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Conserved domains on  [gi|2786665063|ref|WP_369908169|]
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tyrosine-type recombinase/integrase [Limnohabitans sp. Rim28]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves 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.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  10047575|9278480

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
8-201 3.72e-31

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 114.71  E-value: 3.72e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063   8 DYRRTKMAQAKTLTKEELARVLDYIDTRRF-AQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKeeIRllpdMTKG 86
Cdd:COG4974   101 KLPKKPRKLPRVLTEEEIEALLEALDTETPeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIR--VR----RGKG 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  87 RYARTVFVNIKLREELQAYAAQAKCVDRSYPFFASQKSILSgfsANSLAQTFGLLYAGAGLQ-GASSHSGRRTFLTSLAN 165
Cdd:COG4974   175 GKERTVPLSPEALEALREYLEERRPRDSDYLFPTRRGRPLS---RRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLE 251

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2786665063 166 KGTAIHILKTLAGHRSIQTTAAYLYSSPSQLKAAVE 201
Cdd:COG4974   252 AGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
8-201 3.72e-31

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 114.71  E-value: 3.72e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063   8 DYRRTKMAQAKTLTKEELARVLDYIDTRRF-AQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKeeIRllpdMTKG 86
Cdd:COG4974   101 KLPKKPRKLPRVLTEEEIEALLEALDTETPeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIR--VR----RGKG 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  87 RYARTVFVNIKLREELQAYAAQAKCVDRSYPFFASQKSILSgfsANSLAQTFGLLYAGAGLQ-GASSHSGRRTFLTSLAN 165
Cdd:COG4974   175 GKERTVPLSPEALEALREYLEERRPRDSDYLFPTRRGRPLS---RRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLE 251

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2786665063 166 KGTAIHILKTLAGHRSIQTTAAYLYSSPSQLKAAVE 201
Cdd:COG4974   252 AGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 24-189 4.57e-23

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: 90.62  E-value: 4.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  24 ELARVLDYIDTRRFAQ-RNRTMMLLTHLAGLRIGEVACLRWSDvINTDGSVkeeIRLLPDMTKGRYARTVFVNIKLREEL 102
Cdd:cd00397     1 ELEKLLDAIDEDKKIDlRDRAILLLLLETGLRISELLALKVKD-IDLDNGT---IRVRGKKTKGGKERTVPLPKELAEEL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 103 QAY----AAQAKCVDRSYPFFASQKSILSGFSANSLAQTFGLLYAGAGLQGASSHSGRRTFLTSLANKGTAIHILKTLAG 178
Cdd:cd00397    77 KEYlkerRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                         170
                  ....*....|.
gi 2786665063 179 HRSIQTTAAYL 189
Cdd:cd00397   157 HSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 20-193 3.95e-17

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: 75.05  E-value: 3.95e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYIDTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDvINTDGSVkeeIRLlpDMTKGRYARTVFVNIKLR 99
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSD-IDFENGV---IRV--HRGKGNKERTVPLSDAAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 100 EELQAYAAQAKCVDRSYPF-FASQKSilSGFSANSLAQTFGLLYAGAGLQGA-SSHSGRRTFLTSLANKGTAIHILKTLA 177
Cdd:pfam00589  76 ELLKEWLSKRLLEAPKSDYlFASKRG--KPLSRQTVRKIFKRAGKEAGLELPlHPHMLRHSFATHLLEAGVDLRVVQKLL 153

                         170
                  ....*....|....*.
gi 2786665063 178 GHRSIQTTAAYLYSSP 193
Cdd:pfam00589 154 GHSSISTTQIYTHVAD 169
int PHA02601
integrase; Provisional
 7-202 2.24e-08

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 52.81  E-value: 2.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063   7 HDYRRTKMAQAKT--LTKEELARVLDYIDtrrfAQRNRTMMLLTHL---AGLRIGEVACLRWSDVINTdgsvkeeiRLLP 81
Cdd:PHA02601  158 DGIRPFKEAEPELafLTKEEIERLLDACD----GSRSPDLGLIAKIclaTGARWSEAETLKRSQISPY--------KITF 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  82 DMTKGRYARTVFVNIKLREELQAyaAQAKCVDRSYPFFASQksilsgfsanslaqtfgLLYAGAGL-QGASSHSGRRTFL 160
Cdd:PHA02601  226 VKTKGKKNRTVPISEELYKMLPK--RRGRLFKDAYESFERA-----------------VKRAGIDLpEGQATHVLRHTFA 286

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2786665063 161 TSLANKGTAIHILKTLAGHRSIQTTAAYLYSSPSQLKAAVEL 202
Cdd:PHA02601  287 SHFMMNGGNILVLQRILGHATIEMTMAYAHFAPDHLEDAVSL 328
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
8-201 3.72e-31

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 114.71  E-value: 3.72e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063   8 DYRRTKMAQAKTLTKEELARVLDYIDTRRF-AQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKeeIRllpdMTKG 86
Cdd:COG4974   101 KLPKKPRKLPRVLTEEEIEALLEALDTETPeGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIR--VR----RGKG 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  87 RYARTVFVNIKLREELQAYAAQAKCVDRSYPFFASQKSILSgfsANSLAQTFGLLYAGAGLQ-GASSHSGRRTFLTSLAN 165
Cdd:COG4974   175 GKERTVPLSPEALEALREYLEERRPRDSDYLFPTRRGRPLS---RRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLE 251

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2786665063 166 KGTAIHILKTLAGHRSIQTTAAYLYSSPSQLKAAVE 201
Cdd:COG4974   252 AGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVE 287
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 24-189 4.57e-23

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: 90.62  E-value: 4.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  24 ELARVLDYIDTRRFAQ-RNRTMMLLTHLAGLRIGEVACLRWSDvINTDGSVkeeIRLLPDMTKGRYARTVFVNIKLREEL 102
Cdd:cd00397     1 ELEKLLDAIDEDKKIDlRDRAILLLLLETGLRISELLALKVKD-IDLDNGT---IRVRGKKTKGGKERTVPLPKELAEEL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 103 QAY----AAQAKCVDRSYPFFASQKSILSGFSANSLAQTFGLLYAGAGLQGASSHSGRRTFLTSLANKGTAIHILKTLAG 178
Cdd:cd00397    77 KEYlkerRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                         170
                  ....*....|.
gi 2786665063 179 HRSIQTTAAYL 189
Cdd:cd00397   157 HSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
18-188 2.68e-19

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 83.09  E-value: 2.68e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  18 KTLTKEELARVLDYIDTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGsvkeEIRLLpdmTKGRYARTVFVNIK 97
Cdd:COG4973   110 RALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAG----EVRVR---GKTGKSRTVPLGPK 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  98 LREELQAYAAQAKCVDR--SYPFFASQKsilsG--FSANSLAQTFGLLYAGAGLQGA-SSHSGRRTFLTSLANKGTAIHI 172
Cdd:COG4973   183 ALAALREWLAVRPELAApdEGALFPSRR----GtrLSPRNVQKRLRRLAKKAGLPKHvHPHDLRHSFATHLLESGGDLRA 258

                         170
                  ....*....|....*.
gi 2786665063 173 LKTLAGHRSIQTTAAY 188
Cdd:COG4973   259 VQELLGHASISTTQIY 274
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 16-188 9.54e-18

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: 76.60  E-value: 9.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  16 QAKTLTKEELARVLDYIDTRRFAQRNRTMMLLTHLaGLRIGEVACLRWSDVintdgsVKEEIRLLPDMTKGRYARTVFVN 95
Cdd:cd00796     1 RDRFLTEDEEARLLAALEESTNPHLRLIVLLALYT-GARRGEILSLRWDDI------DLEVGLIVLPETKNGKPRTVPLS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  96 IKLREELQAY--AAQAKCVDRSYPFFasqksilsGFSANSLAQTFGLLYAGAGLQGASSHSGRRTFLTSLANKGTAIHIL 173
Cdd:cd00796    74 DEAIAILKELkrKRGKDGFFVDGRFF--------GIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTV 145

                         170
                  ....*....|....*
gi 2786665063 174 KTLAGHRSIQTTAAY 188
Cdd:cd00796   146 AKILGHSSIKMTMRY 160
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 20-193 3.95e-17

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: 75.05  E-value: 3.95e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYIDTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDvINTDGSVkeeIRLlpDMTKGRYARTVFVNIKLR 99
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSD-IDFENGV---IRV--HRGKGNKERTVPLSDAAL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 100 EELQAYAAQAKCVDRSYPF-FASQKSilSGFSANSLAQTFGLLYAGAGLQGA-SSHSGRRTFLTSLANKGTAIHILKTLA 177
Cdd:pfam00589  76 ELLKEWLSKRLLEAPKSDYlFASKRG--KPLSRQTVRKIFKRAGKEAGLELPlHPHMLRHSFATHLLEAGVDLRVVQKLL 153

                         170
                  ....*....|....*.
gi 2786665063 178 GHRSIQTTAAYLYSSP 193
Cdd:pfam00589 154 GHSSISTTQIYTHVAD 169
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 21-189 6.78e-15

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: 69.19  E-value: 6.78e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  21 TKEELARVLDYIDTRR-FAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVkeEIRllpdMTKGRYARTVFVNIKLR 99
Cdd:cd01188     1 SPDEVRRLLAAIDRLTpVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTI--TVR----QKKTGRPVELPLTEPVG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 100 EELQAYAAQA--KCVDRSYpfFASQKSILSGFSANS-LAQTFGLLYAGAGLQGA--SSHSGRRTFLTSLANKGTAIHILK 174
Cdd:cd01188    75 EALADYLRDGrpRTDSREV--FLRARAPYRPLSSTSqISSIVRRYLRKAGIEPShrGTHSLRHSLATRMLRAGTSLKVIA 152

                         170
                  ....*....|....*
gi 2786665063 175 TLAGHRSIQTTAAYL 189
Cdd:cd01188   153 DLLGHRSIETTAIYA 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 20-189 4.35e-12

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: 61.91  E-value: 4.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYIDTrrfaQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKeeIRllpdMTKGRYARTVFVNIKLR 99
Cdd:cd01193     6 LSPDEVRRILGALTE----LRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIR--VR----QGKGGKDRVVPLPEKLL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 100 EELQAYAAQAKcvDRSYPFFASQKSILSGFSANSLA------QTFGLLYAGAGLQG-----ASSHSGRRTFLTSLANKGT 168
Cdd:cd01193    76 EPLRRYLKSAR--PKEELDPAEGRAGVLDPRTGVERrhhiseTTVQRALKKAVEQAgitkrVTPHTLRHSFATHLLEAGT 153

                         170       180
                  ....*....|....*....|.
gi 2786665063 169 AIHILKTLAGHRSIQTTAAYL 189
Cdd:cd01193   154 DIRTIQELLGHSDLSTTMIYT 174
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 22-189 3.09e-11

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: 59.61  E-value: 3.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  22 KEELARVLDYIdtRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINtdgsvKEEIRLLPDMTkGRYaRTVFVNIKLREE 101
Cdd:cd01192     9 KKLIKEIKLYL--KKANPRNYLLFIVGINTGLRISDLLSLKVEDVTN-----KDKLSIKEQKT-GKQ-KTFPLNPTLVKA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 102 LQAYAAQAKCVDRSYPFFASQKSILSGFSANSLAQTFGLLYAGAGLQGA-SSHSGRRTFLTSLANKGTAIHILKTLAGHR 180
Cdd:cd01192    80 LKEYIDDLDLKRNDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYNiGTHSLRKTFGYHVYKQGKDIELLMKLLNHS 159


                  ....*....
gi 2786665063 181 SIQTTAAYL 189
Cdd:cd01192   160 SPSITLRYL 168
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 22-185 3.71e-11

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The 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: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 58.72  E-value: 3.71e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  22 KEELARVLDYIDTRRfaQRNRTMMLLTHLAGLRIGEVACLRWSDV------INTDGSV----KEEIRLLPdmTKGRYA-R 90
Cdd:cd01189     1 PEELKKLLEALKKRG--DRYYLLFLLALLTGLRRGELLALTWSDIdfengtIRINRTLvrkkKGGYVIKP--PKTKSSiR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  91 TVFVNIKLREELQAYAAQAKCVDRsypffasqksilsgfsanslaqtfgllyagAGLQGASSHSGRRTFLTSLANKGTAI 170
Cdd:cd01189    77 TIPLPDELIELLKELKAFKKLLKK------------------------------AGLPRITPHDLRHTFASLLLEAGVPL 126

                         170
                  ....*....|....*
gi 2786665063 171 HILKTLAGHRSIQTT 185
Cdd:cd01189   127 KVIAERLGHSDISTT 141
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 18-188 4.32e-10

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 58.13  E-value: 4.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  18 KTLTKEELARVLDYIDTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDvINTDgsvKEEIRLLPDMTKGRYARTVFVN-- 95
Cdd:COG0582   204 PALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSE-IDLE---AALWTIPAERMKTRRPHIVPLSrq 279

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  96 -IKLREELQAYAAQAKCVdrsypfFASQKSILSGFSANSLAQtfgLLYAgAGLQGASSHSGRRTFLTSLANKGTAIHILK 174
Cdd:COG0582   280 aLEILKELKPLTGDSEYV------FPSRRGPKKPMSENTLNK---ALRR-MGYGRFTPHGFRHTASTLLNEAGFPPDVIE 349

                         170
                  ....*....|....*
gi 2786665063 175 TLAGHRSIQTT-AAY 188
Cdd:COG0582   350 RQLAHKDGNKVrAAY 364
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 23-189 5.29e-10

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: 55.73  E-value: 5.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  23 EELARV--LDYIDTRRFAQRNRtMMLLTHLAGLRIGEVACLRWSDVINTDGsvKEEIRLLPDMTKGRyartvfVNIKLRE 100
Cdd:cd01185     1 EELKRLmaLELSDTSRLELVRD-MFLFSCYTGLRFSDLKNLTWKNIVEASG--RTWIRYRRKKTGKP------VTVPLLP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 101 ELQAYAAQAKCVDRSYPFFasqkSILSGFSANSLAQTFGLLyagAGL-QGASSHSGRRTFLTSLANKGTAIHILKTLAGH 179
Cdd:cd01185    72 VAREILEKYKDDRSEGKLF----PVLSNQKINRYLKEIAKI---AGIdKHLTFHVARHTFATLLLLKGVDIETISKLLGH 144

                         170
                  ....*....|
gi 2786665063 180 RSIQTTAAYL 189
Cdd:cd01185   145 SSIKTTQIYA 154
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 25-189 2.01e-08

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: 51.92  E-value: 2.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  25 LARVLDYIDTRR-FAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGsvkEEIRLLPDMTKG-RYARTVFVNIKLREE- 101
Cdd:cd00799     1 LKAMLATLDDTTlRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVD---GGLLIRLRRSKTdQDGEGEIKALPYGPEt 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 102 -----LQAYAAQAKcvDRSYPFFAS---QKSILSGF-SANSLAQTFGLLYAGAGLQGA--SSHSGRRTFLTSLANKGTAI 170
Cdd:cd00799    78 cpvraLRAWLEAAG--IPSGPLFRRirrGGSVGTTRlSDRSVARIVKRRAALAGLDPGdfSGHSLRRGFATEAARAGASL 155

                         170
                  ....*....|....*....
gi 2786665063 171 HILKTLAGHRSIQTTAAYL 189
Cdd:cd00799   156 PEIMAQGGHKSVATVMRYI 174
int PHA02601
integrase; Provisional
 7-202 2.24e-08

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 52.81  E-value: 2.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063   7 HDYRRTKMAQAKT--LTKEELARVLDYIDtrrfAQRNRTMMLLTHL---AGLRIGEVACLRWSDVINTdgsvkeeiRLLP 81
Cdd:PHA02601  158 DGIRPFKEAEPELafLTKEEIERLLDACD----GSRSPDLGLIAKIclaTGARWSEAETLKRSQISPY--------KITF 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  82 DMTKGRYARTVFVNIKLREELQAyaAQAKCVDRSYPFFASQksilsgfsanslaqtfgLLYAGAGL-QGASSHSGRRTFL 160
Cdd:PHA02601  226 VKTKGKKNRTVPISEELYKMLPK--RRGRLFKDAYESFERA-----------------VKRAGIDLpEGQATHVLRHTFA 286

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2786665063 161 TSLANKGTAIHILKTLAGHRSIQTTAAYLYSSPSQLKAAVEL 202
Cdd:PHA02601  287 SHFMMNGGNILVLQRILGHATIEMTMAYAHFAPDHLEDAVSL 328
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 20-199 2.58e-08

C-terminal catalytic domain of recombinase RitB, 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: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 51.92  E-value: 2.58e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYID--TRRFAQRNRTMMLLTHL---AGLRIGEVACLRWSDVINTDGsvkeeiRLLPDMTKGRYARTVFV 94
Cdd:cd00797     1 YTDAEIRRLLAAADqlPPESPLRPLTYATLFGLlyaTGLRVGEALRLRLEDVDLDSG------ILTIRQTKFGKSRLVPL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  95 NIKLREELQAYAA--QAKCVDR-SYPFFASQKSilSGFSANSLAQTFGLLYAGAGLQGASS------HSGRRTF----LT 161
Cdd:cd00797    75 HPSTVGALRDYLArrDRLLPSPsSSYFFVSQQG--GRLTGGGVYRVFRRLLRRIGLRGAGDgrgprlHDLRHTFavnrLT 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2786665063 162 SLANKGTAIH----ILKTLAGHRSIQTTAAYLYSSPSQLKAA 199
Cdd:cd00797   153 RWYREGADVErklpVLSTYLGHVNVTDTYWYLTATPELMELA 194
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 21-191 8.22e-08

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: 49.96  E-value: 8.22e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  21 TKEELARVLDYIDTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGsvkeEIRLLPDMTKGRYARTVFVN---IK 97
Cdd:cd00801     1 SPDELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEK----TWTIPAERTKNKRPHRVPLSdqaLE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  98 LREELQAYAAQAKCVdrsypfFASQKSILSGFSANSLAQTfgLLYAGAGLQGASSHSGRRTFLTSLANKGTAIHILKTLA 177
Cdd:cd00801    77 ILEELKEFTGDSGYL------FPSRRKKKKPISENTINKA--LKRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLL 148

                         170
                  ....*....|....*
gi 2786665063 178 GH-RSIQTTAAYLYS 191
Cdd:cd00801   149 NHvLGGVVRAAYNRY 163
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 23-196 1.33e-07

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: 49.43  E-value: 1.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  23 EELARVLDYIDTR-RFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKEeirllpdMTKGRYARTVFVNIKLREE 101
Cdd:cd00798     2 DEVERLLDAPDTDtPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRV-------TGKGNKERLVPFGSYAVEA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 102 LQAYAAQA-----KCVDRSYPFFASQKSILSgfsanslAQTFGLL---YAG-AGLQ-GASSHSGRRTFLTSLANKGTAIH 171
Cdd:cd00798    75 LEEYLEERrplllKKKPPDALFLNKRGKRLS-------RRGVWRIlkkYAErAGLPkHVSPHTLRHSFATHLLEGGADLR 147

                         170       180
                  ....*....|....*....|....*
gi 2786665063 172 ILKTLAGHRSIQTTAAYLYSSPSQL 196
Cdd:cd00798   148 VVQELLGHASLSTTQIYTHVSFERL 172
PRK09870 PRK09870
tyrosine recombinase; Provisional
 20-192 1.48e-06

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 46.86  E-value: 1.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYIDTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVintdgSVKEEIRLLPDMTKGrYARTvfvNIKLR 99
Cdd:PRK09870   13 LTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDI-----DLKAKCIYIHRLKKG-FSTT---HPLLN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 100 EELQAYAAQAKcVDRSYPFFASQKSILSGfSANSLA-QTFGLLYAGAGLQG-----ASSHSGRRTFLTSLANKGTAIHIL 173
Cdd:PRK09870   84 KEIQALKNWLS-IRTSYPHAESEWVFLSR-KGNPLSrQQFYHIISTSGGNAglsleIHPHMLRHSCGFALANMGIDTRLI 161

                         170
                  ....*....|....*....
gi 2786665063 174 KTLAGHRSIQTTAAYLYSS 192
Cdd:PRK09870  162 QDYLGHRNIRHTVWYTASN 180
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 20-181 5.63e-06

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing 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: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 44.99  E-value: 5.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYIDTRRFAQRNRTMMLLTHLA---GLRIGEVACLRWSDVINTDGSVKeeIRLLPDMTKGRY-----ART 91
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCKKKDPALYWLPLIGlytGARLNEICQLRVDDIKEEDGIWC--IDINDDAEGRRLktkasRRL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  92 VFVNIKLREE-LQAYAAQAKcVDRSYPFFASQKSILSGFSANsLAQTFGLLYAGAGL---QGASSHSGRRTFLTSLANKG 167
Cdd:cd01184    79 VPIHPRLIELgFLDYVEALR-ADGKLFLFPEKRDKDGKYSKA-ASKWFNRLLRKLGIkddERKSFHSFRHTFITALKRAG 156

                         170
                  ....*....|....
gi 2786665063 168 TAIHILKTLAGHRS 181
Cdd:cd01184   157 VPEELIAQIVGHSR 170
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 18-203 8.29e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 45.15  E-value: 8.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  18 KTLTKEELARVLDYID-TRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGsvkeEIRLLpdmTKGRYARTVFVNI 96
Cdd:PRK00236  114 KPLDVDQAKRLLDAIDeDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASG----TLRVL---GKGNKERTVPLGR 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  97 KLREELQAY-AAQAKCVDRSYPFFASQKsilsG--FSANSLAQTFGLLYAGAGLQG-ASSHSGRRTFLTSLANKGTAIHI 172
Cdd:PRK00236  187 AAREALEAYlALRPLFLPDDDALFLGAR----GgrLSPRVVQRRVKKLGKKAGLPShITPHKLRHSFATHLLESGGDLRA 262

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2786665063 173 LKTLAGHRSIQTTAAYLYSSPSQLKAAVELA 203
Cdd:PRK00236  263 VQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 21-188 1.10e-05

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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 44.00  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  21 TKEELARVLDYIDTR-RFAQRNRTMMLLTHLAGLRIGEVACLRWSDvintdgsVKEEIRLLPDMTKGRYART-VFVNIKL 98
Cdd:cd01195     1 SREEARQRLDAADRHtAKGKRDEALVRLLLDNALRRSEAVALDVED-------LEKEHRRLRILGKGKKQREvVTLPPTT 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  99 REELQAYAAQAKcvDRSYPFFASQKSILSG--FSANSLAQTFGLLYAGAGL-QGASSHSGRRTFLTSLANKGTA-IHILK 174
Cdd:cd01195    74 REALAAWLAARG--EAEGPLFVSLDRASRGrrLSPQAVYRIVRRLAERIGLgKRLSPHGLRHSAITLALDAGAGlIRKVQ 151

                         170
                  ....*....|....
gi 2786665063 175 TLAGHRSIQTTAAY 188
Cdd:cd01195   152 DFSRHADLRTLQVY 165
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 132-188 2.39e-05

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing 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: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 42.42  E-value: 2.39e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2786665063 132 NSLAQTFGLLYAGAGLQGASSHSGRRTFLTSLANKGTAIHILKTLAGHRSIQTTAAY 188
Cdd:cd01187    84 NELSELKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
xerD PRK00283
tyrosine recombinase;
18-188 4.04e-05

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 43.26  E-value: 4.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  18 KTLTKEELARVLDYIDTR-RFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVkeeiRLlpdMTKGRYARTVFVNI 96
Cdd:PRK00283  112 KTLSEAQVEALLDAPDIDtPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVV----RV---TGKGNKERLVPLGE 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  97 KLREELQAYAAQAKcvdrsyPFFASQKSILSGFsANSLA-----QTFGLL---YAG-AGLQGA--SSHSGRRTFLTSLAN 165
Cdd:PRK00283  185 EAVYAIERYLERGR------PALLNGRSSDALF-PSARGgqltrQTFWHRikhYAKrAGIDPKklSPHVLRHAFATHLLN 257

                         170       180
                  ....*....|....*....|...
gi 2786665063 166 KGTAIHILKTLAGHRSIQTTAAY 188
Cdd:PRK00283  258 HGADLRVVQELLGHSDISTTQIY 280
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 17-198 4.48e-05

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 43.20  E-value: 4.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  17 AKTLTKEELARVLDYIDTRR-FAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKeeIRllpdMTKGRYARTVFVN 95
Cdd:PRK01287  134 RQILSEAETEQVLASPDLTTlQGLRDRALLELLWSTGIRRGELARLDLYDVDASRGVVT--VR----QGKGNKDRVVPVG 207

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  96 IKLREELQAYAAQAK-----CVDRSYPFFASQKsilSGFSANSLAQTFGLLYAGAGLQGASS-HSGRRTFLTSLANKGTA 169
Cdd:PRK01287  208 ERALAWLQRYLQDVRpqlavRPDSGALFVAMDG---DGLARNTLTNMVGRYIRAAGIEKAGAcHLFRHAMATQMLENGAD 284

                         170       180
                  ....*....|....*....|....*....
gi 2786665063 170 IHILKTLAGHRSIQTTAAYLYSSPSQLKA 198
Cdd:PRK01287  285 TRHIQAILGHAKLETTQIYTRVSIGHLQA 313
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 20-189 8.16e-05

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: 41.59  E-value: 8.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  20 LTKEELARVLDYI--DTRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVINTDGSVKEEIRllpdmTKGRYARTVFVniK 97
Cdd:cd01194     1 LTLEQARQLLASLpiDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQ-----GKGKTSKDDFV--Y 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  98 LREE----LQAYAAQAKCVDRSYPFFASQK-----SILSGFSANSLAQTFgLLYAGAGLQGASSHSGRRTFLTSLANKGT 168
Cdd:cd01194    74 LRPDvlkaLQAYLKARGKLDFEEPLFTSLSnnskgQRLTTRSIRRIIKKY-LRKAGLDDDRLTAHSLRHTAGTLALKAGK 152

                         170       180
                  ....*....|....*....|.
gi 2786665063 169 AIHILKTLAGHRSIQTTAAYL 189
Cdd:cd01194   153 SLREVQQLLRHSDPNTTMIYA 173
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 21-188 2.67e-03

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: 271196  Cd Length: 183  Bit Score: 37.07  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063  21 TKEELARVLDYID-TRRFAQRNRTMMLLTHLAGLRIGEVACLRWSDVIntDGSVKEEIRLlpdMTKGRYARTVFVNIKLR 99
Cdd:cd01196     1 TAPEARRLLESIDsTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVY--DQGRRLWVRL---AEKGGKQHEMPCHHDLE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786665063 100 EELQAYAAQAKCV-DRSYPFFASQKSILSGFSANSLAQtfGLLYA-------GAGLQGA-SSHSGRRTFLTSLANKGTAI 170
Cdd:cd01196    76 EYLRAYLEAAEIEeDPKGPLFRTTRGGTRKLTHNPLTQ--ANAYRmvrrraiAADIPTAiGNHSFRATGITAYLKNGGTL 153

                         170
                  ....*....|....*...
gi 2786665063 171 HILKTLAGHRSIQTTAAY 188
Cdd:cd01196   154 EDAQNMANHASTRTTQLY 171
 
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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