| HK_33 | 30 | 485 ± 11 | cNMP_binding-HATPase_c | At, Pr, Cy, Ad, B, V, Cf, Dt, F, Nt, Ar | Cytoplasm | GenCon: near thioredoxin reductase |
| HK_34 | 104 | 386 ± 103 | HisKA-HATPase_c | At, F, Pr, B, Sp, Cy, Cf, V | Cytoplasm | |
| HK_35 | 806 | 186 ± 103 | HATPase | F, At, Pr, Cf, Sp, Cy | Cytoplasm | |
| HK_36 | 7 | 217 ± 95 | HisKA | At, F, Pr, Sp, B, Cy, Cf | Cytoplasm | |
| HK_37 | 5 | 249 ± 9 | STAS-HATPase_c | At, Pr, F, Sp, B, Tt, Cf | Cytoplasm | Overrepresented in actinobacteria GenCon: downstream of extracellular solute-binding protein and HK |
| HATPAse-STAS | ||||||
| HK_38 | 170 | 514 ± 86 | GAF1/2-HisKA-HATPase_c | At, F, Pr, Cf, Cy, Dt, Sp | Cytoplasm | |
| HK_39 | 10 | 643 ± 88 | PAS-GAF1/2-(PAS)-HisKA-HATPase_c | At, Pr, Cf, Cy, V, F, Dt | Cytoplasm | |
| HK_40 | 170 | 790 ± 141 | PAS1/2-(GAF1/2)-SpoIIE-HATPase_c | At, F | Cytoplasm | |
| HK_41 | 26 | 815 ± 97 | HATPase_c-(PAS)-GAF1/2-SpoIIE | At, V, Pr | Cytoplasm | Overrepresented in actinobacteria |
| HK_42 | 29 | 486 ± 175 | HATPase_c-SpoIIE | Pr, At, Dt, Cy, F, Ad, Pl, V, B | Cytoplasm | GenCon: part of operon of regulators of sigma B activity |
| HK_43 | 24 | 622 ± 146 | SpoIIE-HATPase_c | At, Pr, F, B, Pl, Sp | Cytoplasm | Overrepresented in actinobacteria |
| HK_44 | 12 | 600 ± 74 | TMH-PAS-HisKA-HATPase | ND | Cytoplasm | |
| HK_45 | 11 | 389 ± 84 | (HAMP)-HisKA-HATPase | ND | Cytoplasm | |
| HK_46 | 167 | 979 ± 191 | TMH-NIT-HAMP-HATPase | At | Cytoplasm | GenCon: part of operon encoding proteins of unknown function |
| HK_47 | 4 | 292 ± 53 | HATPase_c-HTH | At | Cytoplasm | |
| HK_48 | 12 | 692 ± 134 | (PAS/PAS-GAF-PAS)-SpoIIE-HATPase_c-STAS_2 | At | Cytoplasm | |
| HK_49 | 3 | 739 ± 3 | RsbU_N-PAS-SpoIIE-HATPase_c | At | Cytoplasm | GenCon: downstream of 4 anti-anti-sigma regulatory factors |
| HK_50 | 34 | 325 ± 29 | MEDS-HATPase_c | At | Cytoplasm | |
| HK_00 | 12 | TMH2-CHASE3-TMH-HAMP-GAF-PAS-HisKA-HATPase_c | Unique architectures | |||
| HK_CA-GAF-PAS-HisKA-HATPase_c | ||||||
| GAF-PAS2-HisKA-HATPase_c | ||||||
| HAMP-PAS-HisKA-HATPase_c | ||||||
| MASE1-SpoIIE-HATPase_c | ||||||
| HATPase_c-RRXRR-HNH | ||||||
| HATPase-DUF3883 | ||||||
| HATPase_c-PCMT | ||||||
| HATPase-DUF4325 | ||||||
| DNA_ligase_A_M-DNA_ligase_A_C-His_kinase | ||||||
| SSF-HisKA-HATPase_c | ||||||
| ABC_trans-HisKA-HATPase_c |
a
Amino acids (mean ± standard deviation).
b
Protein domain designations as in the Pfam database. aa, amino acids.
c
Ad, Acidobacteria; Ar, Armatimonadetes; At, Actinobacteria; B, Bacteriodetes; Cf, Chloroflexi; Cy, Cyanobacteria; Df, Deferribacteres; Dt, Deinococcus-Thermus; F, Firmicutes; Nt, Nitrospirae; Pl, Plantomyces; Pr, Proteobacteria; Sp, Spirochetes; Sy, Synergistales; T, Tenericutes; Tt, Thermotogae; V, Verrucomicrobia; ND, not determined.
d
GenCon, genomic context conservation.