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Conserved domains on  [gi|1326725339|gb|PMJ06051|]
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integrase [Vibrio lentus]

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 ...
 15-194 1.19e-34

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 cd01188:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 179  Bit Score: 120.81  E-value: 1.19e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  15 PFRLEEIWRIRTRLEiENNLMQLALLNLAIDSKLRASDLLVLRVCDVssqDRIFNRVKHIQRKTDIEVQFEITTRTQQSL 94
Cdd:cd01188     2 PDEVRRLLAAIDRLT-PVGLRDYAILLLLARLGLRAGDVAGLRLDDI---DWRSGTITVRQKKTGRPVELPLTEPVGEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  95 MKWILMA-SLHDSNFIFPSQRR-KQQPISYSYYRYLVRRWASNLGLDPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGH 172
Cdd:cd01188    78 ADYLRDGrPRTDSREVFLRARApYRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGH 157

                         170       180
                  ....*....|....*....|..
gi 1326725339 173 TKVDNTIRYLGVELEDALLLSE 194
Cdd:cd01188   158 RSIETTAIYAKIDVDDLREVAL 179
 
Name Accession Description Interval E-value
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 15-194 1.19e-34

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: 120.81  E-value: 1.19e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  15 PFRLEEIWRIRTRLEiENNLMQLALLNLAIDSKLRASDLLVLRVCDVssqDRIFNRVKHIQRKTDIEVQFEITTRTQQSL 94
Cdd:cd01188     2 PDEVRRLLAAIDRLT-PVGLRDYAILLLLARLGLRAGDVAGLRLDDI---DWRSGTITVRQKKTGRPVELPLTEPVGEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  95 MKWILMA-SLHDSNFIFPSQRR-KQQPISYSYYRYLVRRWASNLGLDPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGH 172
Cdd:cd01188    78 ADYLRDGrPRTDSREVFLRARApYRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGH 157

                         170       180
                  ....*....|....*....|..
gi 1326725339 173 TKVDNTIRYLGVELEDALLLSE 194
Cdd:cd01188   158 RSIETTAIYAKIDVDDLREVAL 179
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
6-188 2.34e-20

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 86.20  E-value: 2.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339   6 KTKRSGVKKPFRL--EEIWRIRTRLEIE--NNLMQLALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnRVKHiqRKTDIE 81
Cdd:COG4974   101 KLPKKPRKLPRVLteEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTI-RVRR--GKGGKE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  82 VQFEITTRTQQSLMKWILMASLHDSNFIFPSQRRKqqPISYSYYRYLVRRWASNLGLDPNLyGTHSMRRTKATLVYAKTK 161
Cdd:COG4974   178 RTVPLSPEALEALREYLEERRPRDSDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIPKRV-TPHSLRHTFATHLLEAGV 254

                         170       180
                  ....*....|....*....|....*..
gi 1326725339 162 NIRAVQLLLGHTKVDNTIRYLGVELED 188
Cdd:COG4974   255 DLRTVQELLGHSSISTTQIYTHVSDEE 281
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 37-181 1.80e-12

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: 62.72  E-value: 1.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  37 LALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnRVKHIQRKTDIEVQFEITTRtqQSLMKWILMASLHD--SNFIFPSQR 114
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVI-RVHRGKGNKERTVPLSDAAL--ELLKEWLSKRLLEApkSDYLFASKR 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1326725339 115 RKqqPISYSYYRYLVRRWASNLGLDPNLyGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRY 181
Cdd:pfam00589 101 GK--PLSRQTVRKIFKRAGKEAGLELPL-HPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 103-184 2.11e-08

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 52.85  E-value: 2.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339 103 LHDSNFIFPSQRRKqqPISYSYYRYLVRRWASNLGLDPNlYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYL 182
Cdd:PRK00236  203 LPDDDALFLGARGG--RLSPRVVQRRVKKLGKKAGLPSH-ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYT 279


                  ..
gi 1326725339 183 GV 184
Cdd:PRK00236  280 HV 281
 
Name Accession Description Interval E-value
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 15-194 1.19e-34

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: 120.81  E-value: 1.19e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  15 PFRLEEIWRIRTRLEiENNLMQLALLNLAIDSKLRASDLLVLRVCDVssqDRIFNRVKHIQRKTDIEVQFEITTRTQQSL 94
Cdd:cd01188     2 PDEVRRLLAAIDRLT-PVGLRDYAILLLLARLGLRAGDVAGLRLDDI---DWRSGTITVRQKKTGRPVELPLTEPVGEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  95 MKWILMA-SLHDSNFIFPSQRR-KQQPISYSYYRYLVRRWASNLGLDPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGH 172
Cdd:cd01188    78 ADYLRDGrPRTDSREVFLRARApYRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGH 157

                         170       180
                  ....*....|....*....|..
gi 1326725339 173 TKVDNTIRYLGVELEDALLLSE 194
Cdd:cd01188   158 RSIETTAIYAKIDVDDLREVAL 179
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 17-188 1.70e-22

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: 89.27  E-value: 1.70e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  17 RLEEIWRIRTRLEIENNLMqLALLNLAIDSKLRASDLLVLRVCDVSSQDRIFNrvkhIQRKTDIEVQFEITTRTQQSLMK 96
Cdd:cd01192     8 DKKLIKEIKLYLKKANPRN-YLLFIVGINTGLRISDLLSLKVEDVTNKDKLSI----KEQKTGKQKTFPLNPTLVKALKE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  97 WI-LMASLHDSNFIFPSQRRKQQPIS-YSYYRYLvRRWASNLGLdPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTK 174
Cdd:cd01192    83 YIdDLDLKRNDYLFKSLKQGPEKPISrKQAYKIL-KKAADDLGL-NYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSS 160

                         170
                  ....*....|....
gi 1326725339 175 VDNTIRYLGVELED 188
Cdd:cd01192   161 PSITLRYLGIDQED 174
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
6-188 2.34e-20

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 86.20  E-value: 2.34e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339   6 KTKRSGVKKPFRL--EEIWRIRTRLEIE--NNLMQLALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnRVKHiqRKTDIE 81
Cdd:COG4974   101 KLPKKPRKLPRVLteEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTI-RVRR--GKGGKE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  82 VQFEITTRTQQSLMKWILMASLHDSNFIFPSQRRKqqPISYSYYRYLVRRWASNLGLDPNLyGTHSMRRTKATLVYAKTK 161
Cdd:COG4974   178 RTVPLSPEALEALREYLEERRPRDSDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIPKRV-TPHSLRHTFATHLLEAGV 254

                         170       180
                  ....*....|....*....|....*..
gi 1326725339 162 NIRAVQLLLGHTKVDNTIRYLGVELED 188
Cdd:COG4974   255 DLRTVQELLGHSSISTTQIYTHVSDEE 281
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
14-181 6.38e-14

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 68.45  E-value: 6.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  14 KPFRLEEIWRI-RTRLEIENNLMQLALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnrvkHIQRKTDIEVQFEITTRTQQ 92
Cdd:COG4973   110 RALTVDELAQLlDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEV----RVRGKTGKSRTVPLGPKALA 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  93 SLMKWILM---ASLHDSNFIFPSQRRKqqPISYSYYRYLVRRWASNLGLDPNLYgTHSMRRTKATLVYAKTKNIRAVQLL 169
Cdd:COG4973   186 ALREWLAVrpeLAAPDEGALFPSRRGT--RLSPRNVQKRLRRLAKKAGLPKHVH-PHDLRHSFATHLLESGGDLRAVQEL 262

                         170
                  ....*....|..
gi 1326725339 170 LGHTKVDNTIRY 181
Cdd:COG4973   263 LGHASISTTQIY 274
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 32-182 4.59e-13

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: 64.04  E-value: 4.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  32 NNLMQLALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnRVKHIQRKTDIEVQFEITTRTQQSLMKWI--LMASLHDSNFI 109
Cdd:cd00397    15 IDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTI-RVRGKKTKGGKERTVPLPKELAEELKEYLkeRRDKRGPLLKS 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1326725339 110 FPSQRRKQQPISYSYYRYLVRRWASNLGLDPNL-YGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYL 182
Cdd:cd00397    94 LYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRkITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 37-181 1.80e-12

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: 62.72  E-value: 1.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  37 LALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnRVKHIQRKTDIEVQFEITTRtqQSLMKWILMASLHD--SNFIFPSQR 114
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVI-RVHRGKGNKERTVPLSDAAL--ELLKEWLSKRLLEApkSDYLFASKR 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1326725339 115 RKqqPISYSYYRYLVRRWASNLGLDPNLyGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRY 181
Cdd:pfam00589 101 GK--PLSRQTVRKIFKRAGKEAGLELPL-HPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 48-182 1.49e-11

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: 59.97  E-value: 1.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  48 LRASDLLVLRVCDVSSqDRIFNRVKHIQRKTDIEVQFEITTRTQQSLMKWILMASlhdSNFIFPsqrrkqqPISYSYYRY 127
Cdd:cd01185    32 LRFSDLKNLTWKNIVE-ASGRTWIRYRRKKTGKPVTVPLLPVAREILEKYKDDRS---EGKLFP-------VLSNQKINR 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1326725339 128 LVRRWASNLGLDPNLYgTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYL 182
Cdd:cd01185   101 YLKEIAKIAGIDKHLT-FHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYA 154
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 38-182 6.35e-11

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: 58.85  E-value: 6.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  38 ALLNLAIDSKLRASDLLVLRVCDVSSQD----RIF-NRVKHIQRKTDIEVQFEITTRT--QQSLMKWILmASLHDSNFIF 110
Cdd:cd00799    20 ALLLLGFAGALRRSELVALRVEDLTRFVdgglLIRlRRSKTDQDGEGEIKALPYGPETcpVRALRAWLE-AAGIPSGPLF 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1326725339 111 PSQRRKQQPIS-----YSYYRYLVRRWASNlGLDPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYL 182
Cdd:cd00799    99 RRIRRGGSVGTtrlsdRSVARIVKRRAALA-GLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYI 174
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 103-184 2.11e-08

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 52.85  E-value: 2.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339 103 LHDSNFIFPSQRRKqqPISYSYYRYLVRRWASNLGLDPNlYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYL 182
Cdd:PRK00236  203 LPDDDALFLGARGG--RLSPRVVQRRVKKLGKKAGLPSH-ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYT 279


                  ..
gi 1326725339 183 GV 184
Cdd:PRK00236  280 HV 281
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 108-182 2.64e-07

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: 48.52  E-value: 2.64e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1326725339 108 FIFPSQRRKQQPISYSYYRYLVRRWASNLGLDPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYL 182
Cdd:cd01194    99 FTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYA 173
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 19-184 9.58e-07

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: 46.88  E-value: 9.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  19 EEIWRIrtrLEIENNLMQLALLNLAIDSKLRASDLLVLRVCDVSSqDRIFNRVKHIQRKTDIEVQfeITTRTQQSLMKWI 98
Cdd:cd01193     9 DEVRRI---LGALTELRHRLILSLLYGAGLRISELLRLRVKDIDF-ERGVIRVRQGKGGKDRVVP--LPEKLLEPLRRYL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  99 LMAslHDSNFIFPSQ-----------RRKQQPISYSYYRYLVRRWASNLGLDPNLyGTHSMRRTKATLVYAKTKNIRAVQ 167
Cdd:cd01193    83 KSA--RPKEELDPAEgragvldprtgVERRHHISETTVQRALKKAVEQAGITKRV-TPHTLRHSFATHLLEAGTDIRTIQ 159

                         170
                  ....*....|....*..
gi 1326725339 168 LLLGHTKVDNTIRYLGV 184
Cdd:cd01193   160 ELLGHSDLSTTMIYTHV 176
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 37-187 8.20e-06

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: 44.58  E-value: 8.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  37 LALLNLAIDSKLRASDLLVLRVCDVSSQDrifNRVKHIQRKTDIEVQFEITTRTQQSLMKWILMASL----HDSNFIFPS 112
Cdd:cd01182    24 HALLLLLYDTGARVQELADLTIRDLRLDD---PATVRLHGKGRKERTVPLWKETVAALKAYLQEFHLtpdpKQLFPLFPN 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339 113 QRRkqQPISYSYYRYLVRRWAS-----NLGLDPNLYgTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIRYLGVELE 187
Cdd:cd01182   101 RRG--QPLTRDGVAYILNKYVAlasnrCPSLPKRIT-PHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEADLE 177
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 105-180 2.31e-05

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: 43.03  E-value: 2.31e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1326725339 105 DSNFIFPSQRRKQQPISYSYYRYLVRRwasnLGLDPNLYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIR 180
Cdd:cd00801    87 DSGYLFPSRRKKKKPISENTINKALKR----LGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRA 158
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 38-184 4.35e-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: 4.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  38 ALLNLAIDSKLRASDLLVLRVCDVSSQDRIFnRVKHIQRKTDIeVQFeiTTRTQQSLMKWI-----LMASLHDSNFIFPS 112
Cdd:cd00798    23 AILELLYASGLRVSELVGLDLSDVDLDEGLV-RVTGKGNKERL-VPF--GSYAVEALEEYLeerrpLLLKKKPPDALFLN 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1326725339 113 QRrkQQPISYSYYRYLVRRWASNLGLDPNLyGTHSMRRTKAT-LVYAKTkNIRAVQLLLGHTKVDNTIRYLGV 184
Cdd:cd00798    99 KR--GKRLSRRGVWRILKKYAERAGLPKHV-SPHTLRHSFAThLLEGGA-DLRVVQELLGHASLSTTQIYTHV 167
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 19-181 7.85e-04

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: 38.46  E-value: 7.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  19 EEIWRIRTRLEIENNLMQLALLNLAIDSKLRASDLLVLRVCDVSSQdrifNRVKHIQR-KTDIEVQFEITTRTQQsLMKW 97
Cdd:cd00796     8 DEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLE----VGLIVLPEtKNGKPRTVPLSDEAIA-ILKE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1326725339  98 ILMASLHDSNFIFPSQRrkqqPISYSYYRYLVRRWASNLGLdPNLyGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDN 177
Cdd:cd00796    83 LKRKRGKDGFFVDGRFF----GIPIASLRRAFKKARKRAGL-EDL-RFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKM 156


                  ....
gi 1326725339 178 TIRY 181
Cdd:cd00796   157 TMRY 160
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 105-180 8.46e-04

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 39.25  E-value: 8.46e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1326725339 105 DSNFIFPSQRRKQQPISYSYYRYLVRRwasnLGLDPnlYGTHSMRRTKATLVYAKTKNIRAVQLLLGHTKVDNTIR 180
Cdd:COG0582   293 DSEYVFPSRRGPKKPMSENTLNKALRR----MGYGR--FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRA 362
 
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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