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Conserved domains on  [gi|507031987|ref|WP_016103690|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Bacillus cereus group]

Protein Classification

site-specific integrase( domain architecture ID 332)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 10-184 8.86e-47

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


The actual alignment was detected with superfamily member cd01192:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 178  Bit Score: 151.29  E-value: 8.86e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  10 VQPIRSKEQIEDMKwALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIvklkrKKRKEFKIKEGKTKKERIINLTSIF 89
Cdd:cd01192    3 VEPIKDKKLIKEIK-LYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDV-----TNKDKLSIKEQKTGKQKTFPLNPTL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  90 -DEIYSYTQTLKST----WLFPSRKG-EQPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEIL 162
Cdd:cd01192   77 vKALKEYIDDLDLKrndyLFKSLKQGpEKPISRKQAYKILKKAADDLGLNyNIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170       180
                 ....*....|....*....|..
gi 507031987 163 NHSTPQITLKYIGINKEEKDNI 184
Cdd:cd01192  157 NHSSPSITLRYLGIDQEDVDKA 178
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 10-184 8.86e-47

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 151.29  E-value: 8.86e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  10 VQPIRSKEQIEDMKwALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIvklkrKKRKEFKIKEGKTKKERIINLTSIF 89
Cdd:cd01192    3 VEPIKDKKLIKEIK-LYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDV-----TNKDKLSIKEQKTGKQKTFPLNPTL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  90 -DEIYSYTQTLKST----WLFPSRKG-EQPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEIL 162
Cdd:cd01192   77 vKALKEYIDDLDLKrndyLFKSLKQGpEKPISRKQAYKILKKAADDLGLNyNIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170       180
                 ....*....|....*....|..
gi 507031987 163 NHSTPQITLKYIGINKEEKDNI 184
Cdd:cd01192  157 NHSSPSITLRYLGIDQEDVDKA 178
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
15-188 7.98e-27

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 103.15  E-value: 7.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  15 SKEQIEDMKWALKRH--CSERDYILFLFGIHTGLRVSDLLQietqtivkLKRK----KRKEFKIKEGKTKKERIINLTS- 87
Cdd:COG4974  114 TEEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSELLG--------LKWSdidlDRGTIRVRRGKGGKERTVPLSPe 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  88 ---IFDEIYSYTQTLKSTWLFPSRKGEqPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEILN 163
Cdd:COG4974  186 aleALREYLEERRPRDSDYLFPTRRGR-PLSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLG 264

                        170       180
                 ....*....|....*....|....*
gi 507031987 164 HSTPQITLKYIGINKEEKDNILDTF 188
Cdd:COG4974  265 HSSISTTQIYTHVSDEELREAVEKL 289
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 16-178 1.64e-20

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 83.52  E-value: 1.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   16 KEQIED-MKWALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIvklkRKKRKEFKIKEGKTKKERIINLTsifDEIYS 94
Cdd:pfam00589   4 EDEVERlLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDI----DFENGVIRVHRGKGNKERTVPLS---DAALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   95 YTQTL---------KSTWLFPSRKGeQPISKIQAYRQLQKAGDFASIES-IGTHTMRNTFGYWFYKQTKDVAMLQEILNH 164
Cdd:pfam00589  77 LLKEWlskrlleapKSDYLFASKRG-KPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGH 155

                         170
                  ....*....|....
gi 507031987  165 STPQITLKYIGINK 178
Cdd:pfam00589 156 SSISTTQIYTHVAD 169
PRK09871 PRK09871
tyrosine recombinase; Provisional
 1-186 1.05e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 63.46  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   1 MNKKPHLIdvqpirSKEQIEDMKWALKRHCSERDYILFLFGIHTGLRVSDLLQIETQtivklkrkkrkEFKIKEGKTKKE 80
Cdd:PRK09871   1 MSKRRYLT------GKEVQAMMQAVCYGATGARDYCLILLAYRHGMRISELLDLHYQ-----------DLDLNEGRINIR 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  81 RIINLTSI-----FDE---IYSYTQtLKSTW--------LFPSRKGeQPISKIQAYRQLQKAGDFA-SIESIGTHTMRNT 143
Cdd:PRK09871  64 RLKNGFSTvhplrFDEreaVERWTQ-ERANWkgadrtdaIFISRRG-SRLSRQQAYRIIRDAGIEAgTVTQTHPHMLRHA 141

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 507031987 144 FGYWFYKQTKDVAMLQEILNHSTPQITLKYIGINKE------EKDNILD 186
Cdd:PRK09871 142 CGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAArfaglwERNNLIN 190
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 10-184 8.86e-47

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 151.29  E-value: 8.86e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  10 VQPIRSKEQIEDMKwALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIvklkrKKRKEFKIKEGKTKKERIINLTSIF 89
Cdd:cd01192    3 VEPIKDKKLIKEIK-LYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDV-----TNKDKLSIKEQKTGKQKTFPLNPTL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  90 -DEIYSYTQTLKST----WLFPSRKG-EQPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEIL 162
Cdd:cd01192   77 vKALKEYIDDLDLKrndyLFKSLKQGpEKPISRKQAYKILKKAADDLGLNyNIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170       180
                 ....*....|....*....|..
gi 507031987 163 NHSTPQITLKYIGINKEEKDNI 184
Cdd:cd01192  157 NHSSPSITLRYLGIDQEDVDKA 178
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
15-188 7.98e-27

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 103.15  E-value: 7.98e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  15 SKEQIEDMKWALKRH--CSERDYILFLFGIHTGLRVSDLLQietqtivkLKRK----KRKEFKIKEGKTKKERIINLTS- 87
Cdd:COG4974  114 TEEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSELLG--------LKWSdidlDRGTIRVRRGKGGKERTVPLSPe 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  88 ---IFDEIYSYTQTLKSTWLFPSRKGEqPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEILN 163
Cdd:COG4974  186 aleALREYLEERRPRDSDYLFPTRRGR-PLSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLG 264

                        170       180
                 ....*....|....*....|....*
gi 507031987 164 HSTPQITLKYIGINKEEKDNILDTF 188
Cdd:COG4974  265 HSSISTTQIYTHVSDEELREAVEKL 289
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 16-178 1.64e-20

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 83.52  E-value: 1.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   16 KEQIED-MKWALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIvklkRKKRKEFKIKEGKTKKERIINLTsifDEIYS 94
Cdd:pfam00589   4 EDEVERlLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDI----DFENGVIRVHRGKGNKERTVPLS---DAALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   95 YTQTL---------KSTWLFPSRKGeQPISKIQAYRQLQKAGDFASIES-IGTHTMRNTFGYWFYKQTKDVAMLQEILNH 164
Cdd:pfam00589  77 LLKEWlskrlleapKSDYLFASKRG-KPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGH 155

                         170
                  ....*....|....
gi 507031987  165 STPQITLKYIGINK 178
Cdd:pfam00589 156 SSISTTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 33-174 1.61e-17

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 75.59  E-value: 1.61e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  33 RDYILFLFGIHTGLRVSDLLQIETQTIVKlkrkKRKEFKIKEGKTK--KERIINLTS-IFDEIYSYTQTLKSTW------ 103
Cdd:cd00397   18 RDRAILLLLLETGLRISELLALKVKDIDL----DNGTIRVRGKKTKggKERTVPLPKeLAEELKEYLKERRDKRgpllks 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507031987 104 -----LFPSRKGEQPISKiQAYRQLQKAGDFASIEsIGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLKYI 174
Cdd:cd00397   94 lylnkLFGTKLGERLSRR-TLRRIFKKAGIEAGRK-ITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
3-185 1.15e-15

Site-specific recombinase XerC [Replication, recombination and repair];


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 73.07  E-value: 1.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   3 KKPHLIDVQPIRskeQIEDMkwALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIvklkRKKRKEFKIKeGKTKKERI 82
Cdd:COG4973  107 KLPRALTVDELA---QLLDA--LADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDV----DLDAGEVRVR-GKTGKSRT 176

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  83 INLTS----IFDEIYSYTQTLK---STWLFPSRKGeQPISKIQAYRQLQKAGDFASIES-IGTHTMRNTFGYWFYKQTKD 154
Cdd:COG4973  177 VPLGPkalaALREWLAVRPELAapdEGALFPSRRG-TRLSPRNVQKRLRRLAKKAGLPKhVHPHDLRHSFATHLLESGGD 255

                        170       180       190
                 ....*....|....*....|....*....|.
gi 507031987 155 VAMLQEILNHSTPQITLKYIGINKEEKDNIL 185
Cdd:COG4973  256 LRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 37-181 2.31e-13

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 64.59  E-value: 2.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  37 LFLFGIHTGLRVSDLLQIETQTIVKLKRKKRKEFKIKegKTKKERIINLTSIFDEIY-SYTQTLKSTWLFPsrkgeqPIS 115
Cdd:cd01185   23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRK--KTGKPVTVPLLPVAREILeKYKDDRSEGKLFP------VLS 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 507031987 116 KIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLKYIGINKEEK 181
Cdd:cd01185   95 NQKINRYLKEIAKIAGIDkHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSKK 161
PRK09871 PRK09871
tyrosine recombinase; Provisional
 1-186 1.05e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 63.46  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   1 MNKKPHLIdvqpirSKEQIEDMKWALKRHCSERDYILFLFGIHTGLRVSDLLQIETQtivklkrkkrkEFKIKEGKTKKE 80
Cdd:PRK09871   1 MSKRRYLT------GKEVQAMMQAVCYGATGARDYCLILLAYRHGMRISELLDLHYQ-----------DLDLNEGRINIR 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  81 RIINLTSI-----FDE---IYSYTQtLKSTW--------LFPSRKGeQPISKIQAYRQLQKAGDFA-SIESIGTHTMRNT 143
Cdd:PRK09871  64 RLKNGFSTvhplrFDEreaVERWTQ-ERANWkgadrtdaIFISRRG-SRLSRQQAYRIIRDAGIEAgTVTQTHPHMLRHA 141

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 507031987 144 FGYWFYKQTKDVAMLQEILNHSTPQITLKYIGINKE------EKDNILD 186
Cdd:PRK09871 142 CGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAArfaglwERNNLIN 190
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 13-173 2.38e-11

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 59.26  E-value: 2.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  13 IRSKEQIEDMKWALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTIVKLKRKKRkefkIKEGKTKKERIINLTSIFDEI 92
Cdd:cd00796    4 FLTEDEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIV----LPETKNGKPRTVPLSDEAIAI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  93 YSYTQTLKSTWLFPSRKGEQPISKIQAYRQLQKAGDFASIESIGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLK 172
Cdd:cd00796   80 LKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMR 159


                 .
gi 507031987 173 Y 173
Cdd:cd00796  160 Y 160
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 1-184 9.76e-11

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 57.90  E-value: 9.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987   1 MNKKPHLIdvqpirSKEQIEDMKWALKRHCSERDYILFLFGIHTGLRVSDLLQIETQTiVKLKRKKRKEFKIKEGKTKKE 80
Cdd:cd01197    1 MKQRKYLT------GKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSD-VDLESRRLHIRRLKNGFSTTH 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  81 RIinltsIFDEIYSYTQTLK---------STWLFPSRKGeQPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYK 150
Cdd:cd01197   74 PL-----RFDEREALEAWLKeranwkgadTDWIFLSRRG-GPLSRQQAYRIIRDLGKEAGTVtQTHPHMLRHACGYALAD 147

                        170       180       190
                 ....*....|....*....|....*....|....
gi 507031987 151 QTKDVAMLQEILNHSTPQITLKYIGINKEEKDNI 184
Cdd:cd01197  148 RGADTRLIQDYLGHRNIRHTVIYTASNAARFANL 181
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 33-176 2.93e-10

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 56.48  E-value: 2.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  33 RDYILFLFGIHTGLRVSDllqietqtIVKLKRK----KRKEFKIKEGKTKKERIINLTS-IFDEIYSYTQ----TLKSTW 103
Cdd:cd01188   21 RDYAILLLLARLGLRAGD--------VAGLRLDdidwRSGTITVRQKKTGRPVELPLTEpVGEALADYLRdgrpRTDSRE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987 104 LFPSRK-------GEQPISKIQAyRQLQKAGdfasIESI--GTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLKYI 174
Cdd:cd01188   93 VFLRARapyrplsSTSQISSIVR-RYLRKAG----IEPShrGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYA 167


                 ..
gi 507031987 175 GI 176
Cdd:cd01188  168 KI 169
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 33-188 5.95e-08

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 50.35  E-value: 5.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  33 RDYILFLFGIHTGLRVSDLLQIetqTIVKLKRKKRKEFKIKeGKTKKERIINL----TSIF----DEIYSYTQTLKSTWL 104
Cdd:cd01182   22 RDHALLLLLYDTGARVQELADL---TIRDLRLDDPATVRLH-GKGRKERTVPLwketVAALkaylQEFHLTPDPKQLFPL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987 105 FPSRKGeQPISKIQAYRQLQKAGDFAS------IESIGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLKYIGINK 178
Cdd:cd01182   98 FPNRRG-QPLTRDGVAYILNKYVALASnrcpslPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEADL 176

                        170
                 ....*....|
gi 507031987 179 EEKDNILDTF 188
Cdd:cd01182  177 EMKREALEKA 186
PRK09870 PRK09870
tyrosine recombinase; Provisional
 33-177 9.82e-08

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 49.94  E-value: 9.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  33 RDYILFLFGIHTGLRVSDLLQIETQTIvKLKRKKRKEFKIKEGKTKKERIINltsifDEIYSYTQTLK---------STW 103
Cdd:PRK09870  33 RNYCLTLLCFIHGFRASEICRLRISDI-DLKAKCIYIHRLKKGFSTTHPLLN-----KEIQALKNWLSirtsyphaeSEW 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 507031987 104 LFPSRKGeQPISKIQAYRQLQKAGDFASIE-SIGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLKYIGIN 177
Cdd:PRK09870 107 VFLSRKG-NPLSRQQFYHIISTSGGNAGLSlEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASN 180
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 17-169 3.46e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 49.00  E-value: 3.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  17 EQIEDMKWAlkrhcSERDY-ILFLF-GihTGLRVSDLLQIetqTIVKLKRKKRkEFKIKeGKTKKERIINLTsifdeiyS 94
Cdd:PRK00236 126 DAIDEDDPL-----ALRDRaILELLyG--SGLRLSELVGL---DIDDLDLASG-TLRVL-GKGNKERTVPLG-------R 186

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  95 YTQTLKSTWL-------------FPSRKGeQPISKIQAYRQLQKAGDFASI-ESIGTHTMRNTFGYWFYKQTKDVAMLQE 160
Cdd:PRK00236 187 AAREALEAYLalrplflpdddalFLGARG-GRLSPRVVQRRVKKLGKKAGLpSHITPHKLRHSFATHLLESGGDLRAVQE 265

                        170
                 ....*....|..
gi 507031987 161 ILNH---STPQI 169
Cdd:PRK00236 266 LLGHaslSTTQI 277
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 15-173 1.21e-06

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 46.60  E-value: 1.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  15 SKEQIEDMKWALKRHCSE---RDYILFLFGIHTGLR--------VSDLLQIETQTIVKLKRKkrkefkikeGKTKKERII 83
Cdd:cd01194    2 TLEQARQLLASLPIDDSIiglRDRAIISLMVTEGLRtveivradVGDLRQEGEGTILYVQGK---------GKTSKDDFV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  84 NLTSIFDE-IYSYTQTLK----STWLFPS---RKGEQPISKIQAYRQLQKAGDFASIES--IGTHTMRNTFGYWFYKQTK 153
Cdd:cd01194   73 YLRPDVLKaLQAYLKARGkldfEEPLFTSlsnNSKGQRLTTRSIRRIIKKYLRKAGLDDdrLTAHSLRHTAGTLALKAGK 152

                        170       180
                 ....*....|....*....|
gi 507031987 154 DVAMLQEILNHSTPQITLKY 173
Cdd:cd01194  153 SLREVQQLLRHSDPNTTMIY 172
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 24-174 7.98e-06

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 43.87  E-value: 7.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  24 WALKRHCSERDYILFLFGIHTGLRVSDLLQIetqtivKLKRKKRKEFKIKEGKTKKERIINLTSIFDEIYSYTQTLK--- 100
Cdd:cd00800    4 AAIYAEAPPLLRLAMELALLTGQRQGDLLRL------KWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRIRALPrkr 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 507031987 101 STWLFPSRKGEQPISKI--QAYRQ-LQKAGDFASIESIGTHTMRNTFGYWFYKQTKDVAMlQEILNHSTPQITLKYI 174
Cdd:cd00800   78 SEYLINSRKGGPLSYDTlkSAWRRaRKAAGLKGETEGFTFHDLRAKAATDYAEQGGSTDA-QALLGHKSDAMTERYT 153
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 36-170 9.56e-06

Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 45.03  E-value: 9.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  36 ILFLFGIHTGLRVSDLLQIEtqtivklkrkkRKEFKIKEG---------KTKKERIINLTS----IFDEIYSYTQtlKST 102
Cdd:COG0582  229 LALRLLLLTGVRPGELRGAR-----------WSEIDLEAAlwtipaermKTRRPHIVPLSRqaleILKELKPLTG--DSE 295

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 507031987 103 WLFPSRKG-EQPISKIQAYRQLQKAGdfasIESIGTHTMRNTFGYWFYKQ--TKDVAMLQeiLNHSTPQIT 170
Cdd:COG0582  296 YVFPSRRGpKKPMSENTLNKALRRMG----YGRFTPHGFRHTASTLLNEAgfPPDVIERQ--LAHKDGNKV 360
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 33-188 2.88e-05

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.


Pssm-ID: 271180  Cd Length: 188  Bit Score: 42.67  E-value: 2.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  33 RDYILFLFGIHTGLRVSDL--LQIEtqtivKLKRKKRKEFKIKEGKTK-----KERIINLTsiFDEIYSYTQTLKStWLF 105
Cdd:cd00799   17 RDRALLLLGFAGALRRSELvaLRVE-----DLTRFVDGGLLIRLRRSKtdqdgEGEIKALP--YGPETCPVRALRA-WLE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987 106 PSRKGEQPI-SKIQAYRQLQkaGDFASIESI------------------GTHTMRNTFGYWFYKQTKDVAMLQEILNHST 166
Cdd:cd00799   89 AAGIPSGPLfRRIRRGGSVG--TTRLSDRSVarivkrraalagldpgdfSGHSLRRGFATEAARAGASLPEIMAQGGHKS 166

                        170       180
                 ....*....|....*....|..
gi 507031987 167 PQITLKYIGINKEEKDNILDTF 188
Cdd:cd00799  167 VATVMRYIREADRFKDNAAAKL 188
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 44-169 4.05e-05

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 42.11  E-value: 4.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  44 TGLRVSDLLQIETQTIvklkRKKRKEFKIKeGKTKKERIINLTSI--------FDEIYSYTQTLKSTW-LFPSRKGeQPI 114
Cdd:cd00798   31 SGLRVSELVGLDLSDV----DLDEGLVRVT-GKGNKERLVPFGSYavealeeyLEERRPLLLKKKPPDaLFLNKRG-KRL 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507031987 115 SKIQAYRQLQKAGDFASIES-IGTHTMRNTF-------GywfykqtKDVAMLQEILNH---STPQI 169
Cdd:cd00798  105 SRRGVWRILKKYAERAGLPKhVSPHTLRHSFathllegG-------ADLRVVQELLGHaslSTTQI 163
int PHA02601
integrase; Provisional
 15-173 1.07e-04

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 41.64  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  15 SKEQIEDMKWALKRHCSERDYILFLFGIHTGLRVSDllqietqtIVKLKRKKRKEFKIK--EGKTKKERIInltSIFDEI 92
Cdd:PHA02601 174 TKEEIERLLDACDGSRSPDLGLIAKICLATGARWSE--------AETLKRSQISPYKITfvKTKGKKNRTV---PISEEL 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  93 YSYTQTlKSTWLFPSrkgeqpiskiqAYRQLQKAGDFASIE---SIGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQI 169
Cdd:PHA02601 243 YKMLPK-RRGRLFKD-----------AYESFERAVKRAGIDlpeGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEM 310


                 ....
gi 507031987 170 TLKY 173
Cdd:PHA02601 311 TMAY 314
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 32-173 1.76e-04

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 40.34  E-value: 1.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  32 ERDYILFLFGihTGLRVSDLLQIETQTIvklkRKKRKEFKIKEGKTKKERIINLT-SIFDEIYSYTQTLK-STWLFPS-- 107
Cdd:cd01193   23 HRLILSLLYG--AGLRISELLRLRVKDI----DFERGVIRVRQGKGGKDRVVPLPeKLLEPLRRYLKSARpKEELDPAeg 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 507031987 108 ----------RKGEQPISKIQAYRQLQKAGDFASIES-IGTHTMRNTFGYWFYKQTKDVAMLQEILNHSTPQITLKY 173
Cdd:cd01193   97 ragvldprtgVERRHHISETTVQRALKKAVEQAGITKrVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIY 173
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 22-165 4.63e-03

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 36.48  E-value: 4.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  22 MKWALKRHCSERDYILFLFGIHTGLRVSDLLQIetqtivklkrkKRKEFKIKEG---------KTKKERIINLTS----I 88
Cdd:cd00801    9 WRALDTANLSPPTKLALRLLLLTGQRIGELARA-----------RWSEIDLEEKtwtipaertKNKRPHRVPLSDqaleI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507031987  89 FDEIYSYTQTlkSTWLFPSRKGE-QPISK---IQAYRQLQKAGDFASiesigTHTMRNTFGYWFYKQTKDVAMLQEILNH 164
Cdd:cd00801   78 LEELKEFTGD--SGYLFPSRRKKkKPISEntiNKALKRLGYKGKEFT-----PHDLRRTFSTLLNELGIDPEVIERLLNH 150


                 .
gi 507031987 165 S 165
Cdd:cd00801  151 V 151
 
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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