Table 1.
Diversity of sensory domains found in association with GGDEF, EAL, and/or HD-GYP domains.a
| Domain nameb | Pfam ID | COGc | PDB ID | PSSM, aad | Domain name origin | GGDEF only | EAL only | GGDEF + EAL | HD-GYP | GGDEF + HD-GYP | Ligands | Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Extracellular (periplasmic) domains | ||||||||||||
| 4HB_MCP_1 | PF12729 | – | 5XUA | 181 | Four-helix bundle of methyl-carrier proteins | + | + | + | + | + | Citrate, fumarate, succinate, pyrene | Hong et al. (2019) |
| 7TMR-DISMED2 | PF07696 | – | 3JYB | 127 | 7TM Receptors with diverse intracellular signaling modules, extracellular domain 2 | + | + | + | – | – | Ca2+, carbohydrates | Jing et al. (2010) |
| 7TMR-HDED | PF07697 | COG1480 | – | 219 | 7TM-HD extracellular domain | – | – | – | + | – | – | |
| ABC_sub_bind | PF04392 | COG2984 | 6HNI | 293 | ABC transporter substrate binding protein | + | – | + | + | – | Tyr? | Bradshaw et al. (2019) |
| Cache3/Cache2 | PF17201 | – | – | 298 | Calcium channels and chemotaxis receptors fused domains 3 and 2 | + | – | + | – | – | – | |
| CBM_2 | PF00553 | – | 2CWR | 101 | Carbohydrate binding module | – | – | – | + | – | Chitin | Nakamura et al. (2008) |
| CBM_4_9 | PF02018 | – | 1GUI | 134 | – same – | + | – | – | – | – | Cellulose, xylan | Boraston et al. (2002) |
| CHASE | PF03924 | COG3614 | 3T4J | 184 | Cyclases/histidine kinases associated sensory extracellular domain | + | + | + | + | – | Cytokinin | Hothorn et al. (2011) |
| CHASE2 | PF05226 | COG4252 | – | 264 | – same – | + | + | + | + | – | – | |
| CHASE3 | PF05227 | COG5278 | 3VA9 | 138 | – same – | + | – | + | – | – | Pyrene | Zhang et al. (unpublished data) |
| CHASE4 | PF05228 | COG3322 | – | 139 | – same – | + | – | + | + | + | – | |
| CHASE5 | PF17149 | – | – | 108 | – same – | + | – | + | – | – | Arg? | |
| CHASE7 | PF17151 | – | – | 187 | – same – | + | – | – | – | – | Taurocholate | |
| CHASE8 | PF17152 | – | – | 102 | – same – | + | + | + | – | – | – | |
| CHASE9 | PF17153 | – | – | 116 | – same – | – | + | – | – | – | – | |
| CSS-motif | PF12792 | COG4943 | – | 209 | Conserved Cys-Ser-Ser motif | – | + | – | – | – | DsbA, DsbB | |
| DAHL | PF19443 | – | – | 221 | Double all-helical ligand-binding | + | + | + | – | – | Asp, Arg, Ile, fucose, galactose, mannose | |
| dCache | Double CACHE (Calcium channel and chemotaxis receptor) domain | Dicarboxylates | ||||||||||
| dCache_1 | PF02743 | – | 3LID | 238 | – same – | + | + | + | + | + | Amino acids, pH, diamines, purines, betaine, succinate | Zhang and Hendrickson (2010) |
| dCache_2 | PF08269 | – | 5G4Z | 297 | – same – | + | – | + | – | + | C2 and C3 carboxylates | Brewster et al. (2016) |
| dCache_3 | PF14827 | – | 5IS1 | 235 | – same – | + | + | + | + | – | – | Kim et al. (2016) |
| DICTe | PF10069 | COG4250 | – | 126 | Diguanylate cyclases and two-component systems | + | + | + | + | – | Light? | |
| DUF3365 | PF11845 | – | 5B82 | 167 | Domain of unknown function | + | – | + | – | + | c-type heme, redox | Motomura et al. (2017) |
| GAPES1 | PF17155 | – | – | 274 | Gammaproteobacterial periplasmic sensor domain | + | – | – | – | – | Autoinducer-2 (AI-2) | |
| GAPES2 | PF17156 | – | – | 204 | – same – | + | – | – | – | – | – | |
| GAPES3 | PF17154 | – | – | 121 | – same – | + | + | + | – | – | – | |
| GAPES4 | PF17157 | – | – | 98 | – same – | + | – | + | – | – | – | |
| LapD_MoxY_N | PF16448 | – | 3PJV_D | 124 | N-terminal periplasmic domain of LapD and MoxY | + | + | + | – | – | LapG protein, methanol | Navarro et al. (2011) |
| LuxQ-periplasm | PF09308 | COG1879 | 3C30 | 239 | Periplasmic domain of LuxQ | – | – | + | – | – | LuxP protein | Slama and Hendrickson (unpublished data) |
| PBP1_AmiC (Peripla_BP_5) | PF13433 | COG0683 | 1PEA | 363 | Periplasmic binding protein AmiC-type | + | – | + | – | – | Acetamide, other amides | Pearl et al. (1994) |
| PBP1_ABC_LivBP (Peripla_BP_6) | PF13458 | COG0683 | 1Z15 | 342 | Periplasmic binding protein LivBP-type | + | – | + | – | – | Leu, Ile, Val | Trakhanov et al. (2005) |
| Peripla_BP_3 | PF13377 | COG1609 | 1JYE | 160 | Periplasmic binding protein-like domain | + | + | + | + | – | Ribose, galactose, glucose 6-phosphate | Bell et al. (2001) |
| Peripla_BP_4 | PF13407 | COG4203 | 3UUG | 259 | – same – | + | – | – | – | – | Fructose, galactose | Hu et al. (2013) |
| Phosphonate-bd | PF12974 | COG3221 | 5LQ5 | 243 | Phosphonate-binding | + | – | + | + | + | Phosphates, phosphonates | Bisson et al. (2017) |
| PilJ/NarX | PF13675 | COG3850 | 6GCV | 112 | Nitrate-binding domain of McpN | + | – | + | – | – | Nitrate, nitrite | Martín-Mora et al. (2019) |
| PBPb (SBP_bac_3) | PF00497 | COG0834 | 2LAO | 221 | Bacterial extracellular solute-binding proteins, family 3 | + | + | + | + | + | Amino acids | Oh et al. (1993) |
| sCache | Single CACHE (Calcium channel and chemotaxis receptor) domain | |||||||||||
| sCache_2 | PF17200 | COG4564 | 3UB6 | 153 | – same – | + | – | + | + | + | Urea, propionate, malate, pyruvate | Goers et al. (2012) |
| sCache_3_2 | PF17203 | – | – | 140 | – same – | – | – | + | – | – | Citrate, malate | |
| sCache_3_3 | PF17202 | – | – | 107 | – same – | + | – | + | + | – | – | |
| sCache_4 | PF09984 | – | 5O7J | 146 | – same – | + | – | + | – | – | – | Ali-Ahmad et al. (2017) |
| TarH | PF02203 | – | 2LIG | 152 | Ligand-binding domain of the bacterial aspartate receptor | + | – | + | – | – | Asp, Glu, Ser, citrate, 4-hydroxybenzoate | Milburn et al. (1991) |
| Integral membrane domains | ||||||||||||
| 5TM-5TMR_LYT | PF07694 | COG3275 | – | 170 | 5TM Receptors of the LytS-YhcK type, 5 TM | + | – | + | + | + | Pyruvate | |
| 7TM-7TMR_HD | PF07698 | – | – | 190 | 7TM Receptor with intracellular HD hydrolase | – | – | – | + | – | – | |
| 7TMR-DISM_7TM | PF07695 | – | – | 207 | 7TM Receptors with diverse intracellular signaling modules, 7 TM domain | + | + | + | + | – | – | |
| AA_permease (SLC12) | PF00324 | COG0531 | – | 415 | Amino acid permease, 9TM | – | – | + | – | – | Amino acids | |
| AA_permease_2 | PF13520 | COG0531 | 5J4I | 427 | Amino acid permease, 12 TM | + | – | + | + | + | Amino acids | Ilgü et al. (2016) |
| Ammonium_transp | PF00909 | COG0004 | 6EU6 | 399 | Ammonium channel transporter Amt, 9–11 TM | + | – | + | – | – | NH4+ | Pflüger et al. (2018) |
| DUF4084 | PF13321 | – | – | 304 | Domain of unknown function, 9–10 TM | + | – | + | – | – | – | |
| DUF4118 | PF13493 | COG2205 | 2KSF | 107 | Transmembrane domain of KdpD, 4 TM | + | + | + | – | – | – | Maslennikov et al. (2010) |
| HisKA_7TM | PF16927 | – | – | 221 | N-terminal 7TM region of histidine kinase, 7TM | + | + | + | + | + | Autoinducer-1 (AI-1) | |
| MASE1 | PF05231 | – | – | 299 | Membrane-associated sensor domain, 5 TM | + | + | + | – | – | – | |
| MASE2 | PF05230 | – | – | 89 | – same –, 6 TM | + | – | + | – | – | – | |
| MASE3 | PF17159 | – | – | 226 | – same –, 5 TM | + | + | + | + | – | – | |
| MASE4 | PF17158 | – | – | 239 | – same –, 8 TM | + | – | + | – | – | – | |
| MASE5 | PF17178 | – | – | 192 | – same –, 6 TM | + | – | – | – | – | – | |
| MHYT | PF03707 | COG3300 | – | 54 (x3) | Met-His-Tyr-Thr motif, 6 TM | + | + | + | – | – | NO, nitrate | |
| PTS_EIIC | PF02378 | COG1455 | – | 315 | Phosphotransferase system, EIIC domain, 9–10 TM | – | + | – | – | – | – | |
| Intracellular (cytoplasmic) domains | ||||||||||||
| BLUFe | PF04940 | – | 2BYC | 89 | Blue light using FAD | – | + | + | – | – | FAD | Jung et al. (2005) |
| CBSe | PF00571 | COG0517 | 2RC3 | 57 (x2) | Regulatory domain in cystathionine-beta synthase | + | + | + | + | + | Adenine derivatives | Dong et al. (unpublished data) |
| C_GCAxxG_C_C | PF09719 | – | 1H21 | 115 | Putative redox-active protein with a CGAxxG motif | – | – | + | – | – | c-type heme | Abreu et al. (2003) |
| cNMP_binding | PF00027 | COG0664 | 2ZCW | 89 | Cyclic nucleotide-binding domain | + | + | + | + | – | Cyclic NMPs | Agari et al. (2008) |
| CZBe | PF13682 | – | – | 64 | Chemoreceptor zinc-binding domain | + | + | + | – | – | Zinc | |
| Diacid_rec | PF05651 | COG3835 | – | 131 | Sugar diacid recognition domain | + | – | + | – | – | Sugar acids | |
| DUF484 | PF04340 | – | 3E98 | 219 | Domain of unknown function | + | – | – | – | – | – | JCSG (unpublished data) |
| DUF1631 | PF07793 | – | – | 742 | – same – | + | + | + | – | – | – | |
| DUF1883 | PF08980 | – | 2B1Y | 86 | – same – | + | – | – | – | – | – | Nocek et al. (unpublished data) |
| DUF2892 | PF11127 | – | – | 66 | – same – | + | – | + | + | – | – | |
| DUF3330e | PF11809 | – | – | 69 | – same – | – | + | – | – | – | – | |
| DUF3369 | PF11849 | COG3437 | – | 168 | – same – | + | + | + | + | – | – | |
| DUF3391 | PF11871 | COG2206 | – | 136 | – same – | – | – | – | + | – | – | |
| FHA | PF00498 | COG1716 | 1G6G | 66 | Forkhead-associated domain | + | + | + | + | – | pThr, pTyr | Durocher et al. (2000) |
| FIST/NosP | PF08495 | COG3287 | – | 129 | F-box and intracellular signal transduction | + | + | + | + | + | NO | |
| FIST_C/NosP | PF10442 | COG3287 | – | 135 | – same – | + | + | + | + | + | NO | |
| GAF | PF01590 | COG2203 | 5VIV | 133 | Common domain in cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA | + | + | + | + | + | Biliverdin, cGMP, phycocyanobilin (+O2, CO, NO) | Baloban et al. (2017) |
| GAF_2 | PF13185 | COG1956 | 4MN7 | 137 | – same – | + | + | + | + | + | O2, CO, NO | Kim et al. (2014) |
| GAF_3 | PF13492 | COG2203 | 3EEA | 129 | – same – | + | + | + | + | + | – | Zhang et al. (unpublished data) |
| HDODe | PF08668 | COG1639 | 3M1T | 196 | HD-related output domain | + | + | + | + | – | – | JCSG (unpublished data) |
| Hemerythrin | PF01814 | COG2703 | 4XPX | 128 | Hemerythrin HHE cation binding domain | + | + | + | + | – | O2 | Chen et al. (2015) |
| HNOBA | PF07701 | – | – | 215 | Heme NO binding associated domain | + | – | + | – | – | Oxygen, NO | |
| Laminin_G_3e | PF13385 | – | 4DQA | 151 | Laminin globular domain | + | + | + | – | – | Arabinan, O-glycans | JCSG (unpublished data) |
| MEDS | PF14417 | – | – | 160 | Methanogen/methylotroph, DcmR sensory domain | + | + | + | + | – | Dichloromethane | |
| NIT | PF08376 | – | 4AKK | 228 | Nitrate- and nitrite sensing domain | + | – | + | – | – | Nitrate, nitrite | Boudes et al. (2012) |
| NMT1 | PF09084 | COG0715 | 2X26 | 216 | NMT1/THI5 protein domain | + | – | + | – | – | Alkanesulfonate | Beale et al. (2010) |
| PAS | PF00989 | COG2202 | 1KOU | 113 | Common domain in Period circadian protein (Per), Ah receptor nuclear translocator protein (ARNT), and Single-minded protein (Sim). | + | + | + | + | + | FAD, FMN, heme, 4-hydroxycinnamic acid (+O2, CO, NO) | van Aalten et al. (2002) |
| PAS_2 | PF08446 | COG4251 | 6G20 | 107 | – same – | + | – | + | – | – | – | Schmidt et al. (2018) |
| PAS_3 | PF08447 | – | 5SY7 | 89 | – same – | + | + | + | + | + | – | Wu et al. (2016) |
| PAS_4 | PF08448 | – | – | 110 | – same – | + | + | + | + | + | Aromatic compounds | |
| PAS_7 | PF12860 | – | – | 115 | – same – | + | + | + | – | – | – | |
| PAS_8 | PF13188 | – | – | 65 | – same – | + | + | + | + | + | O2, CO, NO | |
| PAS_9/LOV | PF13426 | – | – | 102 | – same – | + | + | + | + | + | Light, O2, voltage | |
| PHYe | PF00360 | COG4251 | 2VEA | 178 | Phytochrome region | + | – | + | – | – | Red light | Essen et al. (2008) |
| PilZ | PF07238 | – | 2L74 | 102 | Type IV pili biosynthesis protein | + | + | + | + | – | c-di-GMP | Habazettl et al. (2011) |
| PocR | PF10114 | – | – | 155 | Ligand binding domain of transcriptional regulator PocR | + | + | + | + | + | 1,2-propanediol | |
| Protoglobin | PF11563 | – | 4ZVA | 149 | Globin sensor domain | + | + | + | + | – | O2, CO, NO | Tarnawski et al. (2015) |
| RsbRD_N | PF14361 | – | – | 104 | N-terminal domain of the stressosome component RsbRD | + | – | + | – | – | – | |
| SnoaL_3 | PF13474 | COG4319 | 3CNX | 121 | SnoaL-fold domain 3 | + | – | + | + | – | – | JCSG (unpublished data) |
| T2SSE_N/MshEN | PF05157 | – | 5HTL | 108 | Type II secretion system protein E, N-terminal domain | + | – | – | + | – | c-di-GMP | Wang et al. (2016) |
| TackOD1 | PF18551 | – | – | 188 | Thaumarchaeal output domain 1 | + | – | – | – | – | – | |
| TPR_1 | PF00515 | COG0457 | 2KC7 | 34 | Tetratricopeptide repeat | – | Eletsky et al. (unpublished data) | |||||
| TPR_2 | PF07719 | COG0457 | 4XI0 | – same – | + | – | – | – | – | – | Zeytuni et al. (2015) | |
| TPR_4 | PF07721 | – | – | – same – | + | – | – | – | – | – | ||
| TPR_7 | PF13176 | – | – | – same – | + | + | + | – | – | – | ||
| TPR_8 | PF13181 | – | – | 33 | – same – | + | + | + | + | – | – | |
| TPR_10 | PF13374 | – | – | – same – | + | – | + | – | – | – | ||
| TPR_12 | PF13424 | – | 3ESK | 77 | – same – | + | + | + | + | + | – | Kajander et al. (2009) |
| TPR_16 | PF13432 | – | – | 68 | – same – | + | – | + | – | – | – | |
| TPR_MalT | PF17874 | – | – | MalT-like TPR region | + | – | + | – | + | – | ||
| V4R | PF02830 | COG1719 | 2OSD | 62 | Vinyl 4 reductase | + | – | + | – | – | Hydrocarbons | JCSG (unpublished data) |
| YceI | PF04264 | COG2353 | 3HPE | 118 | YceI-like domain | – | – | + | – | – | Isoprenoids, fatty acids | Sisinni et al. (2010) |
| YkuI_Ce | PF10388 | – | 2BAS | 166 | C-terminal domain of YkuI | – | + | – | – | – | – | Minasov et al. (2009) |
| Y_Y_Y | PF07495 | – | 4A2M | 65 | Tyr-x-Tyr-x-Tyr sequence motif | + | – | + | + | – | Heparin? | Lowe et al. (2012) |
| Total number | 94 | 52 | 88 | 48 | 25 | |||||||
a
The table indicates presence (+) or absence (–) of the respective domain combination in the Pfam database as of 12-12-2022. Domain combinations found in a single protein in UniProt were ignored. For domain counts, additional ligands, and references, see Table S1 (Supporting Information). Additional references for some of these domains can be found in the recent review by Matilla et al. (2022). Some domain combinations in the EAL-only column are listed as absent despite being annotated as such in UniProt because all the respective entries contain a diverged GGDEF domains.
b
Domain names in Pfam (alternative names are in parentheses). The respective entries can be retrieved from InterPro using the https://www.ebi.ac.uk/interpro/entry/pfam/PFxxxxx/format, e.g. https://www.ebi.ac.uk/interpro/entry/pfam/PF12729/for 4HB_MCP_1
c
COG database (https://www.ncbi.nlm.nih.gov/research/cog/) entries that include this domain. A dash in this and other columns indicates the absence of data.
d
Length (in amino acid residues) of the domain sequence model in the CDD database (https://www.ncbi.nlm.nih.gov/cdd).
e
This domain is usually found at the C-termini of the respective CMEs.