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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572  27 DQNPERQLEGVK----VDRAFSDKASGKDVKRPQLEALISFARTGDTVVVHSMDRLARNLDDLRRIVQTLTQRGVHIEFV 102
Cdd:cd03768    11 DQSLERQLEALKaageCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEELREKGVSLRSL 90

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1736663572 103 KEHLSFTgedSPMANLMLSVMGAFAEFERALIRERQREG 141
Cdd:cd03768    91 TEGIDTS---TPSGKLMLTILGAFAEFERELIRERTKEG 126

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572  27 DQNPERQLEGVK----VDRAFSDKASGKDVKRPQLEALISFARTGDTVVVHSMDRLARNLDDLRRIVQTLTQRGVHIEFV 102
Cdd:cd03768    11 DQSLERQLEALKaageCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEELREKGVSLRSL 90

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1736663572 103 KEHLSFTgedSPMANLMLSVMGAFAEFERALIRERQREG 141
Cdd:cd03768    91 TEGIDTS---TPSGKLMLTILGAFAEFERELIRERTKEG 126

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572   27 DQNPERQLE---------GVKVDRAFSDKA-SGKDVKRPQLEALISFARTGD--TVVVHSMDRLARNLDDLRRIVQTLTQ 94
Cdd:smart00857  14 DGSLERQLEalrayaernGWEVVRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSLRDLLALLELLEE 93

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1736663572   95 RGVHIEFVKEHLSFTgeDSPMANLMLSVMGAFAEFERALIRERQREGIALAKQRGAY 151
Cdd:smart00857  94 KGVRLVSLKEGILDT--STPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148

master DNA invertase Mpi family serine-type recombinase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572  36 GVKVDRAFSDKASG-KDVKRPQLEALISFARTGDTVVVHSMDRLARNLDDLRRIVQTLTQRGVHIEFVKEHLSFtGEDSP 114
Cdd:PRK13413   30 NLTIDKWIEETISGtKSYKDRKLGKLLKKMRKGDILIVSELSRLGRNLMEIMSILNICMEKEVIVYTIKEGYEL-GDDIN 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572 115 MANLMLSvMGAFAEFERALIRERQREGIALAKQRGAYRGRKKSLSSERIA------ELRQRVEAGEQKTKLAREFGISRE 188
Cdd:PRK13413  109 SKVLAFA-FGLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTPKKYKltgkeeKIKKLLDKGTSKSEIARKLGVSRT 187

                  ....*...
gi 1736663572 189 TLYQYLRT 196
Cdd:PRK13413  188 TLARFLKT 195

Helix-turn-helix domain of resolvase;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1736663572 153 GRKKSLSSERIAELRQRVEAGEQKTKLAREFGISRETLYQYLRTD 197
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572  27 DQNPERQLEGVK----VDRAFSDKASGKDVKRPQLEALISFARTGDTVVVHSMDRLARNLDDLRRIVQTLTQRGVHIEFV 102
Cdd:cd03768    11 DQSLERQLEALKaageCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEELREKGVSLRSL 90

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1736663572 103 KEHLSFTgedSPMANLMLSVMGAFAEFERALIRERQREG 141
Cdd:cd03768    91 TEGIDTS---TPSGKLMLTILGAFAEFERELIRERTKEG 126

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572   27 DQNPERQLE---------GVKVDRAFSDKA-SGKDVKRPQLEALISFARTGD--TVVVHSMDRLARNLDDLRRIVQTLTQ 94
Cdd:smart00857  14 DGSLERQLEalrayaernGWEVVRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSLRDLLALLELLEE 93

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1736663572   95 RGVHIEFVKEHLSFTgeDSPMANLMLSVMGAFAEFERALIRERQREGIALAKQRGAY 151
Cdd:smart00857  94 KGVRLVSLKEGILDT--STPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572  31 ERQLE---------GVKVDRAFSDKASG--KDVKRPQLEALISFARTG--DTVVVHSMDRLARNLDDLRRIVQTLTQRGV 97
Cdd:cd00338    17 ERQREalreyaarnGLEVVGEYEDAGSSatSLVDRPGLQRLLADVKAGkiDVVLVEKLDRLSRNLVDLLELLELLEAHGV 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1736663572  98 HIEFVKEHLSFtgeDSPMANLMLSVMGAFAEFERALIRERQREG 141
Cdd:cd00338    97 RVVTADGEIDL---DSEDGRLMLGILAAMAEEESKLISERTKRG 137

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1736663572 153 GRKKSLSSERIAELRQRVEAGEQKTKLAREFGISRETLYQYL 194
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1736663572  20 YLQQCPFDQNPERQLE---------GVKVDRAFSDKASGKDVKRPQLEALISFARTGDTVVVHSMDRLAR-NLDDLRRIV 89
Cdd:cd03767     4 YLRASTDEQDATRAKEsleafaterGFYIAGFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWETLK 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1736663572  90 QTLTQRGVHI---EFVKEHLSFTGEDSPMA--------NLMLSVMGAFAEFERALIRERQREG 141
Cdd:cd03767    84 ASIAAKGLRVvslDLPTSHSALAAEDNDFTgrilsainDMLLDLLAAMARKDYEDRRERQKQG 146