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Conserved domains on  [gi|1308680812|gb|PKM50962|]
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hypothetical protein CVV01_00105, partial [Firmicutes bacterium HGW-Firmicutes-6]

Protein Classification

cache domain-containing protein( domain architecture ID 10499564)

cache domain-containing protein adopts a structure with one or two PAS-like subdomains, and may bind ligands

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
dCache_1 pfam02743
Cache domain; Double cache domain 1 covers the last three strands from the membrane distal ...
 44-286 2.61e-18

Cache domain; Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains. This domain when present in chemoreceptors recognize several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognizes C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).


:

Pssm-ID: 460673 [Multi-domain]  Cd Length: 237  Bit Score: 83.16  E-value: 2.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812  44 SITGLTEKQLETESNAAANEIAGVFSKYLEITRQMAVNsqfedmtteitPGFVPTAAQGFAKSEKSLSGVKASDPNIMEA 123
Cdd:pfam02743   2 AIKEQAEEQLLSLAKQLAENIESYLDSLEEILELLASN-----------PDLQDLLSAPAEEELAKLESLLRSNPGISSI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 124 WIGDSDSNQLLLSQGFYSSPDWIMVERPWYTQMMAAGGTT---LTAPYVDAMTNKMVVTAVSPIYRTGTKdIISAAGLDF 200
Cdd:pfam02743  71 YLVDADGRVLASSDESPSYPGLDVSERPWYKEALKGGGGIiwvFSSPYPSSESGEPVLTIARPIYDDDGE-VIGVLVADL 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 201 TLDSVSAMMSEYKLGETGSFILASADGQLIYHPNQEYVNTNIkDSDMSDNIKDAVLNQQTGAIEYTSDGSHNHGYVTMVG 280
Cdd:pfam02743 150 DLDTLQELLSQIKLGEGGYVFIVDSDGRILAHPLGKNLRSLL-APFLGKSLADALPGSGITEIAVDLDGEDYLVAYAPIP 228


                  ....*.
gi 1308680812 281 NTGWTI 286
Cdd:pfam02743 229 GTGWTL 234
 
Name Accession Description Interval E-value
dCache_1 pfam02743
Cache domain; Double cache domain 1 covers the last three strands from the membrane distal ...
 44-286 2.61e-18

Cache domain; Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains. This domain when present in chemoreceptors recognize several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognizes C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460673 [Multi-domain]  Cd Length: 237  Bit Score: 83.16  E-value: 2.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812  44 SITGLTEKQLETESNAAANEIAGVFSKYLEITRQMAVNsqfedmtteitPGFVPTAAQGFAKSEKSLSGVKASDPNIMEA 123
Cdd:pfam02743   2 AIKEQAEEQLLSLAKQLAENIESYLDSLEEILELLASN-----------PDLQDLLSAPAEEELAKLESLLRSNPGISSI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 124 WIGDSDSNQLLLSQGFYSSPDWIMVERPWYTQMMAAGGTT---LTAPYVDAMTNKMVVTAVSPIYRTGTKdIISAAGLDF 200
Cdd:pfam02743  71 YLVDADGRVLASSDESPSYPGLDVSERPWYKEALKGGGGIiwvFSSPYPSSESGEPVLTIARPIYDDDGE-VIGVLVADL 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 201 TLDSVSAMMSEYKLGETGSFILASADGQLIYHPNQEYVNTNIkDSDMSDNIKDAVLNQQTGAIEYTSDGSHNHGYVTMVG 280
Cdd:pfam02743 150 DLDTLQELLSQIKLGEGGYVFIVDSDGRILAHPLGKNLRSLL-APFLGKSLADALPGSGITEIAVDLDGEDYLVAYAPIP 228


                  ....*.
gi 1308680812 281 NTGWTI 286
Cdd:pfam02743 229 GTGWTL 234
PDC2_MCP_like cd12912
second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains; ...
 204-294 2.88e-16

second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains; Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the second PDC domain of Methyl-accepting chemotaxis proteins (MCPs), Histidine kinases (HKs), and other similar domains. Many members contain both HAMP (HK, Adenylyl cyclase, MCP, and Phosphatase) and MCP domains, which are signalling domains that interact with protein partners to relay a signal. MCPs are part of a transmembrane protein complex that controls bacterial chemotaxis. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses.


Pssm-ID: 350337 [Multi-domain]  Cd Length: 92  Bit Score: 73.19  E-value: 2.88e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 204 SVSAMMSEYKLGETGSFILASADGQLIYHPNQEYVNTNIKDSDMSDN-IKDAVLNQQTGAIEYTSDGSHNHGYVTMVGNT 282
Cdd:cd12912     1 ELSEIISSIKIGETGYAFLVDKDGTIIAHPDKELVGKKISDDEAAEEeLAKKMLAGKSGSVEYTFNGEKKYVAYAPIPGT 80

                          90
                  ....*....|..
gi 1308680812 283 GWTITTGLPDKE 294
Cdd:cd12912    81 GWSLVVVVPESE 92
HAMP COG2770
HAMP domain [Signal transduction mechanisms];
153-349 2.85e-04

HAMP domain [Signal transduction mechanisms];


Pssm-ID: 442051 [Multi-domain]  Cd Length: 631  Bit Score: 42.79  E-value: 2.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 153 YTQMMAAGGTTLTAPYVDAMTNKMVVTAVSPIYRTGTKDIISAAGLDFTLDSVSAMMSEYKLGETGSFILASADGQLIYH 232
Cdd:COG2770    66 LLALLLAAALLLLLLLLSLVALAALLLALLLLLLLALLLLLAALLLLLLLAALALLLLLLLLLAALLALLLALALLALLL 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 233 PNQEYVNTNIKDSDMSDNIKDAVLNQQTGAIEYTSDGSHNHGYVTMVGNTGWTITTGLPDKEFnspynLIQIITFIIMLI 312
Cdd:COG2770   146 GLAAARLLLAALLALAAALALALGAGELLLLADLAAAIAALLAALLLLLLGGLLLVVLLEAAL-----AALLLLLLLALL 220

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1308680812 313 VIAGMVLLTVFTSRKIAKPINMLAGVANKLAVGNVDV 349
Cdd:COG2770   221 ALLLALLLALLLARRITRPLRRLAEAARRIAAGDLDV 257
 
Name Accession Description Interval E-value
dCache_1 pfam02743
Cache domain; Double cache domain 1 covers the last three strands from the membrane distal ...
 44-286 2.61e-18

Cache domain; Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains. This domain when present in chemoreceptors recognize several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognizes C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460673 [Multi-domain]  Cd Length: 237  Bit Score: 83.16  E-value: 2.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812  44 SITGLTEKQLETESNAAANEIAGVFSKYLEITRQMAVNsqfedmtteitPGFVPTAAQGFAKSEKSLSGVKASDPNIMEA 123
Cdd:pfam02743   2 AIKEQAEEQLLSLAKQLAENIESYLDSLEEILELLASN-----------PDLQDLLSAPAEEELAKLESLLRSNPGISSI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 124 WIGDSDSNQLLLSQGFYSSPDWIMVERPWYTQMMAAGGTT---LTAPYVDAMTNKMVVTAVSPIYRTGTKdIISAAGLDF 200
Cdd:pfam02743  71 YLVDADGRVLASSDESPSYPGLDVSERPWYKEALKGGGGIiwvFSSPYPSSESGEPVLTIARPIYDDDGE-VIGVLVADL 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 201 TLDSVSAMMSEYKLGETGSFILASADGQLIYHPNQEYVNTNIkDSDMSDNIKDAVLNQQTGAIEYTSDGSHNHGYVTMVG 280
Cdd:pfam02743 150 DLDTLQELLSQIKLGEGGYVFIVDSDGRILAHPLGKNLRSLL-APFLGKSLADALPGSGITEIAVDLDGEDYLVAYAPIP 228


                  ....*.
gi 1308680812 281 NTGWTI 286
Cdd:pfam02743 229 GTGWTL 234
PDC2_MCP_like cd12912
second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains; ...
 204-294 2.88e-16

second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains; Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the second PDC domain of Methyl-accepting chemotaxis proteins (MCPs), Histidine kinases (HKs), and other similar domains. Many members contain both HAMP (HK, Adenylyl cyclase, MCP, and Phosphatase) and MCP domains, which are signalling domains that interact with protein partners to relay a signal. MCPs are part of a transmembrane protein complex that controls bacterial chemotaxis. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses.


Pssm-ID: 350337 [Multi-domain]  Cd Length: 92  Bit Score: 73.19  E-value: 2.88e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 204 SVSAMMSEYKLGETGSFILASADGQLIYHPNQEYVNTNIKDSDMSDN-IKDAVLNQQTGAIEYTSDGSHNHGYVTMVGNT 282
Cdd:cd12912     1 ELSEIISSIKIGETGYAFLVDKDGTIIAHPDKELVGKKISDDEAAEEeLAKKMLAGKSGSVEYTFNGEKKYVAYAPIPGT 80

                          90
                  ....*....|..
gi 1308680812 283 GWTITTGLPDKE 294
Cdd:cd12912    81 GWSLVVVVPESE 92
PDC2_HK_sensor cd18774
second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins, ...
 206-291 3.50e-13

second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins, diguanylate-cyclase and similar domains; Histidine kinase (HK) receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. HK receptors in this family contain double PDC (PhoQ/DcuS/CitA) sensor domains. Signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. The HK family includes not just histidine kinase receptors but also sensors for chemotaxis proteins and diguanylate cyclase receptors, implying a combinatorial molecular evolution.


Pssm-ID: 350342 [Multi-domain]  Cd Length: 89  Bit Score: 64.77  E-value: 3.50e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 206 SAMMSEYKLGETGSFILASADGQLIYHPNQEYVNTNIKDSDMSDNIKdAVLNQQTGAIEYTS-DGSHNHGYVTMVGNTGW 284
Cdd:cd18774     3 SDLLSSIKLGETGYAFLVDSDGTILAHPPKELVGKGKSLDDLALLAA-LLLAGESGTFEYTSdDGVERLVAYRPVPGTPW 81


                  ....*..
gi 1308680812 285 TITTGLP 291
Cdd:cd18774    82 VVVVGVP 88
PDC1_MCP_like cd12913
first PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains; ...
 67-202 4.32e-10

first PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains; Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the first PDC domain of Methyl-accepting chemotaxis proteins (MCPs), Histidine kinases (HKs), and other similar domains. Many members contain both HAMP (HK, Adenylyl cyclase, MCP, and Phosphatase) and MCP domains, which are signalling domains that interact with protein partners to relay a signal. MCPs are part of a transmembrane protein complex that controls bacterial chemotaxis. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses.


Pssm-ID: 350338  Cd Length: 139  Bit Score: 57.15  E-value: 4.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812  67 VFSKYLEITRQMAVNSQFEDMTTEITPGFVPTAAQGFAKSEKSLSGV---------KASDPNIMEAWIGDSDSNQLLLSQ 137
Cdd:cd12913     1 FLEEAESIAEQLASTLESLVSSGSLDRELLENLLKQVLESNPDILGVyvafepnafSDETGRFAPYWYRDDGGIIDLDEP 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1308680812 138 GFYSSPdwimvERPWYTQMMAAGGTTLTAPYVDAM-TNKMVVTAVSPIYRTGTkdIISAAGLDFTL 202
Cdd:cd12913    81 PDYDYR-----TRDWYKLAKETGKPVWTEPYIDEVgTGVLMITISVPIYDNGK--FIGVVGVDISL 139
PDC1_HK_sensor cd18773
first PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins, diguanylate-cyclase ...
 110-186 3.73e-08

first PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins, diguanylate-cyclase and similar domains; Histidine kinase (HK) receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. HK receptors in this family contain double PDC (PhoQ/DcuS/CitA) sensor domains. Signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. The HK family includes not just histidine kinase receptors but also sensors for chemotaxis proteins and diguanylate cyclase receptors, implying a combinatorial molecular evolution.


Pssm-ID: 350341 [Multi-domain]  Cd Length: 125  Bit Score: 51.41  E-value: 3.73e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1308680812 110 LSGVKASDPNIMEAWIGDSDSNQLLLSQGFYSSPDWIM-VERPWYTQMMAAGGTTLTAPYVDAMTNKMVVTAVSPIYR 186
Cdd:cd18773    33 LRRLLERNPEISGIYVVDADGRVVASSDRDPGGGDDDDdRDRFWYQAAKATGKLVISEPYISRVTGKPVITLSRPIRD 110
HAMP COG2770
HAMP domain [Signal transduction mechanisms];
153-349 2.85e-04

HAMP domain [Signal transduction mechanisms];


Pssm-ID: 442051 [Multi-domain]  Cd Length: 631  Bit Score: 42.79  E-value: 2.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 153 YTQMMAAGGTTLTAPYVDAMTNKMVVTAVSPIYRTGTKDIISAAGLDFTLDSVSAMMSEYKLGETGSFILASADGQLIYH 232
Cdd:COG2770    66 LLALLLAAALLLLLLLLSLVALAALLLALLLLLLLALLLLLAALLLLLLLAALALLLLLLLLLAALLALLLALALLALLL 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308680812 233 PNQEYVNTNIKDSDMSDNIKDAVLNQQTGAIEYTSDGSHNHGYVTMVGNTGWTITTGLPDKEFnspynLIQIITFIIMLI 312
Cdd:COG2770   146 GLAAARLLLAALLALAAALALALGAGELLLLADLAAAIAALLAALLLLLLGGLLLVVLLEAAL-----AALLLLLLLALL 220

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1308680812 313 VIAGMVLLTVFTSRKIAKPINMLAGVANKLAVGNVDV 349
Cdd:COG2770   221 ALLLALLLALLLARRITRPLRRLAEAARRIAAGDLDV 257
Pro_Al_protease pfam02983
Alpha-lytic protease prodomain;
158-199 4.28e-03

Alpha-lytic protease prodomain;


Pssm-ID: 460772  Cd Length: 55  Bit Score: 34.97  E-value: 4.28e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1308680812 158 AAGGTTLTAPYVDAMTNKMVVTAVSPIyRTGTKDIISAAGLD 199
Cdd:pfam02983  14 ARAPAAVTAWYVDVRTNKVVVTADSGV-SAAAAALVAAAGVD 54
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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