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Conserved domains on  [gi|1344182771|gb|PPE16920|]
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integrase [Escherichia coli]

Protein Classification

site-specific integrase( domain architecture ID 10557092)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 183-351 1.46e-63

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: 199.49  E-value: 1.46e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 183 DEYLKIYQAAessPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPtalhvdaLGISMKETLDKC 262
Cdd:cd00800     1 AEYAAIYAEA---PPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIP-------WTPSLRALVDRI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 263 KEILG--GETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMAS 340
Cdd:cd00800    71 RALPRkrSEYLINSRKGGPLSYDTLKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQGGSTDAQALLGHKSDAMTE 150

                         170
                  ....*....|.
gi 1344182771 341 QYRDDRGREWD 351
Cdd:cd00800   151 RYTRKRGQKWV 161
Arm-DNA-bind_1 pfam09003
Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of ...
 2-69 7.78e-30

Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage.


:

Pssm-ID: 430365  Cd Length: 73  Bit Score: 109.12  E-value: 7.78e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1344182771   2 GRRRSHERRDLPPNLYIR-----NNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARIN 69
Cdd:pfam09003   1 APRPRKNSLNLPPNLYPKkdkrnGKVYYRYRHPVTGKFFGLGTDKREAIAEAVEANHRLAEQRQPSTLAERIK 73
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
80-158 2.28e-07

Phage integrase, N-terminal SAM-like domain;


The actual alignment was detected with superfamily member pfam02899:

Pssm-ID: 472283 [Multi-domain]  Cd Length: 83  Bit Score: 48.03  E-value: 2.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  80 LDRYEKILAS-RGIKQKTLINYMSKIKAIRRGLPDAP--LEDITTKEIAAMLNGYIDEG-KAASAKLIRSTLSDAFREAI 155
Cdd:pfam02899   1 IDQFLEYLSLeRGLSPHTLRAYRRDLLAFLKFLSEGGssLEQITTSDVRAFLAELRAQGlSASSLARRLSALRSFYQFLI 80


                  ...
gi 1344182771 156 AEG 158
Cdd:pfam02899  81 REG 83
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 183-351 1.46e-63

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: 199.49  E-value: 1.46e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 183 DEYLKIYQAAessPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPtalhvdaLGISMKETLDKC 262
Cdd:cd00800     1 AEYAAIYAEA---PPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIP-------WTPSLRALVDRI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 263 KEILG--GETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMAS 340
Cdd:cd00800    71 RALPRkrSEYLINSRKGGPLSYDTLKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQGGSTDAQALLGHKSDAMTE 150

                         170
                  ....*....|.
gi 1344182771 341 QYRDDRGREWD 351
Cdd:cd00800   151 RYTRKRGQKWV 161
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 179-344 2.50e-45

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: 152.86  E-value: 2.50e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 179 RLTADEYLKIYQAAE--SSPCWLRLAMELAVVTGQRVGDLCEMKWSDI--VDGYLYVEQSKTGVKIAIPTAlhvDALGIS 254
Cdd:pfam00589   1 RLTEDEVERLLDAAEtgPLSIRDKALLELLYATGLRISELCSLRWSDIdfENGVIRVHRGKGNKERTVPLS---DAALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 255 MKETLDKC-KEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSfegDPPTFHELR-SLSARLYEKQISDKFAQHLLG 332
Cdd:pfam00589  78 LKEWLSKRlLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE---LPLHPHMLRhSFATHLLEAGVDLRVVQKLLG 154

                         170
                  ....*....|..
gi 1344182771 333 HKSDTMASQYRD 344
Cdd:pfam00589 155 HSSISTTQIYTH 166
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
73-342 1.33e-36

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 133.55  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  73 SVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGYIDEGKAA-SAKLIRSTLSD 149
Cdd:COG4973     1 KLTLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDAdlPLEELTPADVRRFLARLHRRGLSPrTLNRRLSALRS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 150 AFREAIAEGHITTNPVAATRAAKSEVRRSR-LTADEYLKIYQAAESSP--CWLRLAMELAVVTGQRVGDLCEMKWSDIV- 225
Cdd:COG4973    81 FFNWAVREGLLEANPAAGVKAPKAPRKLPRaLTVDELAQLLDALADDPlaVRDRAIVELLYSTGLRLGELVGLDWEDVDl 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 226 -DGYLYVeQSKTGV--KIAIPTALhVDALgismKETLDKCKEILGGET--IIASTRREPLSSGTVSRYFMRARKASGLSf 300
Cdd:COG4973   161 dAGEVRV-RGKTGKsrTVPLGPKA-LAAL----REWLAVRPELAAPDEgaLFPSRRGTRLSPRNVQKRLRRLAKKAGLP- 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1344182771 301 egDPPTFHELRSLSA-RLYEKQISDKFAQHLLGHKSDTMASQY 342
Cdd:COG4973   234 --KHVHPHDLRHSFAtHLLESGGDLRAVQELLGHASISTTQIY 274
Arm-DNA-bind_1 pfam09003
Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of ...
 2-69 7.78e-30

Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage.


Pssm-ID: 430365  Cd Length: 73  Bit Score: 109.12  E-value: 7.78e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1344182771   2 GRRRSHERRDLPPNLYIR-----NNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARIN 69
Cdd:pfam09003   1 APRPRKNSLNLPPNLYPKkdkrnGKVYYRYRHPVTGKFFGLGTDKREAIAEAVEANHRLAEQRQPSTLAERIK 73
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
80-158 2.28e-07

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 48.03  E-value: 2.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  80 LDRYEKILAS-RGIKQKTLINYMSKIKAIRRGLPDAP--LEDITTKEIAAMLNGYIDEG-KAASAKLIRSTLSDAFREAI 155
Cdd:pfam02899   1 IDQFLEYLSLeRGLSPHTLRAYRRDLLAFLKFLSEGGssLEQITTSDVRAFLAELRAQGlSASSLARRLSALRSFYQFLI 80


                  ...
gi 1344182771 156 AEG 158
Cdd:pfam02899  81 REG 83
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 183-351 1.46e-63

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: 199.49  E-value: 1.46e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 183 DEYLKIYQAAessPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPtalhvdaLGISMKETLDKC 262
Cdd:cd00800     1 AEYAAIYAEA---PPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIP-------WTPSLRALVDRI 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 263 KEILG--GETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMAS 340
Cdd:cd00800    71 RALPRkrSEYLINSRKGGPLSYDTLKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQGGSTDAQALLGHKSDAMTE 150

                         170
                  ....*....|.
gi 1344182771 341 QYRDDRGREWD 351
Cdd:cd00800   151 RYTRKRGQKWV 161
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 179-344 2.50e-45

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: 152.86  E-value: 2.50e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 179 RLTADEYLKIYQAAE--SSPCWLRLAMELAVVTGQRVGDLCEMKWSDI--VDGYLYVEQSKTGVKIAIPTAlhvDALGIS 254
Cdd:pfam00589   1 RLTEDEVERLLDAAEtgPLSIRDKALLELLYATGLRISELCSLRWSDIdfENGVIRVHRGKGNKERTVPLS---DAALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 255 MKETLDKC-KEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSfegDPPTFHELR-SLSARLYEKQISDKFAQHLLG 332
Cdd:pfam00589  78 LKEWLSKRlLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE---LPLHPHMLRhSFATHLLEAGVDLRVVQKLLG 154

                         170
                  ....*....|..
gi 1344182771 333 HKSDTMASQYRD 344
Cdd:pfam00589 155 HSSISTTQIYTH 166
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
73-342 1.33e-36

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 133.55  E-value: 1.33e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  73 SVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGYIDEGKAA-SAKLIRSTLSD 149
Cdd:COG4973     1 KLTLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDAdlPLEELTPADVRRFLARLHRRGLSPrTLNRRLSALRS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 150 AFREAIAEGHITTNPVAATRAAKSEVRRSR-LTADEYLKIYQAAESSP--CWLRLAMELAVVTGQRVGDLCEMKWSDIV- 225
Cdd:COG4973    81 FFNWAVREGLLEANPAAGVKAPKAPRKLPRaLTVDELAQLLDALADDPlaVRDRAIVELLYSTGLRLGELVGLDWEDVDl 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 226 -DGYLYVeQSKTGV--KIAIPTALhVDALgismKETLDKCKEILGGET--IIASTRREPLSSGTVSRYFMRARKASGLSf 300
Cdd:COG4973   161 dAGEVRV-RGKTGKsrTVPLGPKA-LAAL----REWLAVRPELAAPDEgaLFPSRRGTRLSPRNVQKRLRRLAKKAGLP- 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1344182771 301 egDPPTFHELRSLSA-RLYEKQISDKFAQHLLGHKSDTMASQY 342
Cdd:COG4973   234 --KHVHPHDLRHSFAtHLLESGGDLRAVQELLGHASISTTQIY 274
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
74-342 7.60e-33

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 123.95  E-value: 7.60e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  74 VTLHSWLDRY-EKILASRGIKQKTLINYMSKIKAIRR---GLPDAPLEDITTKEIAAMLNGYIDEG-KAASAKLIRSTLS 148
Cdd:COG4974     1 LTLADLLEAFlEELKREKGLSPNTIKAYRRDLRRFLRfleELGKIPLAEITPEDIRAYLNYLRERGlSPSTINRYLAALR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 149 DAFREAIAEGHITTNPVAATRAAKSEVRRSR-LTADEYLKIYQAAESSPCW---LRLAMELAVVTGQRVGDLCEMKWSDI 224
Cdd:COG4974    81 SFFRYAVREGLLEDNPAAKVKLPKKPRKLPRvLTEEEIEALLEALDTETPEglrDRALLLLLYATGLRVSELLGLKWSDI 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 225 V--DGYLYVEQSKTGVKIAIPtalhvdaLGISMKETLDKCKEILGGET---IIASTRREPLSSGTVSRYFMRARKASGLS 299
Cdd:COG4974   161 DldRGTIRVRRGKGGKERTVP-------LSPEALEALREYLEERRPRDsdyLFPTRRGRPLSRRAIRKILKRLAKRAGIP 233

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1344182771 300 fegDPPTFHELR-SLSARLYEKQISDKFAQHLLGHKSDTMASQY 342
Cdd:COG4974   234 ---KRVTPHSLRhTFATHLLEAGVDLRTVQELLGHSSISTTQIY 274
Arm-DNA-bind_1 pfam09003
Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of ...
 2-69 7.78e-30

Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage.


Pssm-ID: 430365  Cd Length: 73  Bit Score: 109.12  E-value: 7.78e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1344182771   2 GRRRSHERRDLPPNLYIR-----NNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARIN 69
Cdd:pfam09003   1 APRPRKNSLNLPPNLYPKkdkrnGKVYYRYRHPVTGKFFGLGTDKREAIAEAVEANHRLAEQRQPSTLAERIK 73
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 9-346 3.76e-26

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 107.43  E-value: 3.76e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771   9 RRDLPPNLYIRNNGYYCYRDPRTGKEFGLG------------RDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVT- 75
Cdd:COG0582    22 GGGLLLLVGPSGGKRWRYRYRFRGKRKRLAlgvypgvslalaRARRAEARALLALGIDPSPARKAAKAAAAAAAANTFEe 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  76 -LHSWLDRYEKilasrGIKQKTLINYMSKIKA-IRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFRE 153
Cdd:COG0582   102 vAEEWLEEKKP-----EWKEKTAAQVRRTLEKhIFPVLGDRPIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRY 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 154 AIAEGHITTNPVAATRAA--KSEVRRSR-LTADEYLKIYQAAESSPCWL--RLAMELAVVTGQRVGDLCEMKWSDI--VD 226
Cdd:COG0582   177 AVARGLIERNPAADLKGAlpKPKVKHHPaLTPEELPELLRALDAYRGSPvtRLALRLLLLTGVRPGELRGARWSEIdlEA 256

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 227 GYLYV--EQSKTGVKIAIPtaLHVDALGIsmketLDKCKEILGGETII---ASTRREPLSSGTVSryfmRARKASGLsfe 301
Cdd:COG0582   257 ALWTIpaERMKTRRPHIVP--LSRQALEI-----LKELKPLTGDSEYVfpsRRGPKKPMSENTLN----KALRRMGY--- 322

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1344182771 302 gDPPTFHELRSLSA-RLYEKQISDKFAQHLLGHKSDTMA------SQYRDDR 346
Cdd:COG0582   323 -GRFTPHGFRHTAStLLNEAGFPPDVIERQLAHKDGNKVraaynrADYLEER 373
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 184-342 8.79e-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: 65.58  E-value: 8.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 184 EYLKIYQAAESS---PCWLRLAMELAVVTGQRVGDLCEMKWSDIVD--GYLYVEQSKTG------VKIAIPTALHVDALg 252
Cdd:cd00397     1 ELEKLLDAIDEDkkiDLRDRAILLLLLETGLRISELLALKVKDIDLdnGTIRVRGKKTKggkertVPLPKELAEELKEY- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 253 isMKETLDKCKEILGGETIIAST---RREPLSSGTVSRYFMRARKASGLSFegdppTFHELRSLSA-RLYEKQISDKFAQ 328
Cdd:cd00397    80 --LKERRDKRGPLLKSLYLNKLFgtkLGERLSRRTLRRIFKKAGIEAGRKI-----TPHSLRHTFAtNLLENGVDIKVVQ 152

                         170
                  ....*....|....
gi 1344182771 329 HLLGHKSDTMASQY 342
Cdd:cd00397   153 KLLGHSSISTTQRY 166
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 176-342 5.73e-12

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: 63.11  E-value: 5.73e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 176 RRSRLTADEYLKIYQAAESSPC-WLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYV--EQSKTGVKIAIPtaLHVDALg 252
Cdd:cd00796     1 RDRFLTEDEEARLLAALEESTNpHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIvlPETKNGKPRTVP--LSDEAI- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 253 ismkETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEgdppTFHELR-SLSARLYEKQISDKFAQHLL 331
Cdd:cd00796    78 ----AILKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDL----RFHDLRhTFASRLVQAGVPIKTVAKIL 149

                         170
                  ....*....|.
gi 1344182771 332 GHKSDTMASQY 342
Cdd:cd00796   150 GHSSIKMTMRY 160
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 182-338 3.16e-08

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: 52.18  E-value: 3.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 182 ADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDI--VDGYLYVEQsktgvkiaiptalhvdalgismkeTL 259
Cdd:cd01189     1 PEELKKLLEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIdfENGTIRINR------------------------TL 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 260 DKCKEILGGETI---IASTRREPLSSGTVS-----RYFMRARKASGLsfegDPPTFHELRSLSA-RLYEKQISDKFAQHL 330
Cdd:cd01189    57 VRKKKGGYVIKPpktKSSIRTIPLPDELIEllkelKAFKKLLKKAGL----PRITPHDLRHTFAsLLLEAGVPLKVIAER 132


                  ....*...
gi 1344182771 331 LGHKSDTM 338
Cdd:cd01189   133 LGHSDIST 140
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
80-158 2.28e-07

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 48.03  E-value: 2.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771  80 LDRYEKILAS-RGIKQKTLINYMSKIKAIRRGLPDAP--LEDITTKEIAAMLNGYIDEG-KAASAKLIRSTLSDAFREAI 155
Cdd:pfam02899   1 IDQFLEYLSLeRGLSPHTLRAYRRDLLAFLKFLSEGGssLEQITTSDVRAFLAELRAQGlSASSLARRLSALRSFYQFLI 80


                  ...
gi 1344182771 156 AEG 158
Cdd:pfam02899  81 REG 83
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 180-342 3.92e-07

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: 49.61  E-value: 3.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 180 LTADEYLKIYQAAESSPC-----WLRLAMELAVVTGQRVGDLCEMKWSDIV--DGYLYV----EQSKTGVKIA-----IP 243
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCkkkdpALYWLPLIGLYTGARLNEICQLRVDDIKeeDGIWCIdindDAEGRRLKTKasrrlVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 244 taLHVDALGIS----MKETLDKCKEILGGETIIASTRReplsSGTVSRYFMRARKASGLSFEGDpPTFHELR-SLSARLY 318
Cdd:cd01184    81 --IHPRLIELGfldyVEALRADGKLFLFPEKRDKDGKY----SKAASKWFNRLLRKLGIKDDER-KSFHSFRhTFITALK 153

                         170       180
                  ....*....|....*....|....
gi 1344182771 319 EKQISDKFAQHLLGHKSDTMASQY 342
Cdd:cd01184   154 RAGVPEELIAQIVGHSRGGVTHDT 177
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 209-338 2.58e-06

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: 46.87  E-value: 2.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 209 TGQRVGDLCEMKWSDIVD----GYLYVEQSKTGVKIAIPtaLHVDALGIsmketLDKCKEILGGETIIastrrEPLSSGT 284
Cdd:cd01185    30 TGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTGKPVTVP--LLPVAREI-----LEKYKDDRSEGKLF-----PVLSNQK 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1344182771 285 VSRYFMRARKASGLsfegDPP-TFHelrslSAR------LYEKQISDKFAQHLLGHKSDTM 338
Cdd:cd01185    98 INRYLKEIAKIAGI----DKHlTFH-----VARhtfatlLLLKGVDIETISKLLGHSSIKT 149
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 200-346 1.31e-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: 44.95  E-value: 1.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 200 RLAMELAVVTGQRVGDLCEMKWSDIV--DGYLYV--EQSKTGVKIAIPtalhvdalgIS--MKETLDKCKEILGGETIIA 273
Cdd:cd00801    22 KLALRLLLLTGQRIGELARARWSEIDleEKTWTIpaERTKNKRPHRVP---------LSdqALEILEELKEFTGDSGYLF 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 274 STRREPLSSGTVSRYFMRARKasgLSFEGDPPTFHELRSL-SARLYEKQISDKFAQHLLGH--KSDTMA----SQYRDDR 346
Cdd:cd00801    93 PSRRKKKKPISENTINKALKR---LGYKGKEFTPHDLRRTfSTLLNELGIDPEVIERLLNHvlGGVVRAaynrYDYLEER 169
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
79-155 9.41e-05

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 40.67  E-value: 9.41e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1344182771  79 WLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAA--SAKLIRSTLSDAFREAI 155
Cdd:pfam13495   1 LLERFREALRLRGYAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHLANERNVSasTQNQALNALSFFYRWVL 79
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 180-311 1.88e-03

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: 38.83  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1344182771 180 LTADEYLKIYQAAESSPC---WLRLAMELAV----VTGQRVGDLCEMKWSDI--VDGYLYVEQSKTG----VKIAIPTal 246
Cdd:cd00797     1 YTDAEIRRLLAAADQLPPespLRPLTYATLFgllyATGLRVGEALRLRLEDVdlDSGILTIRQTKFGksrlVPLHPST-- 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1344182771 247 hVDALGISMKETLDKCKEILGGETIIASTRRePLSSGTVSRYFMRARKASGLSFEGDP--PTFHELR 311
Cdd:cd00797    79 -VGALRDYLARRDRLLPSPSSSYFFVSQQGG-RLTGGGVYRVFRRLLRRIGLRGAGDGrgPRLHDLR 143
 
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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