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Conserved domains on  [gi|498480210|ref|WP_010783490|]
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MULTISPECIES: recombinase family protein [Bacilli]

Protein Classification

recombinase family protein( domain architecture ID 10133033)

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
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-123 1.64e-58

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: 179.60  E-value: 1.64e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   2 KIGYARVSTGLQNLDLQEDSLNKFG-CEKIFSDHMSGAKSNRPGLETAIDFVRSGDTLVVWRLDRLGRNMEDLISIVNRL 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 498480210  81 NERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:cd03768   81 REKGVSLRSLTEGI--DTSTPSGKLMLTILGAFAEFERELIRE 121
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
142-183 8.91e-12

Helix-turn-helix domain of resolvase;


:

Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 57.36  E-value: 8.91e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 498480210  142 PEKLKAQDLELLKTLVDSGTPIKTIAERWNVSRTTIYRYLDK 183
Cdd:pfam02796   3 PPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAA 44
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-123 1.64e-58

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: 179.60  E-value: 1.64e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   2 KIGYARVSTGLQNLDLQEDSLNKFG-CEKIFSDHMSGAKSNRPGLETAIDFVRSGDTLVVWRLDRLGRNMEDLISIVNRL 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 498480210  81 NERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:cd03768   81 REKGVSLRSLTEGI--DTSTPSGKLMLTILGAFAEFERELIRE 121
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-183 6.88e-46

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 155.18  E-value: 6.88e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   1 MKIGYARVSTGLQ---NLDLQEDSLNKF----GCE--KIFSDH-MSGAKSNRPGLETAIDFVRSG--DTLVVWRLDRLGR 68
Cdd:COG1961    3 RAAGYARVSTDDQeglSLERQREALRAYaekaGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210  69 NMEDLISIVNRLNERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILER------------SAAGRAAARARG 136
Cdd:COG1961   83 NLADLLELVEELKERGVRLISLTEGI--DTSTPMGRLLLTILAAFAEFERELISERtraglaaakargKYLGRPPYGYRD 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 498480210 137 RFGGRPEKLKAQDLELLKTLVDSGTPIKTIAERWN------VSRTTIYRYLDK 183
Cdd:COG1961  161 PKKLVIDEEEAEVVRRIFELYLEGKSLREIARELNergiptWSRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-123 2.53e-43

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: 141.64  E-value: 2.53e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210    3 IGYARVSTGLQN--LDLQEDSLNKFGCEK----IFSDH-MSGAKSNRPGLETAIDFVRS--GDTLVVWRLDRLGRNMEDL 73
Cdd:pfam00239   2 IGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 498480210   74 ISIVNRLNERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGI--DTSTPMGRLLLTILAALAEFERALIRE 129
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-123 3.29e-40

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: 133.90  E-value: 3.29e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210     3 IGYARVSTGLQ---NLDLQEDSLNKF----GCE--KIFSDH-MSGAKSNRPGLETAIDFVRSGD--TLVVWRLDRLGRNM 70
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWEvvRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 498480210    71 EDLISIVNRLNERGVSFHSLQENITmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIL-DTSTPAGRLLLDILAALAEFERELISE 133
recomb_XisF NF041201
fdxN element excision recombinase XisF;
2-121 1.84e-20

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 87.71  E-value: 1.84e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   2 KIGYARVSTGLQN-----LDLQEDSLNKFGCEKIFSDHMSGAKSNRPGLETAIDFVRSG--DTLVVWRLDRLGRNMEDLI 74
Cdd:NF041201   1 IVGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIY 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 498480210  75 SIVNRLNERGVSFHSLQENItMDKSSSTGQLMFHLFAAFAEFERNLI 121
Cdd:NF041201  81 KAIEVLQKKGVKLVILDAPL-DDLSSPGGWFTINQLAALAEFESRLL 126
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-186 6.27e-15

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 69.75  E-value: 6.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   1 MKIGYARVSTGLQNLDLQEDSLNKFGCEKIFS------DHMSGAKS-NRPGLETAIDFVRSGDTLVVWRLDRLGRNMEDL 73
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGTKSyKDRKLGKLLKKMRKGDILIVSELSRLGRNLMEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210  74 ISIVNRLNERGVSFHSLQENITMDKSSSTGQLMFhLFAAFAEFERNLILERSAAGRAAARARGRFGGRPE-------KLK 146
Cdd:PRK13413  81 MSILNICMEKEVIVYTIKEGYELGDDINSKVLAF-AFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKgstpkkyKLT 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 498480210 147 AQDlELLKTLVDSGTPIKTIAERWNVSRTTIYRYLDKMEE 186
Cdd:PRK13413 160 GKE-EKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRGL 198
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
142-183 8.91e-12

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 57.36  E-value: 8.91e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 498480210  142 PEKLKAQDLELLKTLVDSGTPIKTIAERWNVSRTTIYRYLDK 183
Cdd:pfam02796   3 PPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAA 44
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 142-181 2.20e-10

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: 53.48  E-value: 2.20e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 498480210 142 PEKLKAQDLELLKTLVDSGTPIKTIAERWNVSRTTIYRYL 181
Cdd:cd00569    3 PPKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
COG3355 COG3355
Predicted transcriptional regulator [Transcription];
145-188 3.08e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 442583 [Multi-domain]  Cd Length: 131  Bit Score: 41.87  E-value: 3.08e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 498480210 145 LKAQDLELLKTLVDSGTP--IKTIAERWNVSRTTIYRYLDKMEEKN 188
Cdd:COG3355   25 LSETDAEVYLILLENGEPltVEELAEALDRSRSTVYRSLQKLLEAG 70
transpos_IS607 NF033518
IS607 family transposase;
3-68 6.82e-04

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 38.78  E-value: 6.82e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 498480210   3 IGYARVSTGLQ--NLDLQEDSL------NKFGCEKIFSDHMSGAKSNRPGLETAIDFVRSGD--TLVVWRLDRLGR 68
Cdd:NF033518  57 VIYARVSSADQkdDLERQVARLtqyataKGWQVDEVVTDIGSGLNEKRKGLLKLLDDILNGEvsRVVVEHKDRLTR 132
cas_HTH TIGR01884
CRISPR locus-related DNA-binding protein; Most but not all examples of this family are ...
 142-187 1.52e-03

CRISPR locus-related DNA-binding protein; Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity. [Regulatory functions, DNA interactions, , ]


Pssm-ID: 273852 [Multi-domain]  Cd Length: 203  Bit Score: 38.11  E-value: 1.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 498480210  142 PEKLKAQDLELLKTLVDSG-TPIKTIAERWNVSRTTIYRYLDKMEEK 187
Cdd:TIGR01884 138 LAGLSREELKILEVLKATGeKSVKNIAKKLGKSLSTISRHLAELEKK 184
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
142-188 3.37e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.65  E-value: 3.37e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 498480210   142 PEKLKAQDLELLKTLVDSGT-PIKTIAERWNVSRTTIYRYLDKMEEKN 188
Cdd:smart00347   5 PLGLTPTQFLVLRILYEEGPlSVSELAKRLGVSPSTVTRVLDRLEKKG 52
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-123 1.64e-58

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: 179.60  E-value: 1.64e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   2 KIGYARVSTGLQNLDLQEDSLNKFG-CEKIFSDHMSGAKSNRPGLETAIDFVRSGDTLVVWRLDRLGRNMEDLISIVNRL 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 498480210  81 NERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:cd03768   81 REKGVSLRSLTEGI--DTSTPSGKLMLTILGAFAEFERELIRE 121
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-183 6.88e-46

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 155.18  E-value: 6.88e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   1 MKIGYARVSTGLQ---NLDLQEDSLNKF----GCE--KIFSDH-MSGAKSNRPGLETAIDFVRSG--DTLVVWRLDRLGR 68
Cdd:COG1961    3 RAAGYARVSTDDQeglSLERQREALRAYaekaGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210  69 NMEDLISIVNRLNERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILER------------SAAGRAAARARG 136
Cdd:COG1961   83 NLADLLELVEELKERGVRLISLTEGI--DTSTPMGRLLLTILAAFAEFERELISERtraglaaakargKYLGRPPYGYRD 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 498480210 137 RFGGRPEKLKAQDLELLKTLVDSGTPIKTIAERWN------VSRTTIYRYLDK 183
Cdd:COG1961  161 PKKLVIDEEEAEVVRRIFELYLEGKSLREIARELNergiptWSRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-123 2.53e-43

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: 141.64  E-value: 2.53e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210    3 IGYARVSTGLQN--LDLQEDSLNKFGCEK----IFSDH-MSGAKSNRPGLETAIDFVRS--GDTLVVWRLDRLGRNMEDL 73
Cdd:pfam00239   2 IGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 498480210   74 ISIVNRLNERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGI--DTSTPMGRLLLTILAALAEFERALIRE 129
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-123 3.29e-40

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: 133.90  E-value: 3.29e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210     3 IGYARVSTGLQ---NLDLQEDSLNKF----GCE--KIFSDH-MSGAKSNRPGLETAIDFVRSGD--TLVVWRLDRLGRNM 70
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWEvvRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 498480210    71 EDLISIVNRLNERGVSFHSLQENITmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIL-DTSTPAGRLLLDILAALAEFERELISE 133
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-123 3.51e-26

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: 97.33  E-value: 3.51e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   5 YARVSTGLQN----LDLQEDSLNKF----GCE--KIFSDHMSGAKSN--RPGLETAIDFVRSG--DTLVVWRLDRLGRNM 70
Cdd:cd00338    2 YARVSTDKQEqgdsLERQREALREYaarnGLEvvGEYEDAGSSATSLvdRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 498480210  71 EDLISIVNRLNERGVSFHSLQENItmDKSSSTGQLMFHLFAAFAEFERNLILE 123
Cdd:cd00338   82 VDLLELLELLEAHGVRVVTADGEI--DLDSEDGRLMLGILAAMAEEESKLISE 132
recomb_XisF NF041201
fdxN element excision recombinase XisF;
2-121 1.84e-20

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 87.71  E-value: 1.84e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   2 KIGYARVSTGLQN-----LDLQEDSLNKFGCEKIFSDHMSGAKSNRPGLETAIDFVRSG--DTLVVWRLDRLGRNMEDLI 74
Cdd:NF041201   1 IVGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIY 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 498480210  75 SIVNRLNERGVSFHSLQENItMDKSSSTGQLMFHLFAAFAEFERNLI 121
Cdd:NF041201  81 KAIEVLQKKGVKLVILDAPL-DDLSSPGGWFTINQLAALAEFESRLL 126
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-186 6.27e-15

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 69.75  E-value: 6.27e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   1 MKIGYARVSTGLQNLDLQEDSLNKFGCEKIFS------DHMSGAKS-NRPGLETAIDFVRSGDTLVVWRLDRLGRNMEDL 73
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGTKSyKDRKLGKLLKKMRKGDILIVSELSRLGRNLMEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210  74 ISIVNRLNERGVSFHSLQENITMDKSSSTGQLMFhLFAAFAEFERNLILERSAAGRAAARARGRFGGRPE-------KLK 146
Cdd:PRK13413  81 MSILNICMEKEVIVYTIKEGYELGDDINSKVLAF-AFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKgstpkkyKLT 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 498480210 147 AQDlELLKTLVDSGTPIKTIAERWNVSRTTIYRYLDKMEE 186
Cdd:PRK13413 160 GKE-EKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRGL 198
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
142-183 8.91e-12

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 57.36  E-value: 8.91e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 498480210  142 PEKLKAQDLELLKTLVDSGTPIKTIAERWNVSRTTIYRYLDK 183
Cdd:pfam02796   3 PPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAA 44
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 142-181 2.20e-10

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: 53.48  E-value: 2.20e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 498480210 142 PEKLKAQDLELLKTLVDSGTPIKTIAERWNVSRTTIYRYL 181
Cdd:cd00569    3 PPKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 4-90 6.47e-10

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: 55.02  E-value: 6.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498480210   4 GYARVSTGLQNLDLQEDSLNKFGCEK------IFSDHMSGAKSNRPGLETAIDFVRSGDTLVVWRLDRLGR-NMEDLISI 76
Cdd:cd03767    3 AYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWETL 82

                         90
                 ....*....|....
gi 498480210  77 VNRLNERGVSFHSL 90
Cdd:cd03767   83 KASIAAKGLRVVSL 96
COG3355 COG3355
Predicted transcriptional regulator [Transcription];
145-188 3.08e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 442583 [Multi-domain]  Cd Length: 131  Bit Score: 41.87  E-value: 3.08e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 498480210 145 LKAQDLELLKTLVDSGTP--IKTIAERWNVSRTTIYRYLDKMEEKN 188
Cdd:COG3355   25 LSETDAEVYLILLENGEPltVEELAEALDRSRSTVYRSLQKLLEAG 70
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
3-74 6.95e-05

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 41.52  E-value: 6.95e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 498480210   3 IGYARVSTGLQNLDL--QEDSLNKFGCEK-----IFSDHMSGAKSNRPGLETAIDFVRSgDTLVVWRLDRLGRNMEDLI 74
Cdd:COG2452   51 VIYARVSSADQKDDLerQVERLEEYATAKgyqdeVIKDVGSGLNYKRKGLLKLLERIEV-ERVVVEHKDRLARFGFELL 128
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 150-188 1.57e-04

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 38.18  E-value: 1.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 498480210  150 LELLKTLVDSGTPI--KTIAERWNVSRTTIYRYLDKMEEKN 188
Cdd:pfam08279   1 LQILQLLLEARGPIsgQELAEKLGVSRRTIRRDIKILEELG 41
transpos_IS607 NF033518
IS607 family transposase;
3-68 6.82e-04

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 38.78  E-value: 6.82e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 498480210   3 IGYARVSTGLQ--NLDLQEDSL------NKFGCEKIFSDHMSGAKSNRPGLETAIDFVRSGD--TLVVWRLDRLGR 68
Cdd:NF033518  57 VIYARVSSADQkdDLERQVARLtqyataKGWQVDEVVTDIGSGLNEKRKGLLKLLDDILNGEvsRVVVEHKDRLTR 132
cas_HTH TIGR01884
CRISPR locus-related DNA-binding protein; Most but not all examples of this family are ...
 142-187 1.52e-03

CRISPR locus-related DNA-binding protein; Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity. [Regulatory functions, DNA interactions, , ]


Pssm-ID: 273852 [Multi-domain]  Cd Length: 203  Bit Score: 38.11  E-value: 1.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 498480210  142 PEKLKAQDLELLKTLVDSG-TPIKTIAERWNVSRTTIYRYLDKMEEK 187
Cdd:TIGR01884 138 LAGLSREELKILEVLKATGeKSVKNIAKKLGKSLSTISRHLAELEKK 184
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 3-68 2.31e-03

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: 36.86  E-value: 2.31e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 498480210   3 IGYARVSTGLQNLDLQ-------EDSLNKFGCEKIFSDHMSGAKSNRPGLETAIDFVRSG--DTLVVWRLDRLGR 68
Cdd:cd03769    2 VLYARVSSHDQKDDLErqierleAYATAQGWIVEVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLAR 76
Lrp COG1522
DNA-binding transcriptional regulator, Lrp family [Transcription];
149-187 2.44e-03

DNA-binding transcriptional regulator, Lrp family [Transcription];


Pssm-ID: 441131 [Multi-domain]  Cd Length: 138  Bit Score: 36.68  E-value: 2.44e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 498480210 149 DLELLKTLV-DSGTPIKTIAERWNVSRTTIYRYLDKMEEK 187
Cdd:COG1522    7 DRRILRLLQeDGRLSFAELAERVGLSESTVLRRVRRLEEA 46
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
142-188 3.37e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.65  E-value: 3.37e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 498480210   142 PEKLKAQDLELLKTLVDSGT-PIKTIAERWNVSRTTIYRYLDKMEEKN 188
Cdd:smart00347   5 PLGLTPTQFLVLRILYEEGPlSVSELAKRLGVSPSTVTRVLDRLEKKG 52
HTH_22 pfam13309
HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding ...
 142-182 4.85e-03

HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.


Pssm-ID: 463841 [Multi-domain]  Cd Length: 63  Bit Score: 34.36  E-value: 4.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 498480210  142 PEKLKAQD-LELLKTLVDSGT-----PIKTIAERWNVSRTTIYRYLD 182
Cdd:pfam13309  17 PARLTKEEkREIVRALDEKGAfllkgAVEKVAKRLGVSRATVYNYLR 63
HTH_23 pfam13384
Homeodomain-like domain;
156-187 5.45e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 33.78  E-value: 5.45e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 498480210  156 LVDSGTPIKTIAERWNVSRTTIYRYLDKMEEK 187
Cdd:pfam13384  13 LLAEGLSVKEIAELLGVSRRTVYRWLKRYNEE 44
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
149-187 6.00e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 33.56  E-value: 6.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 498480210  149 DLELLKTLV-DSGTPIKTIAERWNVSRTTIYRYLDKMEEK 187
Cdd:pfam13412   3 DRKILNLLQeNPRISQRELAERLGLSPSTVNRRLKRLEEE 42
 
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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