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Conserved domains on  [gi|553680586|gb|ESD97266|]
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Helix-turn-helix domain of resolvase [Escherichia coli 908616]

Protein Classification

recombinase family protein( domain architecture ID 230867)

recombinase family protein is a serine recombinase that catalyzes the site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme

CATH:  3.40.50.1390
Gene Ontology:  GO:0000150|GO:0003677|GO:0006310
PubMed:  21645851
SCOP:  3000065

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SpoIVCA super family cl34383
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-108 2.35e-18

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1961:

Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 78.53  E-value: 2.35e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680586   1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEGRQEAKLKGIKFG---------RRRTV 71
Cdd:COG1961   87 LLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGrppygyrdpKKLVI 166

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 553680586  72 DRNV------VLTLHQKGTGATEIAHQL------SIARSTVYKILEDER 108
Cdd:COG1961  167 DEEEaevvrrIFELYLEGKSLREIARELnergipTWSRSTVYRILKNPV 215
 
Name Accession Description Interval E-value
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-108 2.35e-18

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 78.53  E-value: 2.35e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680586   1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEGRQEAKLKGIKFG---------RRRTV 71
Cdd:COG1961   87 LLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGrppygyrdpKKLVI 166

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 553680586  72 DRNV------VLTLHQKGTGATEIAHQL------SIARSTVYKILEDER 108
Cdd:COG1961  167 DEEEaevvrrIFELYLEGKSLREIARELnergipTWSRSTVYRILKNPV 215
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 1-62 2.66e-16

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 69.22  E-value: 2.66e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 553680586    1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEGRQEAKLKG 62
Cdd:pfam00239  81 LLTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARG 142
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 1-54 5.22e-15

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 65.58  E-value: 5.22e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 553680586   1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEG 54
Cdd:cd03768   73 LLEIVEELREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 1-64 1.83e-12

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 59.56  E-value: 1.83e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 553680586     1 MIQLIKEFDAQGVAVRFIDDGISTDGD-MGQMVVTILSAVAQAERRRILERTNEGRQEAKLKGIK 64
Cdd:smart00857  84 LLALLELLEEKGVRLVSLKEGILDTSTpAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
 
Name Accession Description Interval E-value
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-108 2.35e-18

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 78.53  E-value: 2.35e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680586   1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEGRQEAKLKGIKFG---------RRRTV 71
Cdd:COG1961   87 LLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGrppygyrdpKKLVI 166

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 553680586  72 DRNV------VLTLHQKGTGATEIAHQL------SIARSTVYKILEDER 108
Cdd:COG1961  167 DEEEaevvrrIFELYLEGKSLREIARELnergipTWSRSTVYRILKNPV 215
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 1-62 2.66e-16

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 69.22  E-value: 2.66e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 553680586    1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEGRQEAKLKG 62
Cdd:pfam00239  81 LLTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARG 142
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 1-54 5.22e-15

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 65.58  E-value: 5.22e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 553680586   1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEG 54
Cdd:cd03768   73 LLEIVEELREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 1-64 1.83e-12

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 59.56  E-value: 1.83e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 553680586     1 MIQLIKEFDAQGVAVRFIDDGISTDGD-MGQMVVTILSAVAQAERRRILERTNEGRQEAKLKGIK 64
Cdd:smart00857  84 LLALLELLEEKGVRLVSLKEGILDTSTpAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 1-54 7.27e-09

Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium.


Pssm-ID: 238206 [Multi-domain]  Cd Length: 137  Bit Score: 49.95  E-value: 7.27e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 553680586   1 MIQLIKEFDAQGVAVRFIDDGISTDGDMGQMVVTILSAVAQAERRRILERTNEG 54
Cdd:cd00338   84 LLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
66-107 7.91e-07

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 42.34  E-value: 7.91e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 553680586   66 GRRRTVDR---NVVLTLHQKGTGATEIAHQLSIARSTVYKILEDE 107
Cdd:pfam02796   1 GRPPKLNEediNEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
 
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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