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Conserved domains on  [gi|1675067057|ref|WP_138586917|]
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HAMP domain-containing protein, partial [Pseudoalteromonas piscicida]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tar super family cl43297
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
1-104 5.03e-12

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG0840:

Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 60.42  E-value: 5.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675067057   1 DTIDAAFSELRWLMIIDVVVIIIILAVLSSVISNSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYT 80
Cdd:COG0840   171 ALALAAAALALALLAAALLALVALAIILALLLSRSITRPLRELLEVLERIAEG--DLTVRIDVDSKDEIGQLADAFNRMI 248

                          90       100
                  ....*....|....*....|....
gi 1675067057  81 EKMRHSIAQVSENTRHVEQFANQV 104
Cdd:COG0840   249 ENLRELVGQVRESAEQVASASEEL 272
 
Name Accession Description Interval E-value
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
1-104 5.03e-12

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 60.42  E-value: 5.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675067057   1 DTIDAAFSELRWLMIIDVVVIIIILAVLSSVISNSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYT 80
Cdd:COG0840   171 ALALAAAALALALLAAALLALVALAIILALLLSRSITRPLRELLEVLERIAEG--DLTVRIDVDSKDEIGQLADAFNRMI 248

                          90       100
                  ....*....|....*....|....
gi 1675067057  81 EKMRHSIAQVSENTRHVEQFANQV 104
Cdd:COG0840   249 ENLRELVGQVRESAEQVASASEEL 272
HAMP smart00304
HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;
34-88 1.05e-07

HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;


Pssm-ID: 197640 [Multi-domain]  Cd Length: 53  Bit Score: 44.55  E-value: 1.05e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1675067057   34 NSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYTEKMRHSIA 88
Cdd:smart00304   1 RRLLRPLRRLAEAAQRIADG--DLTVRLPVDGRDEIGELARAFNEMADRLEETIA 53
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; ...
 37-87 2.15e-07

Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381743 [Multi-domain]  Cd Length: 45  Bit Score: 43.59  E-value: 2.15e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1675067057  37 LHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNsyteKMRHSI 87
Cdd:cd06225     1 TRPLRRLTEAARRIAEG--DLDVRVPVRSKDEIGELARAFN----QMAERL 45
HAMP pfam00672
HAMP domain;
31-85 2.56e-07

HAMP domain;


Pssm-ID: 459898 [Multi-domain]  Cd Length: 53  Bit Score: 43.77  E-value: 2.56e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1675067057  31 VISNSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYTEKMRH 85
Cdd:pfam00672   1 LLARRILRPLRRLAEAARRIASG--DLDVRLPVSGRDEIGELARAFNQMAERLRE 53
 
Name Accession Description Interval E-value
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
1-104 5.03e-12

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 60.42  E-value: 5.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675067057   1 DTIDAAFSELRWLMIIDVVVIIIILAVLSSVISNSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYT 80
Cdd:COG0840   171 ALALAAAALALALLAAALLALVALAIILALLLSRSITRPLRELLEVLERIAEG--DLTVRIDVDSKDEIGQLADAFNRMI 248

                          90       100
                  ....*....|....*....|....
gi 1675067057  81 EKMRHSIAQVSENTRHVEQFANQV 104
Cdd:COG0840   249 ENLRELVGQVRESAEQVASASEEL 272
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 27-99 2.89e-08

Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms];


Pssm-ID: 444024 [Multi-domain]  Cd Length: 422  Bit Score: 49.58  E-value: 2.89e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1675067057  27 VLSSVISNSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYTEKMRHSIAQVSENTRHVEQ 99
Cdd:COG5000    24 WLALLLARRLTRPLRRLAEATRAVAAG--DLSVRLPVTGDDEIGELARAFNRMTDQLKEQREELEERRRYLET 94
HAMP smart00304
HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;
34-88 1.05e-07

HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;


Pssm-ID: 197640 [Multi-domain]  Cd Length: 53  Bit Score: 44.55  E-value: 1.05e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1675067057   34 NSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYTEKMRHSIA 88
Cdd:smart00304   1 RRLLRPLRRLAEAAQRIADG--DLTVRLPVDGRDEIGELARAFNEMADRLEETIA 53
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; ...
 37-87 2.15e-07

Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381743 [Multi-domain]  Cd Length: 45  Bit Score: 43.59  E-value: 2.15e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1675067057  37 LHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNsyteKMRHSI 87
Cdd:cd06225     1 TRPLRRLTEAARRIAEG--DLDVRVPVRSKDEIGELARAFN----QMAERL 45
HAMP pfam00672
HAMP domain;
31-85 2.56e-07

HAMP domain;


Pssm-ID: 459898 [Multi-domain]  Cd Length: 53  Bit Score: 43.77  E-value: 2.56e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1675067057  31 VISNSVLHPIRLAADMMKDISQGqgDLTQQLDEHGNDEISRLSRYFNSYTEKMRH 85
Cdd:pfam00672   1 LLARRILRPLRRLAEAARRIASG--DLDVRLPVSGRDEIGELARAFNQMAERLRE 53
YesM COG2972
Sensor histidine kinase YesM [Signal transduction mechanisms];
1-92 2.50e-05

Sensor histidine kinase YesM [Signal transduction mechanisms];


Pssm-ID: 442211 [Multi-domain]  Cd Length: 445  Bit Score: 41.16  E-value: 2.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1675067057   1 DTIDAAFSELRWLMIIDVVVIIIILAVLSSVISNSVLHPIRLAADMMKDISQGQGdltQQLDEHGNDEISRLSRYFNSYT 80
Cdd:COG2972   146 SELFRGLFSLRRLILLIILLLLLLALLLSYLLSRSITRPIKRLKKAMKKVEKGDL---VRLEVSGNDEIGILARSFNEMV 222

                          90
                  ....*....|..
gi 1675067057  81 EKMRHSIAQVSE 92
Cdd:COG2972   223 ERIKELIEEVYE 234
 
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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