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Conserved domains on  [gi|493293694|ref|WP_006251368|]
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tyrosine-type recombinase/integrase [Mannheimia haemolytica]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 178-334 2.22e-36

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


The actual alignment was detected with superfamily member cd00800:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 161  Bit Score: 129.00  E-value: 2.22e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 178 FQMVYEVADQDMRDLMDLAYITGQRPVDLVNIRKEHIFDGYLHIVQQKTQAKLRIEIVGKLADIIQD--RLEKATGTHLF 255
Cdd:cd00800    3 YAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRirALPRKRSEYLI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 256 STKKGEKLTARKLGKRFTYIREQA-VKNNPEyaneimAFQFRDLRAKSGTDKALSLGEEAARQQLGHTSVQMTKTYIRKA 334
Cdd:cd00800   83 NSRKGGPLSYDTLKSAWRRARKAAgLKGETE------GFTFHDLRAKAATDYAEQGGSTDAQALLGHKSDAMTERYTRKR 156
Phage_int_SAM_4 super family cl48195
Phage integrase, N-terminal SAM-like domain;
86-140 3.15e-04

Phage integrase, N-terminal SAM-like domain;


The actual alignment was detected with superfamily member pfam13495:

Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.13  E-value: 3.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 493293694   86 KKASTAQTDLCKIKNLLLFFNDAPLEEITPQHIREYMTW----RKDTPGSANNEFSMFS 140
Cdd:pfam13495  14 YAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHlaneRNVSASTQNQALNALS 72
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 178-334 2.22e-36

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: 129.00  E-value: 2.22e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 178 FQMVYEVADQDMRDLMDLAYITGQRPVDLVNIRKEHIFDGYLHIVQQKTQAKLRIEIVGKLADIIQD--RLEKATGTHLF 255
Cdd:cd00800    3 YAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRirALPRKRSEYLI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 256 STKKGEKLTARKLGKRFTYIREQA-VKNNPEyaneimAFQFRDLRAKSGTDKALSLGEEAARQQLGHTSVQMTKTYIRKA 334
Cdd:cd00800   83 NSRKGGPLSYDTLKSAWRRARKAAgLKGETE------GFTFHDLRAKAATDYAEQGGSTDAQALLGHKSDAMTERYTRKR 156
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
69-335 5.22e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 96.99  E-value: 5.22e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694  69 ITFGLVAKRYRDEVIPQKKAS--TAQTDLCKIKNLLLFF---NDAPLEEITPQHIREYMTWRKD---TPGSANNEFSMFS 140
Cdd:COG4974    1 LTLADLLEAFLEELKREKGLSpnTIKAYRRDLRRFLRFLeelGKIPLAEITPEDIRAYLNYLRErglSPSTINRYLAALR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 141 HIWQYAREWGY-TNLPSPNIGMKRYPIRKREIYVENNIFQMVYEVADQDMRDLMD-----LAYITGQRPVDLVNIRKEHI 214
Cdd:COG4974   81 SFFRYAVREGLlEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDralllLLYATGLRVSELLGLKWSDI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 215 F--DGYLHIVQQKTQAKLRIEIVGKLADIIQDRLEKA---TGTHLFSTKKGEKLTARKLGKRFTYIREQAVKNNPeyane 289
Cdd:COG4974  161 DldRGTIRVRRGKGGKERTVPLSPEALEALREYLEERrprDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKR----- 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 493293694 290 imaFQFRDLR-------AKSGTDkalslgEEAARQQLGHTSVQMTKTYIRKAP 335
Cdd:COG4974  236 ---VTPHSLRhtfathlLEAGVD------LRTVQELLGHSSISTTQIYTHVSD 279
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 183-335 1.01e-08

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: 53.86  E-value: 1.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694  183 EVADQDMRD--LMDLAYITGQRPVDLVNIRKEHI--FDGYLHIVQQKTQAK----LRIEIVGKLADIIQDRLEKATGTH- 253
Cdd:pfam00589  15 ETGPLSIRDkaLLELLYATGLRISELCSLRWSDIdfENGVIRVHRGKGNKErtvpLSDAALELLKEWLSKRLLEAPKSDy 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694  254 LFSTKKGEKLTARKLGKRFTYIREQAVKNNPeyaneimaFQFRDLRAKSGTDkalsLGEE-----AARQQLGHTSVQMTK 328
Cdd:pfam00589  95 LFASKRGKPLSRQTVRKIFKRAGKEAGLELP--------LHPHMLRHSFATH----LLEAgvdlrVVQKLLGHSSISTTQ 162


                  ....*..
gi 493293694  329 TYIRKAP 335
Cdd:pfam00589 163 IYTHVAD 169
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
86-140 3.15e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.13  E-value: 3.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 493293694   86 KKASTAQTDLCKIKNLLLFFNDAPLEEITPQHIREYMTW----RKDTPGSANNEFSMFS 140
Cdd:pfam13495  14 YAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHlaneRNVSASTQNQALNALS 72
 
Name Accession Description Interval E-value
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 178-334 2.22e-36

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: 129.00  E-value: 2.22e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 178 FQMVYEVADQDMRDLMDLAYITGQRPVDLVNIRKEHIFDGYLHIVQQKTQAKLRIEIVGKLADIIQD--RLEKATGTHLF 255
Cdd:cd00800    3 YAAIYAEAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRirALPRKRSEYLI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 256 STKKGEKLTARKLGKRFTYIREQA-VKNNPEyaneimAFQFRDLRAKSGTDKALSLGEEAARQQLGHTSVQMTKTYIRKA 334
Cdd:cd00800   83 NSRKGGPLSYDTLKSAWRRARKAAgLKGETE------GFTFHDLRAKAATDYAEQGGSTDAQALLGHKSDAMTERYTRKR 156
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
69-335 5.22e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 96.99  E-value: 5.22e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694  69 ITFGLVAKRYRDEVIPQKKAS--TAQTDLCKIKNLLLFF---NDAPLEEITPQHIREYMTWRKD---TPGSANNEFSMFS 140
Cdd:COG4974    1 LTLADLLEAFLEELKREKGLSpnTIKAYRRDLRRFLRFLeelGKIPLAEITPEDIRAYLNYLRErglSPSTINRYLAALR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 141 HIWQYAREWGY-TNLPSPNIGMKRYPIRKREIYVENNIFQMVYEVADQDMRDLMD-----LAYITGQRPVDLVNIRKEHI 214
Cdd:COG4974   81 SFFRYAVREGLlEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDralllLLYATGLRVSELLGLKWSDI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 215 F--DGYLHIVQQKTQAKLRIEIVGKLADIIQDRLEKA---TGTHLFSTKKGEKLTARKLGKRFTYIREQAVKNNPeyane 289
Cdd:COG4974  161 DldRGTIRVRRGKGGKERTVPLSPEALEALREYLEERrprDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKR----- 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 493293694 290 imaFQFRDLR-------AKSGTDkalslgEEAARQQLGHTSVQMTKTYIRKAP 335
Cdd:COG4974  236 ---VTPHSLRhtfathlLEAGVD------LRTVQELLGHSSISTTQIYTHVSD 279
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
102-332 1.60e-21

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 92.72  E-value: 1.60e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 102 LLFFNDAPLEEITPQHIREYMTWRKDT---PGSANNEFSMFSHIWQYAREWGY--TNlPSPNIGMKRYPIRKREIY-VE- 174
Cdd:COG4973   38 LLGDADLPLEELTPADVRRFLARLHRRglsPRTLNRRLSALRSFFNWAVREGLleAN-PAAGVKAPKAPRKLPRALtVDe 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 175 -NNIFQMVYE-VADQDMRDLMDLAYITGQRPVDLVNIRKEHI--FDGYLHiVQQKTQAKLRIEIVGKLADIIQDRLE--- 247
Cdd:COG4973  117 lAQLLDALADdPLAVRDRAIVELLYSTGLRLGELVGLDWEDVdlDAGEVR-VRGKTGKSRTVPLGPKALAALREWLAvrp 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 248 ---KATGTHLFSTKKGEKLTARKLGKRFTYIREQAVKNNPeyaneimaFQFRDLRAKSGTDKALSLGE-EAARQQLGHTS 323
Cdd:COG4973  196 elaAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKH--------VHPHDLRHSFATHLLESGGDlRAVQELLGHAS 267


                 ....*....
gi 493293694 324 VQMTKTYIR 332
Cdd:COG4973  268 ISTTQIYTH 276
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 183-335 1.01e-08

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: 53.86  E-value: 1.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694  183 EVADQDMRD--LMDLAYITGQRPVDLVNIRKEHI--FDGYLHIVQQKTQAK----LRIEIVGKLADIIQDRLEKATGTH- 253
Cdd:pfam00589  15 ETGPLSIRDkaLLELLYATGLRISELCSLRWSDIdfENGVIRVHRGKGNKErtvpLSDAALELLKEWLSKRLLEAPKSDy 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694  254 LFSTKKGEKLTARKLGKRFTYIREQAVKNNPeyaneimaFQFRDLRAKSGTDkalsLGEE-----AARQQLGHTSVQMTK 328
Cdd:pfam00589  95 LFASKRGKPLSRQTVRKIFKRAGKEAGLELP--------LHPHMLRHSFATH----LLEAgvdlrVVQKLLGHSSISTTQ 162


                  ....*..
gi 493293694  329 TYIRKAP 335
Cdd:pfam00589 163 IYTHVAD 169
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 183-332 1.56e-07

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: 50.40  E-value: 1.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 183 EVADQDMRDLMDLAYITGQRPVDLVNIRKEHI-FD-GYLHIVQQKTQAKLRIEIVGKLADIIQDRLEKATGTHLFSTKKG 260
Cdd:cd00796   19 ESTNPHLRLIVLLALYTGARRGEILSLRWDDIdLEvGLIVLPETKNGKPRTVPLSDEAIAILKELKRKRGKDGFFVDGRF 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 493293694 261 EKLTARKLGKRFTYIREQAvknnpeyanEIMAFQFRDLR---AKSGTDKALSLGEEAArqQLGHTSVQMTKTYIR 332
Cdd:cd00796   99 FGIPIASLRRAFKKARKRA---------GLEDLRFHDLRhtfASRLVQAGVPIKTVAK--ILGHSSIKMTMRYAH 162
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 177-331 4.51e-06

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: 46.32  E-value: 4.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 177 IFQMVYEVADQDMRD--LMDLAYITGQRPVDLVNIRKEHI--FDGYLHIVQQKTQA-KLR-IEIVGKLADIIQDRLEKAt 250
Cdd:cd00397    5 LLDAIDEDKKIDLRDraILLLLLETGLRISELLALKVKDIdlDNGTIRVRGKKTKGgKERtVPLPKELAEELKEYLKER- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 251 GTHLFSTKKGEKLTARKLGKRFTYIREQAVKNNPEYANEIMAFQFR--DLRAKSGTDKALSLG-EEAARQQLGHTSVQMT 327
Cdd:cd00397   84 RDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITphSLRHTFATNLLENGVdIKVVQKLLGHSSISTT 163


                 ....
gi 493293694 328 KTYI 331
Cdd:cd00397  164 QRYL 167
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
86-140 3.15e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.13  E-value: 3.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 493293694   86 KKASTAQTDLCKIKNLLLFFNDAPLEEITPQHIREYMTW----RKDTPGSANNEFSMFS 140
Cdd:pfam13495  14 YAERTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHlaneRNVSASTQNQALNALS 72
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 187-332 2.15e-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: 38.40  E-value: 2.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 187 QDMRDLMDLAYITGQRPVDLVNIRKEHIFD----GYLHIVQQKTQAKLRIEIVGKLADIIQDRLEKATGTHLFSTKKGEK 262
Cdd:cd01185   18 ELVRDMFLFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTGKPVTVPLLPVAREILEKYKDDRSEGKLFPVLSNQK 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493293694 263 LTarklgkrfTYIREQAvknnpEYA--NEIMAFQ-----FRDLRAKSGTDKalslgeEAARQQLGHTSVQMTKTYIR 332
Cdd:cd01185   98 IN--------RYLKEIA-----KIAgiDKHLTFHvarhtFATLLLLKGVDI------ETISKLLGHSSIKTTQIYAK 155
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 199-333 6.21e-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: 271191  Cd Length: 176  Bit Score: 37.02  E-value: 6.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493293694 199 TGQRPVDLVNIRKEHIFDGYLHIVQQKTQAKlRIEIVGKLADIIQDRLEKA--TGTHLFSTKKGEKLTARKLGKRF-TYI 275
Cdd:cd01191   32 TGARVSELIKIKVEHVELGYFDIYSKGGKLR-RLYIPKKLRNEALEWLKSTnrKSGYIFLNRFGERITTRGIAQQLkNYA 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 493293694 276 REQAVKNNPEYANeimafQFRDLRAKSGTDKALSLGEEAarQQLGHTSVQMTKTYIRK 333
Cdd:cd01191  111 RKYGLNPKVVYPH-----SFRHRFAKNFLEKYNDIALLA--DLMGHESIETTRIYLRK 161
 
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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