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Conserved domains on  [gi|1078755024|gb|OFE04230|]
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resolvase [Bacillus mycoides]

Protein Classification

recombinase family protein( domain architecture ID 10657212)

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|GO:0015074
PubMed:  21645851|26104451|11972771|16077726|9348666
SCOP:  3000065

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-143 3.19e-28

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: 101.16  E-value: 3.19e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024    6 VFGYIRVSTEGQVRDgySLAYQVEEIERYCNENNLELLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYVVV 85
Cdd:smart00857   1 AAGYARVSTDDQADG--SLERQLEALRAYAERNGWEVVRIYEDEGVSGKKAD-------RPGLQRLLADLRAGDIDVLVV 71

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1078755024   86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQSSYSiyTHDPNDFLVNGMLELLDQYQ 143
Cdd:smart00857  72 YKLDRLGRSLRDLLALLELLEEKGVRLVSLKEGILD--TSTPAGRLLLDILAALAEFE 127
 
Name Accession Description Interval E-value
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-143 3.19e-28

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: 101.16  E-value: 3.19e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024    6 VFGYIRVSTEGQVRDgySLAYQVEEIERYCNENNLELLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYVVV 85
Cdd:smart00857   1 AAGYARVSTDDQADG--SLERQLEALRAYAERNGWEVVRIYEDEGVSGKKAD-------RPGLQRLLADLRAGDIDVLVV 71

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1078755024   86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQSSYSiyTHDPNDFLVNGMLELLDQYQ 143
Cdd:smart00857  72 YKLDRLGRSLRDLLALLELLEEKGVRLVSLKEGILD--TSTPAGRLLLDILAALAEFE 127
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 9-143 4.35e-27

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: 98.10  E-value: 4.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   9 YIRVSTEGQVrDGYSLAYQVEEIERYCNENNLELLRVYEDRGLSGATvdedglTVERDGLQELLSDMAYKQVSYVVVLNT 88
Cdd:cd00338     2 YARVSTDKQE-QGDSLERQREALREYAARNGLEVVGEYEDAGSSATS------LVDRPGLQRLLADVKAGKIDVVLVEKL 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1078755024  89 SRLWRSDMAKVLIQRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:cd00338    75 DRLSRNLVDLLELLELLEAHGVRVVTADG---EIDLDSEDGRLMLGILAAMAEEE 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-143 1.44e-26

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 102.41  E-value: 1.44e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   4 KKVFGYIRVSTEGQvrDGYSLAYQVEEIERYCNENNLELLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYV 83
Cdd:COG1961     2 MRAAGYARVSTDDQ--EGLSLERQREALRAYAEKAGWEIVRIYVDEGVSGTSKD-------RPGLQRLLADLRAGKFDTL 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078755024  84 VVLNTSRLWRS--DMAKVLiqRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:COG1961    73 VVWKLDRLGRNlaDLLELV--EELKERGVRLISLTE---GIDTSTPMGRLLLTILAAFAEFE 129
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 6-143 1.54e-20

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: 81.55  E-value: 1.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVSTEGQvrdGYSLAYQVEEIERYCNENNLelLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYVVV 85
Cdd:pfam00239   1 AIGYARVSTEDQ---DDSLERQLEALRAYAACNGK--IVEFEDKGVSGRKLD-------RPGLQRLLALLRAGKGDVLVV 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1078755024  86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:pfam00239  69 YKLDRLGRSLRDLLTLVEELREKGVDLVSLDE---GIDTSTPMGRLLLTILAALAEFE 123
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
6-117 7.22e-05

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 40.86  E-value: 7.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVSTEGQvrdgySLAYQVEEIERYCNENNLELLRVYEDRgLSGATVDEDgltveRDgLQELLSDMayKQVSYVVV 85
Cdd:PRK13413    2 IYAYIRVSTDKQ-----TVENQRFEITNFAEKNNLTIDKWIEET-ISGTKSYKD-----RK-LGKLLKKM--RKGDILIV 67

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1078755024  86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQ 117
Cdd:PRK13413   68 SELSRLGRNLMEIMSILNICMEKEVIVYTIKE 99
 
Name Accession Description Interval E-value
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-143 3.19e-28

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: 101.16  E-value: 3.19e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024    6 VFGYIRVSTEGQVRDgySLAYQVEEIERYCNENNLELLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYVVV 85
Cdd:smart00857   1 AAGYARVSTDDQADG--SLERQLEALRAYAERNGWEVVRIYEDEGVSGKKAD-------RPGLQRLLADLRAGDIDVLVV 71

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1078755024   86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQSSYSiyTHDPNDFLVNGMLELLDQYQ 143
Cdd:smart00857  72 YKLDRLGRSLRDLLALLELLEEKGVRLVSLKEGILD--TSTPAGRLLLDILAALAEFE 127
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 9-143 4.35e-27

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: 98.10  E-value: 4.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   9 YIRVSTEGQVrDGYSLAYQVEEIERYCNENNLELLRVYEDRGLSGATvdedglTVERDGLQELLSDMAYKQVSYVVVLNT 88
Cdd:cd00338     2 YARVSTDKQE-QGDSLERQREALREYAARNGLEVVGEYEDAGSSATS------LVDRPGLQRLLADVKAGKIDVVLVEKL 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1078755024  89 SRLWRSDMAKVLIQRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:cd00338    75 DRLSRNLVDLLELLELLEAHGVRVVTADG---EIDLDSEDGRLMLGILAAMAEEE 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-143 1.44e-26

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 102.41  E-value: 1.44e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   4 KKVFGYIRVSTEGQvrDGYSLAYQVEEIERYCNENNLELLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYV 83
Cdd:COG1961     2 MRAAGYARVSTDDQ--EGLSLERQREALRAYAEKAGWEIVRIYVDEGVSGTSKD-------RPGLQRLLADLRAGKFDTL 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078755024  84 VVLNTSRLWRS--DMAKVLiqRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:COG1961    73 VVWKLDRLGRNlaDLLELV--EELKERGVRLISLTE---GIDTSTPMGRLLLTILAAFAEFE 129
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 6-143 1.54e-20

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: 81.55  E-value: 1.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVSTEGQvrdGYSLAYQVEEIERYCNENNLelLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYVVV 85
Cdd:pfam00239   1 AIGYARVSTEDQ---DDSLERQLEALRAYAACNGK--IVEFEDKGVSGRKLD-------RPGLQRLLALLRAGKGDVLVV 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1078755024  86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:pfam00239  69 YKLDRLGRSLRDLLTLVEELREKGVDLVSLDE---GIDTSTPMGRLLLTILAALAEFE 123
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 6-115 4.63e-12

Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. 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. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.


Pssm-ID: 239739 [Multi-domain]  Cd Length: 140  Bit Score: 59.30  E-value: 4.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVST-EGQVRDGYSLAYQVEEIERYCNENNLELLRVYEDRGLSGATVDedgltveRDGLQELLSDMAYKQVSYVV 84
Cdd:cd03770     1 TALYCRLSRdDDLDGESNSIENQKAILEEYAKENGLENIRHYIDDGFSGTTFD-------RPGFNRMIEDIEAGKIDIVI 73

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1078755024  85 VLNTSRLWRsDMAKVLIQRELKKHEVDVKAI 115
Cdd:cd03770    74 VKDMSRLGR-NYLKVGLYMEILFPKKGVRFI 103
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 6-143 7.66e-12

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: 58.26  E-value: 7.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVSTEGQvrdgySLAYQVEEIERYCnennlELLRVYEDRGLSGatvdedglTVERDGLQELLSDMayKQVSYVVV 85
Cdd:cd03768     1 VIGYARVSTDDQ-----SLERQLEALKAAG-----ECDKIFEEKGSGG--------KKERPELQKLLEDL--REGDTLVV 60

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1078755024  86 LNTSRLWRSdMAKVL-IQRELKKHEVDVKAIEQssySIYTHDPNDFLVNGMLELLDQYQ 143
Cdd:cd03768    61 TKLDRLGRS-TKDLLeIVEELREKGVSLRSLTE---GIDTSTPSGKLMLTILGAFAEFE 115
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 6-93 4.04e-05

Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic 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. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.


Pssm-ID: 239738  Cd Length: 134  Bit Score: 40.71  E-value: 4.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVSTEGQVRDgysLAYQVEEIERYCNENNlELLRVYEDRGlsgatvdeDGLTVERDGLQELLSDMAYKQVSYVVV 85
Cdd:cd03769     1 TVLYARVSSHDQKDD---LERQIERLEAYATAQG-WIVEVIKDIG--------SGLNEKRKGLLKLLEDVLAGKVERVVI 68


                  ....*...
gi 1078755024  86 LNTSRLWR 93
Cdd:cd03769    69 TYKDRLAR 76
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
6-117 7.22e-05

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 40.86  E-value: 7.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1078755024   6 VFGYIRVSTEGQvrdgySLAYQVEEIERYCNENNLELLRVYEDRgLSGATVDEDgltveRDgLQELLSDMayKQVSYVVV 85
Cdd:PRK13413    2 IYAYIRVSTDKQ-----TVENQRFEITNFAEKNNLTIDKWIEET-ISGTKSYKD-----RK-LGKLLKKM--RKGDILIV 67

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1078755024  86 LNTSRLWRSDMAKVLIQRELKKHEVDVKAIEQ 117
Cdd:PRK13413   68 SELSRLGRNLMEIMSILNICMEKEVIVYTIKE 99
 
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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