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Conserved domains on  [gi|613253854|gb|EZY59904|]
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hypothetical protein V061_02734 [Staphylococcus aureus R0353]

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 ...
 2-135 1.83e-42

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: 139.15  E-value: 1.83e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   2 IVGYARVSSNDQNLERQLENLKTFC-AEKIFTEKQSGKSiENRPVLQEALNFLRMGDRFVVESIDRLGRNYDEVIHTVNY 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGK-KERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 613253854  81 LKDKEVQLMITSLPMMnevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQG 135
Cdd:cd03768   80 LREKGVSLRSLTEGID--------TSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
147-197 8.03e-10

Helix-turn-helix domain of resolvase;


:

Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 52.36  E-value: 8.03e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 613253854  147 GRPLLYSPNAkdpqkrviYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKN 197
Cdd:pfam02796   1 GRPPKLNEED--------INEVITLLEEGISIKQIAKIFGISRSTVYRYLA 43
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-135 1.83e-42

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: 139.15  E-value: 1.83e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   2 IVGYARVSSNDQNLERQLENLKTFC-AEKIFTEKQSGKSiENRPVLQEALNFLRMGDRFVVESIDRLGRNYDEVIHTVNY 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGK-KERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 613253854  81 LKDKEVQLMITSLPMMnevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQG 135
Cdd:cd03768   80 LREKGVSLRSLTEGID--------TSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-198 3.04e-40

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 140.93  E-value: 3.04e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   1 MIVGYARVSSNDQ---NLERQLENLKTFCAE------KIFTEK-QSGKSIEnRPVLQEALNFLRMG--DRFVVESIDRLG 68
Cdd:COG1961    3 RAAGYARVSTDDQeglSLERQREALRAYAEKagweivRIYVDEgVSGTSKD-RPGLQRLLADLRAGkfDTLVVWKLDRLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854  69 RNYDEVIHTVNYLKDKEVQLMITSLPMMnevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGR 148
Cdd:COG1961   82 RNLADLLELVEELKERGVRLISLTEGID--------TSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGR 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854 149 PLL-YSPNAK---DPQKRVIYHRVVEMLEEGQAISKIAKEVN------ITRQTVYRIKNN 198
Cdd:COG1961  154 PPYgYRDPKKlviDEEEAEVVRRIFELYLEGKSLREIARELNergiptWSRSTVYRILKN 213
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 2-145 1.66e-32

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: 114.26  E-value: 1.66e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854     2 IVGYARVSSNDQ---NLERQLENLKTFCAEK------IFTEK-QSGKSIeNRPVLQEALNFLRMGD--RFVVESIDRLGR 69
Cdd:smart00857   1 AAGYARVSTDDQadgSLERQLEALRAYAERNgwevvrIYEDEgVSGKKA-DRPGLQRLLADLRAGDidVLVVYKLDRLGR 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613253854    70 NYDEVIHTVNYLKDKEVQLMITSLPMMNevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVY 145
Cdd:smart00857  80 SLRDLLALLELLEEKGVRLVSLKEGILD-------TSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 2-145 2.52e-31

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: 111.21  E-value: 2.52e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854    2 IVGYARVSSNDQN--LERQLENLKTFCAEK----IFTEK-QSGKSiENRPVLQEALNFLRM--GDRFVVESIDRLGRNYD 72
Cdd:pfam00239   1 AIGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRK-LDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLR 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613253854   73 EVIHTVNYLKDKEVQLMITSlpmmnevvGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVY 145
Cdd:pfam00239  80 DLLTLVEELREKGVDLVSLD--------EGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-201 1.11e-15

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 72.06  E-value: 1.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   1 MIVGYARVSSNDQNLERQLENLKTFCAEKIFT------EKQSG-KSIENRPvLQEALNFLRMGDRFVVESIDRLGRNYDE 73
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGtKSYKDRK-LGKLLKKMRKGDILIVSELSRLGRNLME 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854  74 VIHTVNYLKDKEVQLMITSlpmMNEVVGNplldkfmkDLIIQILA----MVSEQERNESKRRQAQGIQVAKEKGVYKGRP 149
Cdd:PRK13413  80 IMSILNICMEKEVIVYTIK---EGYELGD--------DINSKVLAfafgLSAEIERNLISQRTKEALARKKAEGVTLGRP 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 613253854 150 LLYSPNAKD--PQKRVIyhrvVEMLEEGQAISKIAKEVNITRQTVYRIKNNKGL 201
Cdd:PRK13413 149 KGSTPKKYKltGKEEKI----KKLLDKGTSKSEIARKLGVSRTTLARFLKTRGL 198
recomb_XisF NF041201
fdxN element excision recombinase XisF;
2-125 8.40e-13

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 66.14  E-value: 8.40e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   2 IVGYARVSSNDQN-----LERQLENLKTFCAEKIFTEKQSGKSiENRPVLQEALNFLRMG--DRFVVESIDRLGRNYDEV 74
Cdd:NF041201   1 IVGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRS-DKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTI 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 613253854  75 IHTVNYLKDKEVQLMItsLPMMNEVVGNPlLDKFMkdliIQILAMVSEQER 125
Cdd:NF041201  80 YKAIEVLQKKGVKLVI--LDAPLDDLSSP-GGWFT----INQLAALAEFES 123
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
147-197 8.03e-10

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 52.36  E-value: 8.03e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 613253854  147 GRPLLYSPNAkdpqkrviYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKN 197
Cdd:pfam02796   1 GRPPKLNEED--------INEVITLLEEGISIKQIAKIFGISRSTVYRYLA 43
transpos_IS607 NF033518
IS607 family transposase;
2-69 3.22e-09

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 54.18  E-value: 3.22e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613253854   2 IVGYARVSSNDQ--NLERQLENLKTFCAEK------IFTEKQSGKSiENRPVLQEALNFLRMGD--RFVVESIDRLGR 69
Cdd:NF033518  56 TVIYARVSSADQkdDLERQVARLTQYATAKgwqvdeVVTDIGSGLN-EKRKGLLKLLDDILNGEvsRVVVEHKDRLTR 132
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 168-195 1.55e-04

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: 37.69  E-value: 1.55e-04
                         10        20
                 ....*....|....*....|....*...
gi 613253854 168 VVEMLEEGQAISKIAKEVNITRQTVYRI 195
Cdd:cd00569   14 ARRLLAAGESVAEIARELGVSRSTLYRY 41
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 167-194 2.60e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 37.91  E-value: 2.60e-03
                         10        20
                 ....*....|....*....|....*...
gi 613253854 167 RVVEMLEEGQAISKIAKEVNITRQTVYR 194
Cdd:COG3415   30 RAVLLLAEGLSVREIAERLGVSRSTVYR 57
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-135 1.83e-42

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: 139.15  E-value: 1.83e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   2 IVGYARVSSNDQNLERQLENLKTFC-AEKIFTEKQSGKSiENRPVLQEALNFLRMGDRFVVESIDRLGRNYDEVIHTVNY 80
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGK-KERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 613253854  81 LKDKEVQLMITSLPMMnevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQG 135
Cdd:cd03768   80 LREKGVSLRSLTEGID--------TSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-198 3.04e-40

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 140.93  E-value: 3.04e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   1 MIVGYARVSSNDQ---NLERQLENLKTFCAE------KIFTEK-QSGKSIEnRPVLQEALNFLRMG--DRFVVESIDRLG 68
Cdd:COG1961    3 RAAGYARVSTDDQeglSLERQREALRAYAEKagweivRIYVDEgVSGTSKD-RPGLQRLLADLRAGkfDTLVVWKLDRLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854  69 RNYDEVIHTVNYLKDKEVQLMITSLPMMnevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVYKGR 148
Cdd:COG1961   82 RNLADLLELVEELKERGVRLISLTEGID--------TSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGR 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854 149 PLL-YSPNAK---DPQKRVIYHRVVEMLEEGQAISKIAKEVN------ITRQTVYRIKNN 198
Cdd:COG1961  154 PPYgYRDPKKlviDEEEAEVVRRIFELYLEGKSLREIARELNergiptWSRSTVYRILKN 213
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 2-145 1.66e-32

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: 114.26  E-value: 1.66e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854     2 IVGYARVSSNDQ---NLERQLENLKTFCAEK------IFTEK-QSGKSIeNRPVLQEALNFLRMGD--RFVVESIDRLGR 69
Cdd:smart00857   1 AAGYARVSTDDQadgSLERQLEALRAYAERNgwevvrIYEDEgVSGKKA-DRPGLQRLLADLRAGDidVLVVYKLDRLGR 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613253854    70 NYDEVIHTVNYLKDKEVQLMITSLPMMNevvgnplLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVY 145
Cdd:smart00857  80 SLRDLLALLELLEEKGVRLVSLKEGILD-------TSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 2-145 2.52e-31

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: 111.21  E-value: 2.52e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854    2 IVGYARVSSNDQN--LERQLENLKTFCAEK----IFTEK-QSGKSiENRPVLQEALNFLRM--GDRFVVESIDRLGRNYD 72
Cdd:pfam00239   1 AIGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRK-LDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLR 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613253854   73 EVIHTVNYLKDKEVQLMITSlpmmnevvGNPLLDKFMKDLIIQILAMVSEQERNESKRRQAQGIQVAKEKGVY 145
Cdd:pfam00239  80 DLLTLVEELREKGVDLVSLD--------EGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-135 8.62e-20

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: 81.15  E-value: 8.62e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   5 YARVSSNDQN----LERQLENLKTFCAE------KIFTEKQ-SGKSIENRPVLQEALNFLRMG--DRFVVESIDRLGRNY 71
Cdd:cd00338    2 YARVSTDKQEqgdsLERQREALREYAARnglevvGEYEDAGsSATSLVDRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613253854  72 DEVIHTVNYLKDKEVQLMItslpmMNEVVGnplLDKFMKDLIIQILAMVSEQERNESKRRQAQG 135
Cdd:cd00338   82 VDLLELLELLEAHGVRVVT-----ADGEID---LDSEDGRLMLGILAAMAEEESKLISERTKRG 137
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 2-135 2.78e-16

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: 72.36  E-value: 2.78e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   2 IVGYARVSSNDQNLERQLENLKTFCAEK------IFTEKQSGKSIEnRPVLQEALNFLRMGDRFVVESIDRLGR-NYDEV 74
Cdd:cd03767    1 IRAYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLD-RPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDW 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 613253854  75 IHTVNYLKDKEVQLMITSLPMMNEVVGN--PLLDKFMK----DLIIQILAMVSEQERNESKRRQAQG 135
Cdd:cd03767   80 ETLKASIAAKGLRVVSLDLPTSHSALAAedNDFTGRILsainDMLLDLLAAMARKDYEDRRERQKQG 146
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-201 1.11e-15

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 72.06  E-value: 1.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   1 MIVGYARVSSNDQNLERQLENLKTFCAEKIFT------EKQSG-KSIENRPvLQEALNFLRMGDRFVVESIDRLGRNYDE 73
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGtKSYKDRK-LGKLLKKMRKGDILIVSELSRLGRNLME 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854  74 VIHTVNYLKDKEVQLMITSlpmMNEVVGNplldkfmkDLIIQILA----MVSEQERNESKRRQAQGIQVAKEKGVYKGRP 149
Cdd:PRK13413  80 IMSILNICMEKEVIVYTIK---EGYELGD--------DINSKVLAfafgLSAEIERNLISQRTKEALARKKAEGVTLGRP 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 613253854 150 LLYSPNAKD--PQKRVIyhrvVEMLEEGQAISKIAKEVNITRQTVYRIKNNKGL 201
Cdd:PRK13413 149 KGSTPKKYKltGKEEKI----KKLLDKGTSKSEIARKLGVSRTTLARFLKTRGL 198
recomb_XisF NF041201
fdxN element excision recombinase XisF;
2-125 8.40e-13

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 66.14  E-value: 8.40e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613253854   2 IVGYARVSSNDQN-----LERQLENLKTFCAEKIFTEKQSGKSiENRPVLQEALNFLRMG--DRFVVESIDRLGRNYDEV 74
Cdd:NF041201   1 IVGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRS-DKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTI 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 613253854  75 IHTVNYLKDKEVQLMItsLPMMNEVVGNPlLDKFMkdliIQILAMVSEQER 125
Cdd:NF041201  80 YKAIEVLQKKGVKLVI--LDAPLDDLSSP-GGWFT----INQLAALAEFES 123
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
147-197 8.03e-10

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 52.36  E-value: 8.03e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 613253854  147 GRPLLYSPNAkdpqkrviYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKN 197
Cdd:pfam02796   1 GRPPKLNEED--------INEVITLLEEGISIKQIAKIFGISRSTVYRYLA 43
transpos_IS607 NF033518
IS607 family transposase;
2-69 3.22e-09

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 54.18  E-value: 3.22e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613253854   2 IVGYARVSSNDQ--NLERQLENLKTFCAEK------IFTEKQSGKSiENRPVLQEALNFLRMGD--RFVVESIDRLGR 69
Cdd:NF033518  56 TVIYARVSSADQkdDLERQVARLTQYATAKgwqvdeVVTDIGSGLN-EKRKGLLKLLDDILNGEvsRVVVEHKDRLTR 132
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 2-69 1.11e-08

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: 51.49  E-value: 1.11e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 613253854   2 IVGYARVSSNDQ--NLERQLENLKTFCAEK-----IFTEKQSGKSiENRPVLQEALNFLRMG--DRFVVESIDRLGR 69
Cdd:cd03769    1 TVLYARVSSHDQkdDLERQIERLEAYATAQgwiveVIKDIGSGLN-EKRKGLLKLLEDVLAGkvERVVITYKDRLAR 76
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
2-69 2.46e-08

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 51.53  E-value: 2.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 613253854   2 IVGYARVSSNDQ--NLERQLENLKTFCAEK-----IFTEKQSGKSiENRPVLQEALNFLRMgDRFVVESIDRLGR 69
Cdd:COG2452   50 TVIYARVSSADQkdDLERQVERLEEYATAKgyqdeVIKDVGSGLN-YKRKGLLKLLERIEV-ERVVVEHKDRLAR 122
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 168-195 1.55e-04

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: 37.69  E-value: 1.55e-04
                         10        20
                 ....*....|....*....|....*...
gi 613253854 168 VVEMLEEGQAISKIAKEVNITRQTVYRI 195
Cdd:cd00569   14 ARRLLAAGESVAEIARELGVSRSTLYRY 41
HTH_23 pfam13384
Homeodomain-like domain;
167-198 5.78e-04

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 36.48  E-value: 5.78e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 613253854  167 RVVEMLEEGQAISKIAKEVNITRQTVYRIKNN 198
Cdd:pfam13384   9 RALLLLAEGLSVKEIAELLGVSRRTVYRWLKR 40
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 167-194 2.60e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 37.91  E-value: 2.60e-03
                         10        20
                 ....*....|....*....|....*...
gi 613253854 167 RVVEMLEEGQAISKIAKEVNITRQTVYR 194
Cdd:COG3415   30 RAVLLLAEGLSVREIAERLGVSRSTVYR 57
 
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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