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Conserved domains on  [gi|16129103|ref|NP_415658|]
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putative integrase [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

site-specific integrase( domain architecture ID 10557089)

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:  10047575|9278480|10577069
SCOP:  4002347

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; ...
 197-371 1.07e-56

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: 182.54  E-value: 1.07e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 197 EEWKKIFDIADathRYMGNAMLLALVTGQRLGDISRMKFSDIWDDHLHVIQEKTGSKIAIPLSLrlnainwSLRDVVARC 276
Cdd:cd00800   1 AEYAAIYAEAP---PLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTP-------SLRALVDRI 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 277 RDYAV--SAYLVHFfrstsqaERGAQVKANTLTMNFSKARDLARIDWgEGSPATFHEQRSLSERLYKEQGLDT--QKLLG 352
Cdd:cd00800  71 RALPRkrSEYLINS-------RKGGPLSYDTLKSAWRRARKAAGLKG-ETEGFTFHDLRAKAATDYAEQGGSTdaQALLG 142

                       170
                ....*....|....*....
gi 16129103 353 HKTQQQTDRYHDDRGKGWS 371
Cdd:cd00800 143 HKSDAMTERYTRKRGQKWV 161
Arm-DNA-bind_1 pfam09003
Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of ...
 2-73 3.28e-25

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: 97.18  E-value: 3.28e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129103     2 AARPRKNNVSVP-NLYPLYSRKVNKVYWRYKHPVTGKFHALGTNEAEAIAIATEANTRLAEQRTRQILAISDR 73
Cdd:pfam09003   1 APRPRKNSLNLPpNLYPKKDKRNGKVYYRYRHPVTGKFFGLGTDKREAIAEAVEANHRLAEQRQPSTLAERIK 73
FimB super family cl43194
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 15-259 1.85e-10

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


The actual alignment was detected with superfamily member COG0582:

Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 61.98  E-value: 1.85e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  15 LYPLYSRKVNKVYWRYKHPVTGKFHALG------TNEAEAIAIATEANTRLAEQRTRQILAISDRIATSKGKAITTSTWL 88
Cdd:COG0582  24 GLLLLVGPSGGKRWRYRYRFRGKRKRLAlgvypgVSLALARARRAEARALLALGIDPSPARKAAKAAAAAAAANTFEEVA 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  89 DRYQAIQDDRLKSGDIR--LNTYKQKAKPVslLRERagmkLISAVDVRDIAQLLDEYIAAGRPRMAQVVRSVLIDVFKEA 166
Cdd:COG0582 104 EEWLEEKKPEWKEKTAAqvRRTLEKHIFPV--LGDR----PIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYA 177

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 167 QHYGEVPpgYNPA--LATKQPRRKITRQR-LSLEEWKKIFDIADA--THRYMGNAMLLALVTGQRLGDISRMKFSDI-WD 240
Cdd:COG0582 178 VARGLIE--RNPAadLKGALPKPKVKHHPaLTPEELPELLRALDAyrGSPVTRLALRLLLLTGVRPGELRGARWSEIdLE 255

                       250       260
                ....*....|....*....|..
gi 16129103 241 DHLHVIQE---KTGSKIAIPLS 259
Cdd:COG0582 256 AALWTIPAermKTRRPHIVPLS 277
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 197-371 1.07e-56

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: 182.54  E-value: 1.07e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 197 EEWKKIFDIADathRYMGNAMLLALVTGQRLGDISRMKFSDIWDDHLHVIQEKTGSKIAIPLSLrlnainwSLRDVVARC 276
Cdd:cd00800   1 AEYAAIYAEAP---PLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTP-------SLRALVDRI 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 277 RDYAV--SAYLVHFfrstsqaERGAQVKANTLTMNFSKARDLARIDWgEGSPATFHEQRSLSERLYKEQGLDT--QKLLG 352
Cdd:cd00800  71 RALPRkrSEYLINS-------RKGGPLSYDTLKSAWRRARKAAGLKG-ETEGFTFHDLRAKAATDYAEQGGSTdaQALLG 142

                       170
                ....*....|....*....
gi 16129103 353 HKTQQQTDRYHDDRGKGWS 371
Cdd:cd00800 143 HKSDAMTERYTRKRGQKWV 161
Arm-DNA-bind_1 pfam09003
Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of ...
 2-73 3.28e-25

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: 97.18  E-value: 3.28e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129103     2 AARPRKNNVSVP-NLYPLYSRKVNKVYWRYKHPVTGKFHALGTNEAEAIAIATEANTRLAEQRTRQILAISDR 73
Cdd:pfam09003   1 APRPRKNSLNLPpNLYPKKDKRNGKVYYRYRHPVTGKFFGLGTDKREAIAEAVEANHRLAEQRQPSTLAERIK 73
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
82-362 1.68e-16

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 78.88  E-value: 1.68e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  82 ITTSTWLDRYQaiqDDRLKSGDIRLNTYKQKAKPVSLLR---ERAGMKLISAVDVRDIAQLLDEYIAAGR-PRMAQVVRS 157
Cdd:COG4974   1 LTLADLLEAFL---EELKREKGLSPNTIKAYRRDLRRFLrflEELGKIPLAEITPEDIRAYLNYLRERGLsPSTINRYLA 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 158 VLIDVFKEAQHYGEVPpgYNPALATKQPRRKITRQR-LSLEEWKKIFDIADATHRY---MGNAMLLALVTGQRLGDISRM 233
Cdd:COG4974  78 ALRSFFRYAVREGLLE--DNPAAKVKLPKKPRKLPRvLTEEEIEALLEALDTETPEglrDRALLLLLYATGLRVSELLGL 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 234 KFSDI-WDDH-LHVIQEKTGSKIAIPLSLRLNAInwsLRDVVARCRDYAvSAYLvhfFRSTsqaeRGAQVKANTLTMNFS 311
Cdd:COG4974 156 KWSDIdLDRGtIRVRRGKGGKERTVPLSPEALEA---LREYLEERRPRD-SDYL---FPTR----RGRPLSRRAIRKILK 224

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16129103 312 KARDLARIDWgegsPATFHeqrSLseR-----LYKEQGLD---TQKLLGHKTQQQTDRY 362
Cdd:COG4974 225 RLAKRAGIPK----RVTPH---SL--RhtfatHLLEAGVDlrtVQELLGHSSISTTQIY 274
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 193-362 2.48e-11

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: 61.57  E-value: 2.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103   193 RLSLEEWKKIFDIADATHRYMGNAML--LALVTGQRLGDISRMKFSDIWDDH--LHVIQEKTGSKIAIPLSLrlnAINWS 268
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALleLLYATGLRISELCSLRWSDIDFENgvIRVHRGKGNKERTVPLSD---AALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103   269 LRDVVARCRDYAVSAYLVhfFRSTsqaeRGAQVKANTLTMNFSKARDLARIDwgegSPATFHEQR-SLSERLYKEqGLDT 347
Cdd:pfam00589  78 LKEWLSKRLLEAPKSDYL--FASK----RGKPLSRQTVRKIFKRAGKEAGLE----LPLHPHMLRhSFATHLLEA-GVDL 146

                         170
                  ....*....|....*...
gi 16129103   348 ---QKLLGHKTQQQTDRY 362
Cdd:pfam00589 147 rvvQKLLGHSSISTTQIY 164
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 15-259 1.85e-10

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 61.98  E-value: 1.85e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  15 LYPLYSRKVNKVYWRYKHPVTGKFHALG------TNEAEAIAIATEANTRLAEQRTRQILAISDRIATSKGKAITTSTWL 88
Cdd:COG0582  24 GLLLLVGPSGGKRWRYRYRFRGKRKRLAlgvypgVSLALARARRAEARALLALGIDPSPARKAAKAAAAAAAANTFEEVA 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  89 DRYQAIQDDRLKSGDIR--LNTYKQKAKPVslLRERagmkLISAVDVRDIAQLLDEYIAAGRPRMAQVVRSVLIDVFKEA 166
Cdd:COG0582 104 EEWLEEKKPEWKEKTAAqvRRTLEKHIFPV--LGDR----PIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYA 177

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 167 QHYGEVPpgYNPA--LATKQPRRKITRQR-LSLEEWKKIFDIADA--THRYMGNAMLLALVTGQRLGDISRMKFSDI-WD 240
Cdd:COG0582 178 VARGLIE--RNPAadLKGALPKPKVKHHPaLTPEELPELLRALDAyrGSPVTRLALRLLLLTGVRPGELRGARWSEIdLE 255

                       250       260
                ....*....|....*....|..
gi 16129103 241 DHLHVIQE---KTGSKIAIPLS 259
Cdd:COG0582 256 AALWTIPAermKTRRPHIVPLS 277
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 197-371 1.07e-56

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: 182.54  E-value: 1.07e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 197 EEWKKIFDIADathRYMGNAMLLALVTGQRLGDISRMKFSDIWDDHLHVIQEKTGSKIAIPLSLrlnainwSLRDVVARC 276
Cdd:cd00800   1 AEYAAIYAEAP---PLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTP-------SLRALVDRI 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 277 RDYAV--SAYLVHFfrstsqaERGAQVKANTLTMNFSKARDLARIDWgEGSPATFHEQRSLSERLYKEQGLDT--QKLLG 352
Cdd:cd00800  71 RALPRkrSEYLINS-------RKGGPLSYDTLKSAWRRARKAAGLKG-ETEGFTFHDLRAKAATDYAEQGGSTdaQALLG 142

                       170
                ....*....|....*....
gi 16129103 353 HKTQQQTDRYHDDRGKGWS 371
Cdd:cd00800 143 HKSDAMTERYTRKRGQKWV 161
Arm-DNA-bind_1 pfam09003
Bacteriophage lambda integrase, Arm DNA-binding domain; The amino terminal domain of ...
 2-73 3.28e-25

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: 97.18  E-value: 3.28e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129103     2 AARPRKNNVSVP-NLYPLYSRKVNKVYWRYKHPVTGKFHALGTNEAEAIAIATEANTRLAEQRTRQILAISDR 73
Cdd:pfam09003   1 APRPRKNSLNLPpNLYPKKDKRNGKVYYRYRHPVTGKFFGLGTDKREAIAEAVEANHRLAEQRQPSTLAERIK 73
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
82-362 1.68e-16

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 78.88  E-value: 1.68e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  82 ITTSTWLDRYQaiqDDRLKSGDIRLNTYKQKAKPVSLLR---ERAGMKLISAVDVRDIAQLLDEYIAAGR-PRMAQVVRS 157
Cdd:COG4974   1 LTLADLLEAFL---EELKREKGLSPNTIKAYRRDLRRFLrflEELGKIPLAEITPEDIRAYLNYLRERGLsPSTINRYLA 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 158 VLIDVFKEAQHYGEVPpgYNPALATKQPRRKITRQR-LSLEEWKKIFDIADATHRY---MGNAMLLALVTGQRLGDISRM 233
Cdd:COG4974  78 ALRSFFRYAVREGLLE--DNPAAKVKLPKKPRKLPRvLTEEEIEALLEALDTETPEglrDRALLLLLYATGLRVSELLGL 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 234 KFSDI-WDDH-LHVIQEKTGSKIAIPLSLRLNAInwsLRDVVARCRDYAvSAYLvhfFRSTsqaeRGAQVKANTLTMNFS 311
Cdd:COG4974 156 KWSDIdLDRGtIRVRRGKGGKERTVPLSPEALEA---LREYLEERRPRD-SDYL---FPTR----RGRPLSRRAIRKILK 224

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16129103 312 KARDLARIDWgegsPATFHeqrSLseR-----LYKEQGLD---TQKLLGHKTQQQTDRY 362
Cdd:COG4974 225 RLAKRAGIPK----RVTPH---SL--RhtfatHLLEAGVDlrtVQELLGHSSISTTQIY 274
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
81-362 1.44e-14

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 73.46  E-value: 1.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  81 AITTSTWLDRYQAIQDDRLKSgdirLNTYKQKAKPVSLLRERAGMKL--ISAVDVRDIAQLLDEYIAAGR-PRMAQVVRS 157
Cdd:COG4973   1 KLTLAEALEAYLEHLRERRLS----PKTLEAYRRDLRRLIPLLGDADlpLEELTPADVRRFLARLHRRGLsPRTLNRRLS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 158 VLIDVFKEAQHYGEVPPgyNPALATKQPRRKITRQR-LSLEEWKKIFDI--ADATHRYMGNAMLLALVTGQRLGDISRMK 234
Cdd:COG4973  77 ALRSFFNWAVREGLLEA--NPAAGVKAPKAPRKLPRaLTVDELAQLLDAlaDDPLAVRDRAIVELLYSTGLRLGELVGLD 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 235 FSDI-WDDHLHVIQEKTGSKIAIPLSLRLNAI--NW-SLRDVVARCRDYAVsaylvhfFRSTsqaeRGAQVKANTLTMNF 310
Cdd:COG4973 155 WEDVdLDAGEVRVRGKTGKSRTVPLGPKALAAlrEWlAVRPELAAPDEGAL-------FPSR----RGTRLSPRNVQKRL 223

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 16129103 311 SKARDLAridwGEGSPATFHEQRSLSERLYKEQGLD---TQKLLGHKTQQQTDRY 362
Cdd:COG4973 224 RRLAKKA----GLPKHVHPHDLRHSFATHLLESGGDlraVQELLGHASISTTQIY 274
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 193-362 2.48e-11

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: 61.57  E-value: 2.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103   193 RLSLEEWKKIFDIADATHRYMGNAML--LALVTGQRLGDISRMKFSDIWDDH--LHVIQEKTGSKIAIPLSLrlnAINWS 268
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALleLLYATGLRISELCSLRWSDIDFENgvIRVHRGKGNKERTVPLSD---AALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103   269 LRDVVARCRDYAVSAYLVhfFRSTsqaeRGAQVKANTLTMNFSKARDLARIDwgegSPATFHEQR-SLSERLYKEqGLDT 347
Cdd:pfam00589  78 LKEWLSKRLLEAPKSDYL--FASK----RGKPLSRQTVRKIFKRAGKEAGLE----LPLHPHMLRhSFATHLLEA-GVDL 146

                         170
                  ....*....|....*...
gi 16129103   348 ---QKLLGHKTQQQTDRY 362
Cdd:pfam00589 147 rvvQKLLGHSSISTTQIY 164
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 15-259 1.85e-10

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 61.98  E-value: 1.85e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  15 LYPLYSRKVNKVYWRYKHPVTGKFHALG------TNEAEAIAIATEANTRLAEQRTRQILAISDRIATSKGKAITTSTWL 88
Cdd:COG0582  24 GLLLLVGPSGGKRWRYRYRFRGKRKRLAlgvypgVSLALARARRAEARALLALGIDPSPARKAAKAAAAAAAANTFEEVA 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103  89 DRYQAIQDDRLKSGDIR--LNTYKQKAKPVslLRERagmkLISAVDVRDIAQLLDEYIAAGRPRMAQVVRSVLIDVFKEA 166
Cdd:COG0582 104 EEWLEEKKPEWKEKTAAqvRRTLEKHIFPV--LGDR----PIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYA 177

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 167 QHYGEVPpgYNPA--LATKQPRRKITRQR-LSLEEWKKIFDIADA--THRYMGNAMLLALVTGQRLGDISRMKFSDI-WD 240
Cdd:COG0582 178 VARGLIE--RNPAadLKGALPKPKVKHHPaLTPEELPELLRALDAyrGSPVTRLALRLLLLTGVRPGELRGARWSEIdLE 255

                       250       260
                ....*....|....*....|..
gi 16129103 241 DHLHVIQE---KTGSKIAIPLS 259
Cdd:COG0582 256 AALWTIPAermKTRRPHIVPLS 277
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 192-363 1.06e-08

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: 53.87  E-value: 1.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 192 QRLSLEEWKKIFDIADATHRYM-GNAMLLALVTGQRLGDISRMKFSDIWDDH-LHVIQE-KTGSKIAIPLSLRLNAInws 268
Cdd:cd00796   3 RFLTEDEEARLLAALEESTNPHlRLIVLLALYTGARRGEILSLRWDDIDLEVgLIVLPEtKNGKPRTVPLSDEAIAI--- 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 269 lRDVVARCRDYAVSAYLVHFFRSTSQAERGAqvkantltmnFSKARDLARIdwgegSPATFHEQR-SLSERLYkEQGLD- 346
Cdd:cd00796  80 -LKELKRKRGKDGFFVDGRFFGIPIASLRRA----------FKKARKRAGL-----EDLRFHDLRhTFASRLV-QAGVPi 142

                       170
                ....*....|....*....
gi 16129103 347 --TQKLLGHKTQQQTDRYH 363
Cdd:cd00796 143 ktVAKILGHSSIKMTMRYA 161
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 198-362 1.17e-05

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: 45.16  E-value: 1.17e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 198 EWKKIFDIADAT------HRYMgnaMLLALVTGQRLGDISRMKFSDI--WDDHLHVIQEK--TGSKIAIPLSLRLNAinw 267
Cdd:cd00397   1 ELEKLLDAIDEDkkidlrDRAI---LLLLLETGLRISELLALKVKDIdlDNGTIRVRGKKtkGGKERTVPLPKELAE--- 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 268 SLRDVVARCRDYAVSAYLVHFFRSTSQAERGAQVKANTLTMNFSKARDLAridwgeGSPATFHEQRSLSERLYKEQGLD- 346
Cdd:cd00397  75 ELKEYLKERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEA------GRKITPHSLRHTFATNLLENGVDi 148

                       170
                ....*....|....*...
gi 16129103 347 --TQKLLGHKTQQQTDRY 362
Cdd:cd00397 149 kvVQKLLGHSSISTTQRY 166
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 194-362 8.61e-05

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: 42.68  E-value: 8.61e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 194 LSLEEWKKIFD-------IADATHRYMgnAMLLALVTGQRLGDISRMKFSDI-WDDHLHVI-----QEKTGSKIA----- 255
Cdd:cd01184   1 FTPEELAKIFSsplytgcKKKDPALYW--LPLIGLYTGARLNEICQLRVDDIkEEDGIWCIdinddAEGRRLKTKasrrl 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 256 IPLSLRLnaINWSLRDVVARCRDyavsaylVHFFRSTSQAERGAQVKANTLTMNFSKARDLARIDWGEGspATFHEQRSL 335
Cdd:cd01184  79 VPIHPRL--IELGFLDYVEALRA-------DGKLFLFPEKRDKDGKYSKAASKWFNRLLRKLGIKDDER--KSFHSFRHT 147

                       170       180       190
                ....*....|....*....|....*....|.
gi 16129103 336 SERLYKEQGLD---TQKLLGHKTQQQT-DRY 362
Cdd:cd01184 148 FITALKRAGVPeelIAQIVGHSRGGVThDTY 178
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 217-362 7.90e-04

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: 39.92  E-value: 7.90e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 217 MLLALVTGQRLGDISRMKFSDI-WDDH-LHVIQEKTGSKIAIPLslrLNAINWSLRDVVARCRDYAVSAYLvhFFRSTsq 294
Cdd:cd01188  26 LLLLARLGLRAGDVAGLRLDDIdWRSGtITVRQKKTGRPVELPL---TEPVGEALADYLRDGRPRTDSREV--FLRAR-- 98

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 295 AERGAQVKANTLTMNFSKARDLARIDWGEGSPATFheQRSLSERLYKE-QGLDT-QKLLGHKTQQQTDRY 362
Cdd:cd01188  99 APYRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSL--RHSLATRMLRAgTSLKViADLLGHRSIETTAIY 166
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 218-362 1.12e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 39.58  E-value: 1.12e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 218 LLALVTGQRLGDISRMKFSDI-WDDHLHVIQEKTGsKIAIplsLRLNAINwsLRDVVARCRDYAVSAYLVHFFRSTSQAE 296
Cdd:cd01192  31 IVGINTGLRISDLLSLKVEDVtNKDKLSIKEQKTG-KQKT---FPLNPTL--VKALKEYIDDLDLKRNDYLFKSLKQGPE 104

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16129103 297 RGAQVK-ANTLtmnFSKARDLARIDWGEGSpatfHEQR-SLSERLYKeQGLD---TQKLLGHKTQQQTDRY 362
Cdd:cd01192 105 KPISRKqAYKI---LKKAADDLGLNYNIGT----HSLRkTFGYHVYK-QGKDielLMKLLNHSSPSITLRY 167
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 197-259 7.39e-03

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: 36.86  E-value: 7.39e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129103 197 EEWKKIFDI---ADATHRYMGNAMLLALVTGQRLGDISRMKFSDIWDDH----LHVIQEKTGSKIAIPLS 259
Cdd:cd01185   1 EELKRLMALelsDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEASgrtwIRYRRKKTGKPVTVPLL 70
 
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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