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Conserved domains on  [gi|1398205099|ref|WP_110233175|]
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recombinase family protein [Aurantimicrobium photophilum]

Protein Classification

recombinase family protein( domain architecture ID 10132968)

recombinase family protein is a serine recombinase that catalyzes the site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme

CATH:  3.40.50.1390
Gene Ontology:  GO:0000150|GO:0003677|GO:0006310|GO:0015074
PubMed:  21645851|26104451|11972771|16077726|9348666
SCOP:  3000065

Graphical summary

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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 ...
 5-129 5.44e-56

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: 172.66  E-value: 5.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQNLESQSDALKAAG-ADKIFVEKITGTKASRPELDKVKEQLREGDTLVITRMDRLGRSAKDLLNIVSEL 83
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1398205099  84 DALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDG 129
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-183 3.33e-12

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: 58.11  E-value: 3.33e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1398205099 141 GRKPKMTPARAAEAERLYkEKNMTVQEIADIFGVSRPTIYRAV 183
Cdd:cd00569     1 GRPPKLTPEQIAEARRLL-AAGESVAEIARELGVSRSTLYRYL 42
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-129 5.44e-56

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: 172.66  E-value: 5.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQNLESQSDALKAAG-ADKIFVEKITGTKASRPELDKVKEQLREGDTLVITRMDRLGRSAKDLLNIVSEL 83
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1398205099  84 DALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDG 129
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-184 7.04e-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: 7.04e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   4 RRIGYGRVSTLDQ---NLESQSDALKA----AGAD--KIFVEK-ITGTKASRPELDKVKEQLREG--DTLVITRMDRLGR 71
Cdd:COG1961     3 RAAGYARVSTDDQeglSLERQREALRAyaekAGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099  72 SAKDLLNIVSELDALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGRVGGRKP------- 144
Cdd:COG1961    83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPygyrdpk 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1398205099 145 --KMTPARAAEAERLYKE--KNMTVQEIADIF---GV---SRPTIYRAVA 184
Cdd:COG1961   163 klVIDEEEAEVVRRIFELylEGKSLREIARELnerGIptwSRSTVYRILK 212
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 5-139 1.33e-44

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: 144.72  E-value: 1.33e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQN--LESQSDALKAAGADK----IFVEK-ITGTKASRPELDKVKEQLRE--GDTLVITRMDRLGRSAKD 75
Cdd:pfam00239   1 AIGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRD 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1398205099  76 LLNIVSELDALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGRV 139
Cdd:pfam00239  81 LLTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-138 1.18e-37

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: 126.97  E-value: 1.18e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099    6 IGYGRVSTLDQ---NLESQSDALKAAGA------DKIFVEK-ITGTKASRPELDKVKEQLREGD--TLVITRMDRLGRSA 73
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYAErngwevVRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1398205099   74 KDLLNIVSELDALGVDLEIIEQNI-DTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGR 138
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
recomb_XisF NF041201
fdxN element excision recombinase XisF;
5-172 2.58e-27

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 106.58  E-value: 2.58e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQN-----LESQSDALKAAGADKIFVEKITGTKASRPELDKVKEQLREG--DTLVITRMDRLGRSAKDLL 77
Cdd:NF041201    1 IVGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099  78 NIVSELDALGVDLEIIEQ-NIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGRVGGRKP---KMTPARAAE 153
Cdd:NF041201   81 KAIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPPfgyVRIDDKYAP 160

                         170       180
                  ....*....|....*....|...
gi 1398205099 154 AERLYKEKNMTVQEIA----DIF 172
Cdd:NF041201  161 DCLLYDKSELTVWEIAreiiEIF 183
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
6-181 2.52e-14

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 67.82  E-value: 2.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   6 IGYGRVSTLDQNLESQSDAL------KAAGADKIFVEKITGTKASRP-ELDKVKEQLREGDTLVITRMDRLGRsakDLLN 78
Cdd:PRK13413    3 YAYIRVSTDKQTVENQRFEItnfaekNNLTIDKWIEETISGTKSYKDrKLGKLLKKMRKGDILIVSELSRLGR---NLME 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099  79 IVSELDALgVDLEIIEQNIDTKTPEGKLFFTMVAGFA-----EFEHSMMVARTKDGLAAARAR----GRVGGRKPKMTPA 149
Cdd:PRK13413   80 IMSILNIC-MEKEVIVYTIKEGYELGDDINSKVLAFAfglsaEIERNLISQRTKEALARKKAEgvtlGRPKGSTPKKYKL 158

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1398205099 150 RAAEAE-RLYKEKNMTVQEIADIFGVSRPTIYR 181
Cdd:PRK13413  159 TGKEEKiKKLLDKGTSKSEIARKLGVSRTTLAR 191
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-183 3.33e-12

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: 58.11  E-value: 3.33e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1398205099 141 GRKPKMTPARAAEAERLYkEKNMTVQEIADIFGVSRPTIYRAV 183
Cdd:cd00569     1 GRPPKLTPEQIAEARRLL-AAGESVAEIARELGVSRSTLYRYL 42
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
141-181 1.64e-07

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 45.81  E-value: 1.64e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1398205099 141 GRKPKMTPARAAEAERLYKEKnMTVQEIADIFGVSRPTIYR 181
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEG-ISIKQIAKIFGISRSTVYR 40
transpos_IS630 NF033545
IS630 family transposase;
157-181 2.55e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 37.62  E-value: 2.55e-03
                          10        20
                  ....*....|....*....|....*
gi 1398205099 157 LYKEKNMTVQEIADIFGVSRPTIYR 181
Cdd:NF033545    7 LLAAEGLSITEIAERLGVSRSTVYR 31
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
131-187 2.76e-03

Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];


Pssm-ID: 440498  Cd Length: 140  Bit Score: 36.47  E-value: 2.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1398205099 131 AAARARGRVGGRKPKMTPARAAEAERLYKEKN-MTVQEIADIF-----GVSRPTIYRAVAQLT 187
Cdd:COG0735     3 ALEEAEELLREAGLRLTPQRLAILELLLESDRhLSAEEIYEALrkkgpSISLATVYRTLDLLV 65
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 148-186 3.52e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.56  E-value: 3.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1398205099 148 PARAAEAERLYKEKNMTVQEIADIFGVSRPTI----YRAVAQL 186
Cdd:TIGR02937 112 PEREREVLVLRYLEGLSYKEIAEILGISVGTVkrrlKRARKKL 154
transpos_IS481 NF033577
IS481 family transposase; null
 156-181 6.35e-03

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 36.42  E-value: 6.35e-03
                          10        20
                  ....*....|....*....|....*.
gi 1398205099 156 RLYKEKNMTVQEIADIFGVSRPTIYR 181
Cdd:NF033577    7 RLVLEDGWSVREAARRFGISRKTVYK 32
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-129 5.44e-56

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: 172.66  E-value: 5.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQNLESQSDALKAAG-ADKIFVEKITGTKASRPELDKVKEQLREGDTLVITRMDRLGRSAKDLLNIVSEL 83
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1398205099  84 DALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDG 129
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-184 7.04e-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: 7.04e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   4 RRIGYGRVSTLDQ---NLESQSDALKA----AGAD--KIFVEK-ITGTKASRPELDKVKEQLREG--DTLVITRMDRLGR 71
Cdd:COG1961     3 RAAGYARVSTDDQeglSLERQREALRAyaekAGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099  72 SAKDLLNIVSELDALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGRVGGRKP------- 144
Cdd:COG1961    83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPygyrdpk 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1398205099 145 --KMTPARAAEAERLYKE--KNMTVQEIADIF---GV---SRPTIYRAVA 184
Cdd:COG1961   163 klVIDEEEAEVVRRIFELylEGKSLREIARELnerGIptwSRSTVYRILK 212
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 5-139 1.33e-44

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: 144.72  E-value: 1.33e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQN--LESQSDALKAAGADK----IFVEK-ITGTKASRPELDKVKEQLRE--GDTLVITRMDRLGRSAKD 75
Cdd:pfam00239   1 AIGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRD 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1398205099  76 LLNIVSELDALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGRV 139
Cdd:pfam00239  81 LLTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-138 1.18e-37

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: 126.97  E-value: 1.18e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099    6 IGYGRVSTLDQ---NLESQSDALKAAGA------DKIFVEK-ITGTKASRPELDKVKEQLREGD--TLVITRMDRLGRSA 73
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYAErngwevVRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1398205099   74 KDLLNIVSELDALGVDLEIIEQNI-DTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGR 138
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
recomb_XisF NF041201
fdxN element excision recombinase XisF;
5-172 2.58e-27

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 106.58  E-value: 2.58e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   5 RIGYGRVSTLDQN-----LESQSDALKAAGADKIFVEKITGTKASRPELDKVKEQLREG--DTLVITRMDRLGRSAKDLL 77
Cdd:NF041201    1 IVGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099  78 NIVSELDALGVDLEIIEQ-NIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDGLAAARARGRVGGRKP---KMTPARAAE 153
Cdd:NF041201   81 KAIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPPfgyVRIDDKYAP 160

                         170       180
                  ....*....|....*....|...
gi 1398205099 154 AERLYKEKNMTVQEIA----DIF 172
Cdd:NF041201  161 DCLLYDKSELTVWEIAreiiEIF 183
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 8-129 1.74e-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: 82.69  E-value: 1.74e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   8 YGRVSTLDQN----LESQSDALKAAGA------DKIFVEKITG--TKASRPELDKVKEQLREG--DTLVITRMDRLGRSA 73
Cdd:cd00338     2 YARVSTDKQEqgdsLERQREALREYAArnglevVGEYEDAGSSatSLVDRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1398205099  74 KDLLNIVSELDALGVDLEIIEQNIDTKTPEGKLFFTMVAGFAEFEHSMMVARTKDG 129
Cdd:cd00338    82 VDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
6-181 2.52e-14

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 67.82  E-value: 2.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   6 IGYGRVSTLDQNLESQSDAL------KAAGADKIFVEKITGTKASRP-ELDKVKEQLREGDTLVITRMDRLGRsakDLLN 78
Cdd:PRK13413    3 YAYIRVSTDKQTVENQRFEItnfaekNNLTIDKWIEETISGTKSYKDrKLGKLLKKMRKGDILIVSELSRLGR---NLME 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099  79 IVSELDALgVDLEIIEQNIDTKTPEGKLFFTMVAGFA-----EFEHSMMVARTKDGLAAARAR----GRVGGRKPKMTPA 149
Cdd:PRK13413   80 IMSILNIC-MEKEVIVYTIKEGYELGDDINSKVLAFAfglsaEIERNLISQRTKEALARKKAEgvtlGRPKGSTPKKYKL 158

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1398205099 150 RAAEAE-RLYKEKNMTVQEIADIFGVSRPTIYR 181
Cdd:PRK13413  159 TGKEEKiKKLLDKGTSKSEIARKLGVSRTTLAR 191
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 141-183 3.33e-12

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: 58.11  E-value: 3.33e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1398205099 141 GRKPKMTPARAAEAERLYkEKNMTVQEIADIFGVSRPTIYRAV 183
Cdd:cd00569     1 GRPPKLTPEQIAEARRLL-AAGESVAEIARELGVSRSTLYRYL 42
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 7-88 2.65e-09

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: 53.10  E-value: 2.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   7 GYGRVSTLDQNLESQSDALKAAGADK------IFVEKITGTKASRPELDKVKEQLREGDTLVITRMDRLGR-SAKDLLNI 79
Cdd:cd03767     3 AYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWETL 82


                  ....*....
gi 1398205099  80 VSELDALGV 88
Cdd:cd03767    83 KASIAAKGL 91
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
141-181 1.64e-07

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 45.81  E-value: 1.64e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1398205099 141 GRKPKMTPARAAEAERLYKEKnMTVQEIADIFGVSRPTIYR 181
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEG-ISIKQIAKIFGISRSTVYR 40
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 6-103 1.11e-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: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1398205099   6 IGYGRVSTLDQ--NLESQSDALKAAGADKIFVEKITGTKAS-----RPELDKVKEQLREG--DTLVITRMDRLGRSAKDL 76
Cdd:cd03769     2 VLYARVSSHDQkdDLERQIERLEAYATAQGWIVEVIKDIGSglnekRKGLLKLLEDVLAGkvERVVITYKDRLARFGFEL 81

                          90       100
                  ....*....|....*....|....*..
gi 1398205099  77 LniVSELDALGVDLEIIEQNIDTKTPE 103
Cdd:cd03769    82 L--EELFKAYGVEIVVINQEENEELEQ 106
transpos_IS630 NF033545
IS630 family transposase;
157-181 2.55e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 37.62  E-value: 2.55e-03
                          10        20
                  ....*....|....*....|....*
gi 1398205099 157 LYKEKNMTVQEIADIFGVSRPTIYR 181
Cdd:NF033545    7 LLAAEGLSITEIAERLGVSRSTVYR 31
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 163-185 2.68e-03

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 34.74  E-value: 2.68e-03
                          10        20
                  ....*....|....*....|...
gi 1398205099 163 MTVQEIADIFGVSRPTIYRAVAQ 185
Cdd:pfam12728   2 LTVEEAAELLGVSRRTVYRLIRS 24
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 155-187 2.76e-03

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: 34.72  E-value: 2.76e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1398205099 155 ERLYKEK-NMTVQEIADIFGVSRPTIYRAVAQLT 187
Cdd:pfam08279   5 QLLLEARgPISGQELAEKLGVSRRTIRRDIKILE 38
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
131-187 2.76e-03

Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];


Pssm-ID: 440498  Cd Length: 140  Bit Score: 36.47  E-value: 2.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1398205099 131 AAARARGRVGGRKPKMTPARAAEAERLYKEKN-MTVQEIADIF-----GVSRPTIYRAVAQLT 187
Cdd:COG0735     3 ALEEAEELLREAGLRLTPQRLAILELLLESDRhLSAEEIYEALrkkgpSISLATVYRTLDLLV 65
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 148-186 3.52e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.56  E-value: 3.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1398205099 148 PARAAEAERLYKEKNMTVQEIADIFGVSRPTI----YRAVAQL 186
Cdd:TIGR02937 112 PEREREVLVLRYLEGLSYKEIAEILGISVGTVkrrlKRARKKL 154
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
150-186 3.53e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 37.03  E-value: 3.53e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1398205099 150 RAAeaeRLYKEKNMTVQEIADIFGVSRPTIYRAVAQL 186
Cdd:COG2390     1 RAA---WLYYVEGLTQREIAERLGISRRTVSRLLAEA 34
transpos_IS481 NF033577
IS481 family transposase; null
 156-181 6.35e-03

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 36.42  E-value: 6.35e-03
                          10        20
                  ....*....|....*....|....*.
gi 1398205099 156 RLYKEKNMTVQEIADIFGVSRPTIYR 181
Cdd:NF033577    7 RLVLEDGWSVREAARRFGISRKTVYK 32
HTH_23 pfam13384
Homeodomain-like domain;
156-185 6.50e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 33.40  E-value: 6.50e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1398205099 156 RLYKEKnMTVQEIADIFGVSRPTIYRAVAQ 185
Cdd:pfam13384  12 LLLAEG-LSVKEIAELLGVSRRTVYRWLKR 40
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
150-179 7.79e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 34.41  E-value: 7.79e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1398205099 150 RAAEAERLYKEkNMTVQEIADIFGVSRPTI 179
Cdd:COG2522    17 RALLAKELVER-GLSQSEIAKLLGITQAAV 45
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 155-186 8.67e-03

Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription];


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 35.82  E-value: 8.67e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1398205099 155 ERLYKEKNMTVQEIADIFGVSRPTIYRAVAQL 186
Cdd:COG2378    12 QLLQSRRGVTAAELAERLEVSERTIYRDIDAL 43
 
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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