TABLE 4.
Genomic diversity and abundance of chemoreceptor ligand binding domainsa
| Domain superfamilyb | LBD type | Domain model | No. of domains |
|---|---|---|---|
| 4HB_MCP | Single 4HB | 4HB_MCP_1 | 3,998 |
| TarH | 861 | ||
| CHASE3 | 392 | ||
| Double 4HB | HBM | 231 | |
| Cache-like | Double Cache | dCache_1 | 3,515 |
| Cache_3-Cache_2 | 307 | ||
| dCache_3 | 202 | ||
| dCache_2 | 183 | ||
| Ykul_C | 2 | ||
| Single Cache | sCache_2 | 1,165 | |
| sCache_3_2 | 60 | ||
| sCache_3_3 | 368 | ||
| Diacid_rec | 40 | ||
| CHASE4 | 19 | ||
| CHASE8 | 7 | ||
| PAS | PAS | PAS_3 | 1,930 |
| PAS_9 | 682 | ||
| PAS_4 | 459 | ||
| PAS_8 | 97 | ||
| PAS | 111 | ||
| PAS_7 | 8 | ||
| PAS_6 | 1 | ||
| PAS_10 | 1 | ||
| GAF | GAF | GAF | 463 |
| GAF_2 | 74 | ||
| Protoglobin | Protoglobin | Protoglobin | 552 |
| Globin | 8 | ||
| Bac_globin | 2 | ||
| PBP | Periplasmic binding protein | Phosphonate-bd | 30 |
| SBP_bac_5 | 29 | ||
| SBP_bac_3 | 23 | ||
| SBP_bac_8 | 7 | ||
| Peripla_BP_4 | 16 | ||
| Peripla_BP_5 | 2 | ||
| Peripla_BP_3 | 1 | ||
| Peripla_BP_6 | 1 | ||
| OpuAC | 5 | ||
| DctP | 2 | ||
| NMT1 | 2 | ||
| HNOX-like | Heme and NO binding | HNOB | 75 |
| 4Fe-4S | Iron-sulfur cluster binding | Fer4 | 14 |
| Fe4_10 | 20 | ||
| Fer4_7 | 6 | ||
| Fer4_9 | 4 | ||
| Fer4_6 | 1 | ||
| FeS | 33 | ||
| GPCR_A | GPCR-like | 7TMR-DISM_7TM | 16 |
| NADP_Rossman | NAD binding | GFO_IDH_MocA | 9 |
| Semialdhyde_dh | 1 | ||
| Gx_transp | Transporter | 5TM-5TMR_LYT | 9 |
| Beta_propeller | Extracellular binding | Reg_prop | 8 |
| GBD | Galactose binding | 7TMR-DISMED2 | 6 |
| CBM_4_9 | 2 | ||
| TPR | Protein-protein interactions | TPR_19 | 4 |
| ANAPC3 | 1 | ||
| Cupin | Nucleotide binding | cNMP_binding | 3 |
| HHH | Helix turn helix | HHH_5 | 2 |
| E-set | Sugar binding | Y_Y_Y | 2 |
| Phosphatase | Cyanide binding | Rhodanese | 2 |
| P-loop_NTPase | Nucleotide binding | ABC_tran | 1 |
| 2heme_cytochrom | Heme binding | Ni_hydr_CYTB | 1 |
| ATP-grasp | Glutathione binding | GSH-S_ATP | 1 |
| Flavodoxin | FMN/FAD binding | Falvodoxin_2 | 1 |
| No assigned superfamily | Zinc binding | CZB | 582 |
| PilJ | PilJ | 326 | |
| Nitrate and nitrite binding | NIT | 318 | |
| c-di-GMP binding | PilZ | 137 | |
| Oxygen binding | Hemerythrin | 98 | |
| PocR | 91 | ||
| Domain of unknown function | DUF3365 | 83 | |
| Amino acid binding | FIST | 62 | |
| Hydrogen binding | Fe_hyd_lg_C | 45 | |
| Integral membrane sensor | MHYT | 28 | |
| Adenosyl group binding | CBS | 21 | |
| Ammonium transporter | Ammonium_trans | 16 | |
| Ligand binding | PrpR_N | 9 | |
| Domain of unknown function | DUF4077 | 5 | |
| Integral membrane domain | MASE3 | 5 | |
| Quorum sensing | AI-2E_transport | 1 | |
| Nucleoside binding | Gate | 1 | |
| Phosphate/sugar binding | PTS_EIIC | 1 |
a
Data from Pfam 31.0 and the underlying UniProt reference proteome databases (178) as of March 2017. A total of 26,530 sequences were retrieved by using the MCPsignal domain model. A total of 17,907 LBDs matching Pfam domain models were identified. GPCR, G-protein-coupled receptor; GBD, galactose-binding domain.
b
Pfam clan.