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Conserved domains on  [gi|327200479|pdb|2Y0T|B]
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Chain B, AF1503

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; ...
 4-49 1.46e-09

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: 47.05  E-value: 1.46e-09
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
2Y0T_B       4 TRPIIELSNTFDKIAEGNLEAEVPHqNRADEIGILAKSIERLRRSL 49
Cdd:cd06225  1 TRPLRRLTEAARRIAEGDLDVRVPV-RSKDEIGELARAFNQMAERL 45
 
Name Accession Description Interval E-value
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; ...
 4-49 1.46e-09

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: 47.05  E-value: 1.46e-09
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
2Y0T_B       4 TRPIIELSNTFDKIAEGNLEAEVPHqNRADEIGILAKSIERLRRSL 49
Cdd:cd06225  1 TRPLRRLTEAARRIAEGDLDVRVPV-RSKDEIGELARAFNQMAERL 45
HAMP pfam00672
HAMP domain;
2-50 2.05e-07

HAMP domain;


Pssm-ID: 459898 [Multi-domain]  Cd Length: 53  Bit Score: 41.84  E-value: 2.05e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
2Y0T_B         2 TITRPIIELSNTFDKIAEGNLEAEVPHqNRADEIGILAKSIERLRRSLK 50
Cdd:pfam00672  5 RILRPLRRLAEAARRIASGDLDVRLPV-SGRDEIGELARAFNQMAERLR 52
HAMP smart00304
HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;
2-54 5.17e-07

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


Pssm-ID: 197640 [Multi-domain]  Cd Length: 53  Bit Score: 41.08  E-value: 5.17e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
2Y0T_B          2 TITRPIIELSNTFDKIAEGNLEAEVPHQNRaDEIGILAKSIERLRRSLKVAME 54
Cdd:smart00304  2 RLLRPLRRLAEAAQRIADGDLTVRLPVDGR-DEIGELARAFNEMADRLEETIA 53
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 3-54 1.38e-06

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: 42.64  E-value: 1.38e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
2Y0T_B        3 ITRPIIELSNTFDKIAEGNLEAEVPhQNRADEIGILAKSIERLRRSLKVAME 54
Cdd:COG5000  33 LTRPLRRLAEATRAVAAGDLSVRLP-VTGDDEIGELARAFNRMTDQLKEQRE 83
 
Name Accession Description Interval E-value
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; ...
 4-49 1.46e-09

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: 47.05  E-value: 1.46e-09
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
2Y0T_B       4 TRPIIELSNTFDKIAEGNLEAEVPHqNRADEIGILAKSIERLRRSL 49
Cdd:cd06225  1 TRPLRRLTEAARRIAEGDLDVRVPV-RSKDEIGELARAFNQMAERL 45
HAMP pfam00672
HAMP domain;
2-50 2.05e-07

HAMP domain;


Pssm-ID: 459898 [Multi-domain]  Cd Length: 53  Bit Score: 41.84  E-value: 2.05e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
2Y0T_B         2 TITRPIIELSNTFDKIAEGNLEAEVPHqNRADEIGILAKSIERLRRSLK 50
Cdd:pfam00672  5 RILRPLRRLAEAARRIASGDLDVRLPV-SGRDEIGELARAFNQMAERLR 52
HAMP smart00304
HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;
2-54 5.17e-07

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


Pssm-ID: 197640 [Multi-domain]  Cd Length: 53  Bit Score: 41.08  E-value: 5.17e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
2Y0T_B          2 TITRPIIELSNTFDKIAEGNLEAEVPHQNRaDEIGILAKSIERLRRSLKVAME 54
Cdd:smart00304  2 RLLRPLRRLAEAAQRIADGDLTVRLPVDGR-DEIGELARAFNEMADRLEETIA 53
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 3-54 1.38e-06

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: 42.64  E-value: 1.38e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
2Y0T_B        3 ITRPIIELSNTFDKIAEGNLEAEVPhQNRADEIGILAKSIERLRRSLKVAME 54
Cdd:COG5000  33 LTRPLRRLAEATRAVAAGDLSVRLP-VTGDDEIGELARAFNRMTDQLKEQRE 83
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
3-50 5.98e-05

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


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 38.08  E-value: 5.98e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
2Y0T_B        3 ITRPIIELSNTFDKIAEGNLEAEVPHQNRaDEIGILAKSIERLRRSLK 50
Cdd:COG0840 206 ITRPLRELLEVLERIAEGDLTVRIDVDSK-DEIGQLADAFNRMIENLR 252
HAMP COG2770
HAMP domain [Signal transduction mechanisms];
2-54 1.43e-03

HAMP domain [Signal transduction mechanisms];


Pssm-ID: 442051 [Multi-domain]  Cd Length: 631  Bit Score: 34.32  E-value: 1.43e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
2Y0T_B        2 TITRPIIELSNTFDKIAEGNLEAEVPhQNRADEIGILAKSIERLRRSLKVAME 54
Cdd:COG2770 235 RITRPLRRLAEAARRIAAGDLDVRIP-VSRKDEIGELARAFNRMADSLRESIE 286
 
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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