NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446827802|ref|WP_000905058|]
View 

MULTISPECIES: recombinase family protein [Enterobacteriaceae]

Protein Classification

recombinase family protein( domain architecture ID 10132968)

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-122 2.72e-63

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: 191.54  E-value: 2.72e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   2 LIGYVRVSTNDQNTDLQRNALVCAG-CEQIFEDKLSGTKTDRPGLKRALKRLQKGDTLVVWKLDRLGRSMKHLISLVGEL 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446827802  81 RERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:cd03768   81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRER 122
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-178 1.13e-08

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


:

Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 48.86  E-value: 1.13e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446827802 141 PKLTKEQHEQIARLIKNGHDRKQLAIIYGIGISTIYRY 178
Cdd:cd00569    4 PKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRY 41
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-122 2.72e-63

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: 191.54  E-value: 2.72e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   2 LIGYVRVSTNDQNTDLQRNALVCAG-CEQIFEDKLSGTKTDRPGLKRALKRLQKGDTLVVWKLDRLGRSMKHLISLVGEL 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446827802  81 RERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:cd03768   81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRER 122
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-122 2.39e-50

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: 159.36  E-value: 2.39e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802    3 IGYVRVSTNDQNTDL--QRNALVCAGCEQ----IFEDK-LSGTKTDRPGLKRALKRLQ--KGDTLVVWKLDRLGRSMKHL 73
Cdd:pfam00239   2 IGYARVSTEDQDDSLerQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRagKGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 446827802   74 ISLVGELRERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRER 130
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-122 2.92e-46

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 156.34  E-value: 2.92e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   1 MLIGYVRVSTNDQ---NTDLQRNALV----CAGCE--QIFEDK-LSGTKTDRPGLKRALKRLQKG--DTLVVWKLDRLGR 68
Cdd:COG1961    3 RAAGYARVSTDDQeglSLERQREALRayaeKAGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446827802  69 SMKHLISLVGELRERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:COG1961   83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISER 136
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-122 1.23e-42

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: 140.07  E-value: 1.23e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802     3 IGYVRVSTNDQ---NTDLQRNALVCA----GCE--QIFEDK-LSGTKTDRPGLKRALKRLQKGD--TLVVWKLDRLGRSM 70
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWEvvRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 446827802    71 KHLISLVGELRERGINFRSLTDSI-DTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISER 134
recomb_XisF NF041201
fdxN element excision recombinase XisF;
3-122 3.59e-26

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 103.89  E-value: 3.59e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   3 IGYVRVSTNDQNTD---L--QRNALVCAGCEQIFEDKLSGTKTDRPGLKRALKRLQKG--DTLVVWKLDRLGRSMKHLIS 75
Cdd:NF041201   2 VGYARVSTREQADDghaLeqQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIYK 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446827802  76 LVGELRERGINFRSLTD-SIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:NF041201  82 AIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSER 129
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-178 2.38e-12

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 62.81  E-value: 2.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   1 MLIGYVRVSTNDQNTDLQRNALVcAGCEQ-------IFEDKLSGTK--TDRPgLKRALKRLQKGDTLVVWKLDRLGRSMK 71
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEIT-NFAEKnnltidkWIEETISGTKsyKDRK-LGKLLKKMRKGDILIVSELSRLGRNLM 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802  72 HLISLVGELRERGINFRSLTDSI----DTSSPMGRFFFhvmGALAEMERELIVERTLAGLAAARAR-------GRTGGRR 140
Cdd:PRK13413  79 EIMSILNICMEKEVIVYTIKEGYelgdDINSKVLAFAF---GLSAEIERNLISQRTKEALARKKAEgvtlgrpKGSTPKK 155

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446827802 141 PKLTKeQHEQIARLIKNGHDRKQLAIIYGIGISTIYRY 178
Cdd:PRK13413 156 YKLTG-KEEKIKKLLDKGTSKSEIARKLGVSRTTLARF 192
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-178 1.13e-08

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 48.86  E-value: 1.13e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446827802 141 PKLTKEQHEQIARLIKNGHDRKQLAIIYGIGISTIYRY 178
Cdd:cd00569    4 PKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRY 41
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
141-182 1.63e-08

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 48.89  E-value: 1.63e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 446827802  141 PKLTKEQHEQIARLIKNGHDRKQLAIIYGIGISTIYRYHPAG 182
Cdd:pfam02796   4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-122 2.72e-63

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: 191.54  E-value: 2.72e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   2 LIGYVRVSTNDQNTDLQRNALVCAG-CEQIFEDKLSGTKTDRPGLKRALKRLQKGDTLVVWKLDRLGRSMKHLISLVGEL 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446827802  81 RERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:cd03768   81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRER 122
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-122 2.39e-50

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: 159.36  E-value: 2.39e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802    3 IGYVRVSTNDQNTDL--QRNALVCAGCEQ----IFEDK-LSGTKTDRPGLKRALKRLQ--KGDTLVVWKLDRLGRSMKHL 73
Cdd:pfam00239   2 IGYARVSTEDQDDSLerQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRagKGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 446827802   74 ISLVGELRERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRER 130
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-122 2.92e-46

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 156.34  E-value: 2.92e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   1 MLIGYVRVSTNDQ---NTDLQRNALV----CAGCE--QIFEDK-LSGTKTDRPGLKRALKRLQKG--DTLVVWKLDRLGR 68
Cdd:COG1961    3 RAAGYARVSTDDQeglSLERQREALRayaeKAGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446827802  69 SMKHLISLVGELRERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:COG1961   83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISER 136
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-122 1.23e-42

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: 140.07  E-value: 1.23e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802     3 IGYVRVSTNDQ---NTDLQRNALVCA----GCE--QIFEDK-LSGTKTDRPGLKRALKRLQKGD--TLVVWKLDRLGRSM 70
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWEvvRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 446827802    71 KHLISLVGELRERGINFRSLTDSI-DTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISER 134
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-122 1.50e-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: 101.18  E-value: 1.50e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   5 YVRVSTNDQN----TDLQRNAL--VCA--GCE--QIFEDKLSGTKT--DRPGLKRALKRLQKG--DTLVVWKLDRLGRSM 70
Cdd:cd00338    2 YARVSTDKQEqgdsLERQREALreYAArnGLEvvGEYEDAGSSATSlvDRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446827802  71 KHLISLVGELRERGINFRSLTDSIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:cd00338   82 VDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISER 133
recomb_XisF NF041201
fdxN element excision recombinase XisF;
3-122 3.59e-26

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 103.89  E-value: 3.59e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   3 IGYVRVSTNDQNTD---L--QRNALVCAGCEQIFEDKLSGTKTDRPGLKRALKRLQKG--DTLVVWKLDRLGRSMKHLIS 75
Cdd:NF041201   2 VGYARVSTREQADDghaLeqQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIYK 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446827802  76 LVGELRERGINFRSLTD-SIDTSSPMGRFFFHVMGALAEMERELIVER 122
Cdd:NF041201  82 AIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSER 129
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-178 2.38e-12

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 62.81  E-value: 2.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   1 MLIGYVRVSTNDQNTDLQRNALVcAGCEQ-------IFEDKLSGTK--TDRPgLKRALKRLQKGDTLVVWKLDRLGRSMK 71
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEIT-NFAEKnnltidkWIEETISGTKsyKDRK-LGKLLKKMRKGDILIVSELSRLGRNLM 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802  72 HLISLVGELRERGINFRSLTDSI----DTSSPMGRFFFhvmGALAEMERELIVERTLAGLAAARAR-------GRTGGRR 140
Cdd:PRK13413  79 EIMSILNICMEKEVIVYTIKEGYelgdDINSKVLAFAF---GLSAEIERNLISQRTKEALARKKAEgvtlgrpKGSTPKK 155

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446827802 141 PKLTKeQHEQIARLIKNGHDRKQLAIIYGIGISTIYRY 178
Cdd:PRK13413 156 YKLTG-KEEKIKKLLDKGTSKSEIARKLGVSRTTLARF 192
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 4-85 4.01e-11

Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, 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 subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain.


Pssm-ID: 239736 [Multi-domain]  Cd Length: 146  Bit Score: 58.49  E-value: 4.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   4 GYVRVSTNDQNTDLQRNALVCAGCEQ------IFEDKLSGTKTDRPGLKRALKRLQKGDTLVVWKLDRLGR-SMKHLISL 76
Cdd:cd03767    3 AYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWETL 82


                 ....*....
gi 446827802  77 VGELRERGI 85
Cdd:cd03767   83 KASIAAKGL 91
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-178 1.13e-08

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 48.86  E-value: 1.13e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446827802 141 PKLTKEQHEQIARLIKNGHDRKQLAIIYGIGISTIYRY 178
Cdd:cd00569    4 PKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRY 41
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
141-182 1.63e-08

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 48.89  E-value: 1.63e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 446827802  141 PKLTKEQHEQIARLIKNGHDRKQLAIIYGIGISTIYRYHPAG 182
Cdd:pfam02796   4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 3-68 1.04e-06

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: 46.10  E-value: 1.04e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446827802   3 IGYVRVSTNDQNTDLQRNA-LVCAGCE------QIFEDKLSGTKTDRPGLKRALKRLQKG--DTLVVWKLDRLGR 68
Cdd:cd03769    2 VLYARVSSHDQKDDLERQIeRLEAYATaqgwivEVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLAR 76
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 4-96 1.78e-05

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: 42.74  E-value: 1.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446827802   4 GYVRVSTNDqntDLQRNALVCAGCEQIFE----------------DKLSGTKTDRPGLKRALKRLQKG--DTLVVWKLDR 65
Cdd:cd03770    3 LYCRLSRDD---DLDGESNSIENQKAILEeyakenglenirhyidDGFSGTTFDRPGFNRMIEDIEAGkiDIVIVKDMSR 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446827802  66 LGRSMKHLISLVGELR-ERGINFRSLTDSIDT 96
Cdd:cd03770   80 LGRNYLKVGLYMEILFpKKGVRFIAINDGVDS 111
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH