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Conserved domains on  [gi|490200340|ref|WP_004098835|]
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MULTISPECIES: recombinase family protein [Enterobacteriaceae]

Protein Classification

recombinase family protein( domain architecture ID 18951323)

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:0015074|GO:0000150|GO:0003677|GO:0006310
PubMed:  11972771|16077726|9348666|21645851|26104451
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 ...
 3-129 5.53e-48

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: 152.63  E-value: 5.53e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   3 LFGYARVSTSQQSLDIQIRALKNAGvKANRIFTDKASGSSAAREGLELLRMKVEDGDVILVKKLDRLGRDTADMIQLIKE 82
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAG-ECDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490200340  83 FDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEG 129
Cdd:cd03768   80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 141-182 9.17e-07

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member pfam02796:

Pssm-ID: 481199 [Multi-domain]  Cd Length: 45  Bit Score: 43.88  E-value: 9.17e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 490200340  141 GRKRKIDRNKI---KFMHDKGTGATEIAKHMGIARSTVYKIINSE 182
Cdd:pfam02796   1 GRPPKLNEEDInevITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 3-129 5.53e-48

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: 152.63  E-value: 5.53e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   3 LFGYARVSTSQQSLDIQIRALKNAGvKANRIFTDKASGSSAAREGLELLRMKVEDGDVILVKKLDRLGRDTADMIQLIKE 82
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAG-ECDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490200340  83 FDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEG 129
Cdd:cd03768   80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-183 1.40e-44

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 151.72  E-value: 1.40e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   1 MRLFGYARVSTSQQ---SLDIQIRALKN----AGVKANRIFTDKA-SGSSAAREGLELLRMKVEDG--DVILVKKLDRLG 70
Cdd:COG1961    2 MRAAGYARVSTDDQeglSLERQREALRAyaekAGWEIVRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340  71 RDTADMIQLIKEFDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEGRIEAKSKGIKFGR-------K 143
Cdd:COG1961   82 RNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRppygyrdP 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 490200340 144 RKIDRN--------KIKFMHDKGTGATEIAKHM---GIA---RSTVYKIINSER 183
Cdd:COG1961  162 KKLVIDeeeaevvrRIFELYLEGKSLREIARELnerGIPtwsRSTVYRILKNPV 215
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 4-137 9.48e-40

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: 132.01  E-value: 9.48e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340    4 FGYARVSTSQQ--SLDIQIRALKNAGVKANRI--FTDK-ASGSSAAREGLELLRMKVED--GDVILVKKLDRLGRDTADM 76
Cdd:pfam00239   2 IGYARVSTEDQddSLERQLEALRAYAACNGKIveFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490200340   77 IQLIKEFDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEGRIEAKSKG 137
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARG 142
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 4-139 3.26e-35

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: 120.81  E-value: 3.26e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340     4 FGYARVSTSQQ---SLDIQIRALKNA----GVKANRIFTDKA-SGSSAAREGLELLRMKVEDGD--VILVKKLDRLGRDT 73
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWEVVRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490200340    74 ADMIQLIKEFDALGVAVRFIDDGIS-TDGEMGKMIVTILSAVAQAERTRIFERTNEGRIEAKSKGIK 139
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGILdTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
recomb_XisF NF041201
fdxN element excision recombinase XisF;
5-130 2.65e-20

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 87.32  E-value: 2.65e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   5 GYARVSTSQQ-----SLDIQIRALKNAGvkANRIFTDKASGSSAAREGL-ELLRMkVEDGDV--ILVKKLDRLGRDTADM 76
Cdd:NF041201   3 GYARVSTREQaddghALEQQIARLKKAG--ASEIFFDIESGRSDKRKGFnQLLKL-VKSGKVteIIITRIDRLTRSVVTI 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490200340  77 IQLIKEFDALGVAVRFIDDG-ISTDGEMGKMIVTILSAVAQAERTRIFERTNEGR 130
Cdd:NF041201  80 YKAIEVLQKKGVKLVILDAPlDDLSSPGGWFTINQLAALAEFESRLLSERVRHGL 134
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
3-181 6.79e-13

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 63.97  E-value: 6.79e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   3 LFGYARVSTSQQSLDIQ----IRALKNAGVKANRIFTDKASGSSAA--REGLELLRmKVEDGDVILVKKLDRLGRDTADM 76
Cdd:PRK13413   2 IYAYIRVSTDKQTVENQrfeiTNFAEKNNLTIDKWIEETISGTKSYkdRKLGKLLK-KMRKGDILIVSELSRLGRNLMEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340  77 IQLIKEFDALGVAVRFIDDGIstdgEMG-----KMIVTILSAVAQAERTRIFERTNEGRIEAKSKGIKFGRKR------- 144
Cdd:PRK13413  81 MSILNICMEKEVIVYTIKEGY----ELGddinsKVLAFAFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKgstpkky 156

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 490200340 145 --KIDRNKIKFMHDKGTGATEIAKHMGIARSTVYKIINS 181
Cdd:PRK13413 157 klTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKT 195
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
141-182 9.17e-07

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 43.88  E-value: 9.17e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 490200340  141 GRKRKIDRNKI---KFMHDKGTGATEIAKHMGIARSTVYKIINSE 182
Cdd:pfam02796   1 GRPPKLNEEDInevITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
transpos_IS607 NF033518
IS607 family transposase;
5-111 1.03e-06

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 46.86  E-value: 1.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   5 GYARVSTSQQ--SLDIQIRALKN----AGVKANRIFTDKASGSSAAREGLELLRMKVEDGDV--ILVKKLDRLGRDTADM 76
Cdd:NF033518  58 IYARVSSADQkdDLERQVARLTQyataKGWQVDEVVTDIGSGLNEKRKGLLKLLDDILNGEVsrVVVEHKDRLTRFGFEY 137

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490200340  77 IQLIkeFDALGVAVRFI-DDGISTDGEMGKMIVTIL 111
Cdd:NF033518 138 LEAL--FKANGVEIVVVnEDEKSPEEELVEDLIEIL 171
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-179 1.11e-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: 38.08  E-value: 1.11e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 490200340 141 GRKRKI---DRNKIKFMHDKGTGATEIAKHMGIARSTVYKII 179
Cdd:cd00569    1 GRPPKLtpeQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
147-180 3.57e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 37.17  E-value: 3.57e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 490200340 147 DRNKIKFMHDKGTGATEIAKHMGIARSTVYKIIN 180
Cdd:COG2826   11 EREEIEALLKAGLSVREIARRLGRSPSTISRELK 44
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 3-129 5.53e-48

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: 152.63  E-value: 5.53e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   3 LFGYARVSTSQQSLDIQIRALKNAGvKANRIFTDKASGSSAAREGLELLRMKVEDGDVILVKKLDRLGRDTADMIQLIKE 82
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAG-ECDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490200340  83 FDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEG 129
Cdd:cd03768   80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-183 1.40e-44

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 151.72  E-value: 1.40e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   1 MRLFGYARVSTSQQ---SLDIQIRALKN----AGVKANRIFTDKA-SGSSAAREGLELLRMKVEDG--DVILVKKLDRLG 70
Cdd:COG1961    2 MRAAGYARVSTDDQeglSLERQREALRAyaekAGWEIVRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340  71 RDTADMIQLIKEFDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEGRIEAKSKGIKFGR-------K 143
Cdd:COG1961   82 RNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRppygyrdP 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 490200340 144 RKIDRN--------KIKFMHDKGTGATEIAKHM---GIA---RSTVYKIINSER 183
Cdd:COG1961  162 KKLVIDeeeaevvrRIFELYLEGKSLREIARELnerGIPtwsRSTVYRILKNPV 215
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 4-137 9.48e-40

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: 132.01  E-value: 9.48e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340    4 FGYARVSTSQQ--SLDIQIRALKNAGVKANRI--FTDK-ASGSSAAREGLELLRMKVED--GDVILVKKLDRLGRDTADM 76
Cdd:pfam00239   2 IGYARVSTEDQddSLERQLEALRAYAACNGKIveFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490200340   77 IQLIKEFDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEGRIEAKSKG 137
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARG 142
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 4-139 3.26e-35

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: 120.81  E-value: 3.26e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340     4 FGYARVSTSQQ---SLDIQIRALKNA----GVKANRIFTDKA-SGSSAAREGLELLRMKVEDGD--VILVKKLDRLGRDT 73
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWEVVRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490200340    74 ADMIQLIKEFDALGVAVRFIDDGIS-TDGEMGKMIVTILSAVAQAERTRIFERTNEGRIEAKSKGIK 139
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGILdTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 6-129 9.38e-27

Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium.


Pssm-ID: 238206 [Multi-domain]  Cd Length: 137  Bit Score: 98.87  E-value: 9.38e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   6 YARVSTSQQ----SLDIQIRALKNA----GVKANRIFTDKASGSSAA--REGLELLRMKVEDG--DVILVKKLDRLGRDT 73
Cdd:cd00338    2 YARVSTDKQeqgdSLERQREALREYaarnGLEVVGEYEDAGSSATSLvdRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490200340  74 ADMIQLIKEFDALGVAVRFIDDGISTDGEMGKMIVTILSAVAQAERTRIFERTNEG 129
Cdd:cd00338   82 VDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
recomb_XisF NF041201
fdxN element excision recombinase XisF;
5-130 2.65e-20

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 87.32  E-value: 2.65e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   5 GYARVSTSQQ-----SLDIQIRALKNAGvkANRIFTDKASGSSAAREGL-ELLRMkVEDGDV--ILVKKLDRLGRDTADM 76
Cdd:NF041201   3 GYARVSTREQaddghALEQQIARLKKAG--ASEIFFDIESGRSDKRKGFnQLLKL-VKSGKVteIIITRIDRLTRSVVTI 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490200340  77 IQLIKEFDALGVAVRFIDDG-ISTDGEMGKMIVTILSAVAQAERTRIFERTNEGR 130
Cdd:NF041201  80 YKAIEVLQKKGVKLVILDAPlDDLSSPGGWFTINQLAALAEFESRLLSERVRHGL 134
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
3-181 6.79e-13

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 63.97  E-value: 6.79e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   3 LFGYARVSTSQQSLDIQ----IRALKNAGVKANRIFTDKASGSSAA--REGLELLRmKVEDGDVILVKKLDRLGRDTADM 76
Cdd:PRK13413   2 IYAYIRVSTDKQTVENQrfeiTNFAEKNNLTIDKWIEETISGTKSYkdRKLGKLLK-KMRKGDILIVSELSRLGRNLMEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340  77 IQLIKEFDALGVAVRFIDDGIstdgEMG-----KMIVTILSAVAQAERTRIFERTNEGRIEAKSKGIKFGRKR------- 144
Cdd:PRK13413  81 MSILNICMEKEVIVYTIKEGY----ELGddinsKVLAFAFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKgstpkky 156

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 490200340 145 --KIDRNKIKFMHDKGTGATEIAKHMGIARSTVYKIINS 181
Cdd:PRK13413 157 klTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKT 195
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
141-182 9.17e-07

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 43.88  E-value: 9.17e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 490200340  141 GRKRKIDRNKI---KFMHDKGTGATEIAKHMGIARSTVYKIINSE 182
Cdd:pfam02796   1 GRPPKLNEEDInevITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
transpos_IS607 NF033518
IS607 family transposase;
5-111 1.03e-06

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 46.86  E-value: 1.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   5 GYARVSTSQQ--SLDIQIRALKN----AGVKANRIFTDKASGSSAAREGLELLRMKVEDGDV--ILVKKLDRLGRDTADM 76
Cdd:NF033518  58 IYARVSSADQkdDLERQVARLTQyataKGWQVDEVVTDIGSGLNEKRKGLLKLLDDILNGEVsrVVVEHKDRLTRFGFEY 137

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490200340  77 IQLIkeFDALGVAVRFI-DDGISTDGEMGKMIVTIL 111
Cdd:NF033518 138 LEAL--FKANGVEIVVVnEDEKSPEEELVEDLIEIL 171
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 5-115 1.18e-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: 45.72  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   5 GYARVSTSQQSLDI--QIRALKN---AGVKANRIFTDKASGSSAAREGLELLRMKVEDGDV--ILVKKLDRLGRDTADMI 77
Cdd:cd03769    3 LYARVSSHDQKDDLerQIERLEAyatAQGWIVEVIKDIGSGLNEKRKGLLKLLEDVLAGKVerVVITYKDRLARFGFELL 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 490200340  78 QLIkeFDALGVAVRFIDDG--ISTDGEMGKMIVTILSAVA 115
Cdd:cd03769   83 EEL--FKAYGVEIVVINQEenEELEQELVEDLIEIITSFS 120
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 5-90 7.88e-06

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: 43.85  E-value: 7.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   5 GYARVSTSQQSLDIQIRAL----KNAGVKANRIFTDKASGSSAAREGLELLRMKVEDGDVILVKKLDRLGR-DTADMIQL 79
Cdd:cd03767    3 AYLRASTDEQDATRAKESLeafaTERGFYIAGFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWETL 82

                         90
                 ....*....|.
gi 490200340  80 IKEFDALGVAV 90
Cdd:cd03767   83 KASIAAKGLRV 93
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
2-113 1.86e-05

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 43.06  E-value: 1.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340   2 RLFGYARVSTSQQ--SLDIQIRALKNAGVKAN---RIFTDKASGSSAAREGLELLRMKVEDGDVILVKKlDRLGRDTADM 76
Cdd:COG2452   49 RTVIYARVSSADQkdDLERQVERLEEYATAKGyqdEVIKDVGSGLNYKRKGLLKLLERIEVERVVVEHK-DRLARFGFEL 127

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490200340  77 IQLIkeFDALGVAVRFIDDGISTDGEMGKM--IVTILSA 113
Cdd:COG2452  128 LEAL--CEAYGVEIVVVNQESPEQELVEDLiaIITSFSA 164
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 24-99 7.31e-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: 40.81  E-value: 7.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200340  24 KNAGVKANRIFTDKA-SGSSAAREGLELLRMKVEDG--DVILVKKLDRLGRDTADMIQLIKE-FDALGVAVRFIDDGIST 99
Cdd:cd03770   32 KENGLENIRHYIDDGfSGTTFDRPGFNRMIEDIEAGkiDIVIVKDMSRLGRNYLKVGLYMEIlFPKKGVRFIAINDGVDS 111
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-179 1.11e-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: 38.08  E-value: 1.11e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 490200340 141 GRKRKI---DRNKIKFMHDKGTGATEIAKHMGIARSTVYKII 179
Cdd:cd00569    1 GRPPKLtpeQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
147-180 3.57e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 37.17  E-value: 3.57e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 490200340 147 DRNKIKFMHDKGTGATEIAKHMGIARSTVYKIIN 180
Cdd:COG2826   11 EREEIEALLKAGLSVREIARRLGRSPSTISRELK 44
 
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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