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Conserved domains on  [gi|2321158271|ref|WP_263972598|]
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MULTISPECIES: recombinase family protein [Pseudoalteromonas]

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 ...
 16-140 1.60e-58

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


:

Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 179.98  E-value: 1.60e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  16 KIGYARVSSTGQSLEVQLDKLNQVG-CDKIYHEKQSGKTAARPEFQKCMNYLREGDTFVITRLDRLARSVIHLSQVAERF 94
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2321158271  95 QAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEG 140
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 152-196 8.22e-06

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: 41.57  E-value: 8.22e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2321158271 152 GRPTKRTDEIDLEIYNKRKEGVPIGQLAKDYDLGSATIYRILNDV 196
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 ...
 16-140 1.60e-58

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 179.98  E-value: 1.60e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  16 KIGYARVSSTGQSLEVQLDKLNQVG-CDKIYHEKQSGKTAARPEFQKCMNYLREGDTFVITRLDRLARSVIHLSQVAERF 94
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2321158271  95 QAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEG 140
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 13-194 4.60e-49

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 164.43  E-value: 4.60e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  13 KMSKIGYARVSSTGQ---SLEVQLDKL------NQVGCDKIYHEK-QSGKTAARPEFQKCMNYLREG--DTFVITRLDRL 80
Cdd:COG1961     1 MMRAAGYARVSTDDQeglSLERQREALrayaekAGWEIVRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  81 ARSVIHLSQVAERFQAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVKFGRP-----T 155
Cdd:COG1961    81 GRNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPpygyrD 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2321158271 156 KRTDEID-------LEIYNKRKEGVPIGQLAKDYD------LGSATIYRILN 194
Cdd:COG1961   161 PKKLVIDeeeaevvRRIFELYLEGKSLREIARELNergiptWSRSTVYRILK 212
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 17-150 7.06e-47

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: 151.27  E-value: 7.06e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQ--SLEVQLDKLNQVGCDK----IYHEK-QSGKTAARPEFQKCMNYLRE--GDTFVITRLDRLARSVIHL 87
Cdd:pfam00239   2 IGYARVSTEDQddSLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2321158271  88 SQVAERFQAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVK 150
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 17-150 4.78e-40

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 133.90  E-value: 4.78e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271   17 IGYARVSSTGQ---SLEVQLDKL----NQVGC--DKIYHEK-QSGKTAARPEFQKCMNYLREGD--TFVITRLDRLARSV 84
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALrayaERNGWevVRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2321158271   85 IHLSQVAERFQAENIDLVVIDQAI-DTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVK 150
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
recomb_XisF NF041201
fdxN element excision recombinase XisF;
16-199 1.48e-34

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 127.39  E-value: 1.48e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  16 KIGYARVSSTGQ-----SLEVQLDKLNQVGCDKIYHEKQSGKTAARPEFQKCMNYLREG--DTFVITRLDRLARSVIHLS 88
Cdd:NF041201    1 IVGYARVSTREQaddghALEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  89 QVAERFQAENIDLVVIDQ-AIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVKFGRPT---KRTDE---I 161
Cdd:NF041201   81 KAIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPPfgyVRIDDkyaP 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2321158271 162 DLEIYNKRkeGVPIGQLAK---DYDLGSATIYRILNDVFEK 199
Cdd:NF041201  161 DCLLYDKS--ELTVWEIAReiiEIFLENGSLRGTCRYLNEK 199
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
17-171 6.80e-08

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 50.87  E-value: 6.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQSLEVQ------LDKLNQVGCDKIYHEKQSG-KTAARPEFQKCMNYLREGDTFVITRLDRLAR------S 83
Cdd:PRK13413    3 YAYIRVSTDKQTVENQrfeitnFAEKNNLTIDKWIEETISGtKSYKDRKLGKLLKKMRKGDILIVSELSRLGRnlmeimS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  84 VIH--------LSQVAERFQ-AENIDLVVIDQAIDTStptgrlmfnmlaaiAEFETDLRSERQLEGIAKAKEHGVKFGRP 154
Cdd:PRK13413   83 ILNicmekeviVYTIKEGYElGDDINSKVLAFAFGLS--------------AEIERNLISQRTKEALARKKAEGVTLGRP 148

                         170
                  ....*....|....*..
gi 2321158271 155 TKRTDEIdLEIYNKRKE 171
Cdd:PRK13413  149 KGSTPKK-YKLTGKEEK 164
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
152-196 8.22e-06

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 41.57  E-value: 8.22e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2321158271 152 GRPTKRTDEIDLEIYNKRKEGVPIGQLAKDYDLGSATIYRILNDV 196
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
transpos_IS607 NF033518
IS607 family transposase;
17-106 8.95e-05

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 41.47  E-value: 8.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQ--SLEVQLDKL------NQVGCDKIYHEKQSGKTAARPEFQKCMNYLREGD--TFVITRLDRLARSVIH 86
Cdd:NF033518   57 VIYARVSSADQkdDLERQVARLtqyataKGWQVDEVVTDIGSGLNEKRKGLLKLLDDILNGEvsRVVVEHKDRLTRFGFE 136

                          90       100
                  ....*....|....*....|
gi 2321158271  87 LsqVAERFQAENIDLVVIDQ 106
Cdd:NF033518  137 Y--LEALFKANGVEIVVVNE 154
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 152-193 1.71e-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: 1.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2321158271 152 GRPTKRTDEIDLEIYNKRKEGVPIGQLAKDYDLGSATIYRIL 193
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
PLN00158 PLN00158
histone H2B; Provisional
 142-208 4.59e-04

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 38.52  E-value: 4.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2321158271 142 AKAKEHGVKFGRPTKRTDEIDLEIYNKRKEGVPIGQLAKDydlGSATIYRILNDVFEKVSTEATKLS 208
Cdd:PLN00158   10 AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSK---AMSIMNSFINDIFEKIATEAGKLA 73
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 16-140 1.60e-58

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 179.98  E-value: 1.60e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  16 KIGYARVSSTGQSLEVQLDKLNQVG-CDKIYHEKQSGKTAARPEFQKCMNYLREGDTFVITRLDRLARSVIHLSQVAERF 94
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2321158271  95 QAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEG 140
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 13-194 4.60e-49

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 164.43  E-value: 4.60e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  13 KMSKIGYARVSSTGQ---SLEVQLDKL------NQVGCDKIYHEK-QSGKTAARPEFQKCMNYLREG--DTFVITRLDRL 80
Cdd:COG1961     1 MMRAAGYARVSTDDQeglSLERQREALrayaekAGWEIVRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  81 ARSVIHLSQVAERFQAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVKFGRP-----T 155
Cdd:COG1961    81 GRNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPpygyrD 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2321158271 156 KRTDEID-------LEIYNKRKEGVPIGQLAKDYD------LGSATIYRILN 194
Cdd:COG1961   161 PKKLVIDeeeaevvRRIFELYLEGKSLREIARELNergiptWSRSTVYRILK 212
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 17-150 7.06e-47

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: 151.27  E-value: 7.06e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQ--SLEVQLDKLNQVGCDK----IYHEK-QSGKTAARPEFQKCMNYLRE--GDTFVITRLDRLARSVIHL 87
Cdd:pfam00239   2 IGYARVSTEDQddSLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2321158271  88 SQVAERFQAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVK 150
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 17-150 4.78e-40

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 133.90  E-value: 4.78e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271   17 IGYARVSSTGQ---SLEVQLDKL----NQVGC--DKIYHEK-QSGKTAARPEFQKCMNYLREGD--TFVITRLDRLARSV 84
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALrayaERNGWevVRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2321158271   85 IHLSQVAERFQAENIDLVVIDQAI-DTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVK 150
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
recomb_XisF NF041201
fdxN element excision recombinase XisF;
16-199 1.48e-34

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 127.39  E-value: 1.48e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  16 KIGYARVSSTGQ-----SLEVQLDKLNQVGCDKIYHEKQSGKTAARPEFQKCMNYLREG--DTFVITRLDRLARSVIHLS 88
Cdd:NF041201    1 IVGYARVSTREQaddghALEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  89 QVAERFQAENIDLVVIDQ-AIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEGIAKAKEHGVKFGRPT---KRTDE---I 161
Cdd:NF041201   81 KAIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPPfgyVRIDDkyaP 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2321158271 162 DLEIYNKRkeGVPIGQLAK---DYDLGSATIYRILNDVFEK 199
Cdd:NF041201  161 DCLLYDKS--ELTVWEIAReiiEIFLENGSLRGTCRYLNEK 199
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 19-140 2.18e-24

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: 93.48  E-value: 2.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  19 YARVSS----TGQSLEVQLDKL----NQVGCD--KIYHEKQSGKTAA--RPEFQKCMNYLREG--DTFVITRLDRLARSV 84
Cdd:cd00338     2 YARVSTdkqeQGDSLERQREALreyaARNGLEvvGEYEDAGSSATSLvdRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2321158271  85 IHLSQVAERFQAENIDLVVIDQAIDTSTPTGRLMFNMLAAIAEFETDLRSERQLEG 140
Cdd:cd00338    82 VDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
17-171 6.80e-08

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 50.87  E-value: 6.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQSLEVQ------LDKLNQVGCDKIYHEKQSG-KTAARPEFQKCMNYLREGDTFVITRLDRLAR------S 83
Cdd:PRK13413    3 YAYIRVSTDKQTVENQrfeitnFAEKNNLTIDKWIEETISGtKSYKDRKLGKLLKKMRKGDILIVSELSRLGRnlmeimS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  84 VIH--------LSQVAERFQ-AENIDLVVIDQAIDTStptgrlmfnmlaaiAEFETDLRSERQLEGIAKAKEHGVKFGRP 154
Cdd:PRK13413   83 ILNicmekeviVYTIKEGYElGDDINSKVLAFAFGLS--------------AEIERNLISQRTKEALARKKAEGVTLGRP 148

                         170
                  ....*....|....*..
gi 2321158271 155 TKRTDEIdLEIYNKRKE 171
Cdd:PRK13413  149 KGSTPKK-YKLTGKEEK 164
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 17-136 9.00e-07

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: 46.49  E-value: 9.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQS--LEVQLDKL-----NQVGCDKIYHEKQSGKTAARPEFQKCMNYLREG--DTFVITRLDRLARSVIHL 87
Cdd:cd03769     2 VLYARVSSHDQKddLERQIERLeayatAQGWIVEVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLARFGFEL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2321158271  88 sqVAERFQAENIDLVVIDQAIDTSTPTgRLMFNMLAAIAEFETDLRSER 136
Cdd:cd03769    82 --LEELFKAYGVEIVVINQEENEELEQ-ELVEDLIEIITSFSARLYGKR 127
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 18-140 1.22e-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: 46.16  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  18 GYARVSSTGQSLEVQLDKLNQVGCDK------IYHEKQSGKTAARPEFQKCMNYLREGDTFVITRLDRLARsvihLSQ-- 89
Cdd:cd03767     3 AYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSR----LPLdd 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2321158271  90 ---VAERFQAENIDLVVIDQAID----TSTPTG----------RLMFNMLAAIAEFETDLRSERQLEG 140
Cdd:cd03767    79 wetLKASIAAKGLRVVSLDLPTShsalAAEDNDftgrilsainDMLLDLLAAMARKDYEDRRERQKQG 146
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
152-196 8.22e-06

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 41.57  E-value: 8.22e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2321158271 152 GRPTKRTDEIDLEIYNKRKEGVPIGQLAKDYDLGSATIYRILNDV 196
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
transpos_IS607 NF033518
IS607 family transposase;
17-106 8.95e-05

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 41.47  E-value: 8.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQ--SLEVQLDKL------NQVGCDKIYHEKQSGKTAARPEFQKCMNYLREGD--TFVITRLDRLARSVIH 86
Cdd:NF033518   57 VIYARVSSADQkdDLERQVARLtqyataKGWQVDEVVTDIGSGLNEKRKGLLKLLDDILNGEvsRVVVEHKDRLTRFGFE 136

                          90       100
                  ....*....|....*....|
gi 2321158271  87 LsqVAERFQAENIDLVVIDQ 106
Cdd:NF033518  137 Y--LEALFKANGVEIVVVNE 154
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
17-106 1.25e-04

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 41.13  E-value: 1.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321158271  17 IGYARVSSTGQ--SLEVQLDKL-----NQVGCDKIYHEKQSGKTAARPEFQKCMNyLREGDTFVITRLDRLARSVIHLsq 89
Cdd:COG2452    51 VIYARVSSADQkdDLERQVERLeeyatAKGYQDEVIKDVGSGLNYKRKGLLKLLE-RIEVERVVVEHKDRLARFGFEL-- 127

                          90
                  ....*....|....*..
gi 2321158271  90 VAERFQAENIDLVVIDQ 106
Cdd:COG2452   128 LEALCEAYGVEIVVVNQ 144
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 152-193 1.71e-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: 1.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2321158271 152 GRPTKRTDEIDLEIYNKRKEGVPIGQLAKDYDLGSATIYRIL 193
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
PLN00158 PLN00158
histone H2B; Provisional
 142-208 4.59e-04

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 38.52  E-value: 4.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2321158271 142 AKAKEHGVKFGRPTKRTDEIDLEIYNKRKEGVPIGQLAKDydlGSATIYRILNDVFEKVSTEATKLS 208
Cdd:PLN00158   10 AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSK---AMSIMNSFINDIFEKIATEAGKLA 73
 
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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