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Conserved domains on  [gi|1586009570|ref|WP_131121710|]
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tyrosine-type recombinase/integrase, partial [Bacillus subtilis]

Protein Classification

site-specific integrase( domain architecture ID 332)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10577069|10047575|9278480

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 ...
 2-127 4.49e-32

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 cd01192:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 178  Bit Score: 111.23  E-value: 4.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570   2 NFVQPIRDPECIFYIKRFLKEQNMRNYMLFVTGINSGLRISDILQLRVRD-AKRPYFNLIEKK----KRIDMTPALQREF 76
Cdd:cd01192     1 QIVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDvTNKDKLSIKEQKtgkqKTFPLNPTLVKAL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1586009570  77 KAYVEGKEDHE---FLFKSREGINKPISRSMAYKILRAAAEYVGL-DDIGTHTLR 127
Cdd:cd01192    81 KEYIDDLDLKRndyLFKSLKQGPEKPISRKQAYKILKKAADDLGLnYNIGTHSLR 135
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 2-127 4.49e-32

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: 111.23  E-value: 4.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570   2 NFVQPIRDPECIFYIKRFLKEQNMRNYMLFVTGINSGLRISDILQLRVRD-AKRPYFNLIEKK----KRIDMTPALQREF 76
Cdd:cd01192     1 QIVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDvTNKDKLSIKEQKtgkqKTFPLNPTLVKAL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1586009570  77 KAYVEGKEDHE---FLFKSREGINKPISRSMAYKILRAAAEYVGL-DDIGTHTLR 127
Cdd:cd01192    81 KEYIDDLDLKRndyLFKSLKQGPEKPISRKQAYKILKKAADDLGLnYNIGTHSLR 135
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
16-127 1.95e-14

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 67.33  E-value: 1.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  16 IKRFLKE------QNMRNYMLFVTGINSGLRISDILQLRVRD--AKRPYFNLIEKKKR----IDMTPALQREFKAYVE-- 81
Cdd:COG4974   118 IEALLEAldtetpEGLRDRALLLLLYATGLRVSELLGLKWSDidLDRGTIRVRRGKGGkertVPLSPEALEALREYLEer 197

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1586009570  82 GKEDHEFLFKSREGinKPISRSMAYKILRAAAEYVGLD-DIGTHTLR 127
Cdd:COG4974   198 RPRDSDYLFPTRRG--RPLSRRAIRKILKRLAKRAGIPkRVTPHSLR 242
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 25-127 2.64e-10

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: 54.63  E-value: 2.64e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  25 MRNYMLFVTGINSGLRISDILQLRVRD--AKRPYFNLIEKKKRIDMT--------PALQREFKAYVEGKEDHEFLFKSRE 94
Cdd:pfam00589  21 IRDKALLELLYATGLRISELCSLRWSDidFENGVIRVHRGKGNKERTvplsdaalELLKEWLSKRLLEAPKSDYLFASKR 100

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1586009570  95 GinKPISRSMAYKILRAAAEYVGLDD-IGTHTLR 127
Cdd:pfam00589 101 G--KPLSRQTVRKIFKRAGKEAGLELpLHPHMLR 132
PRK09870 PRK09870
tyrosine recombinase; Provisional
 26-127 1.03e-05

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 42.62  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRD----AKRPYFNLIekKKRIDMT-PALQREFKAYVE--------GKEDHEFLFKS 92
Cdd:PRK09870   33 RNYCLTLLCFIHGFRASEICRLRISDidlkAKCIYIHRL--KKGFSTThPLLNKEIQALKNwlsirtsyPHAESEWVFLS 110

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1586009570  93 REGinKPISRSMAYKILRAAAEYVGLD-DIGTHTLR 127
Cdd:PRK09870  111 RKG--NPLSRQQFYHIISTSGGNAGLSlEIHPHMLR 144
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 2-127 4.49e-32

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: 111.23  E-value: 4.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570   2 NFVQPIRDPECIFYIKRFLKEQNMRNYMLFVTGINSGLRISDILQLRVRD-AKRPYFNLIEKK----KRIDMTPALQREF 76
Cdd:cd01192     1 QIVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDvTNKDKLSIKEQKtgkqKTFPLNPTLVKAL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1586009570  77 KAYVEGKEDHE---FLFKSREGINKPISRSMAYKILRAAAEYVGL-DDIGTHTLR 127
Cdd:cd01192    81 KEYIDDLDLKRndyLFKSLKQGPEKPISRKQAYKILKKAADDLGLnYNIGTHSLR 135
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
16-127 1.95e-14

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 67.33  E-value: 1.95e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  16 IKRFLKE------QNMRNYMLFVTGINSGLRISDILQLRVRD--AKRPYFNLIEKKKR----IDMTPALQREFKAYVE-- 81
Cdd:COG4974   118 IEALLEAldtetpEGLRDRALLLLLYATGLRVSELLGLKWSDidLDRGTIRVRRGKGGkertVPLSPEALEALREYLEer 197

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1586009570  82 GKEDHEFLFKSREGinKPISRSMAYKILRAAAEYVGLD-DIGTHTLR 127
Cdd:COG4974   198 RPRDSDYLFPTRRG--RPLSRRAIRKILKRLAKRAGIPkRVTPHSLR 242
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 25-127 2.64e-10

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: 54.63  E-value: 2.64e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  25 MRNYMLFVTGINSGLRISDILQLRVRD--AKRPYFNLIEKKKRIDMT--------PALQREFKAYVEGKEDHEFLFKSRE 94
Cdd:pfam00589  21 IRDKALLELLYATGLRISELCSLRWSDidFENGVIRVHRGKGNKERTvplsdaalELLKEWLSKRLLEAPKSDYLFASKR 100

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1586009570  95 GinKPISRSMAYKILRAAAEYVGLDD-IGTHTLR 127
Cdd:pfam00589 101 G--KPLSRQTVRKIFKRAGKEAGLELpLHPHMLR 132
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
26-127 3.07e-08

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 50.35  E-value: 3.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVR--DAKRPYFNLIEK--KKR-IDMTPALQREFKAYVE-----GKEDHEFLFKSREG 95
Cdd:COG4973   132 RDRAIVELLYSTGLRLGELVGLDWEdvDLDAGEVRVRGKtgKSRtVPLGPKALAALREWLAvrpelAAPDEGALFPSRRG 211

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1586009570  96 inKPISRSMAYKILRAAAEYVGLDD-IGTHTLR 127
Cdd:COG4973   212 --TRLSPRNVQKRLRRLAKKAGLPKhVHPHDLR 242
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 13-127 1.19e-07

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: 47.86  E-value: 1.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  13 IFYIKRFLKEQNMRNYMLFVTGINSGLRISDILQLRVRD--AKRPYFNLIEKKK------RIDMTPALQREFKAYVE--- 81
Cdd:cd00397     5 LLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDidLDNGTIRVRGKKTkggkerTVPLPKELAEELKEYLKerr 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1586009570  82 -----GKEDHEFLFKSREGINKPISRSMAYKILRAAAEYVGlDDIGTHTLR 127
Cdd:cd00397    85 dkrgpLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG-RKITPHSLR 134
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 37-127 1.32e-06

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 44.81  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  37 SGLRISDILQLRVRD--AKRPYFNLIEKKKRIDMTP-------ALQR---EFKAYVEGKEDHEFLFKSREGinKPISRSM 104
Cdd:cd00798    31 SGLRVSELVGLDLSDvdLDEGLVRVTGKGNKERLVPfgsyaveALEEyleERRPLLLKKKPPDALFLNKRG--KRLSRRG 108

                          90       100
                  ....*....|....*....|....
gi 1586009570 105 AYKILRAAAEYVGL-DDIGTHTLR 127
Cdd:cd00798   109 VWRILKKYAERAGLpKHVSPHTLR 132
PRK09870 PRK09870
tyrosine recombinase; Provisional
 26-127 1.03e-05

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 42.62  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRD----AKRPYFNLIekKKRIDMT-PALQREFKAYVE--------GKEDHEFLFKS 92
Cdd:PRK09870   33 RNYCLTLLCFIHGFRASEICRLRISDidlkAKCIYIHRL--KKGFSTThPLLNKEIQALKNwlsirtsyPHAESEWVFLS 110

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1586009570  93 REGinKPISRSMAYKILRAAAEYVGLD-DIGTHTLR 127
Cdd:PRK09870  111 RKG--NPLSRQQFYHIISTSGGNAGLSlEIHPHMLR 144
PRK09871 PRK09871
tyrosine recombinase; Provisional
 26-125 9.33e-05

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 39.97  E-value: 9.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRDakrpyFNLIEKK---------------KRIDMTPALQR--EFKAYVEGKEDHEF 88
Cdd:PRK09871   27 RDYCLILLAYRHGMRISELLDLHYQD-----LDLNEGRinirrlkngfstvhpLRFDEREAVERwtQERANWKGADRTDA 101

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1586009570  89 LFKSREGinKPISRSMAYKILRAAAEYVGlddIGTHT 125
Cdd:PRK09871  102 IFISRRG--SRLSRQQAYRIIRDAGIEAG---TVTQT 133
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 36-127 1.15e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 40.14  E-value: 1.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  36 NSGLRISDILQLRVRDAKRPYFNLI----EKKKR-IDMTPALQREFKAYVE----GKEDHEFLFKSREGinKPISRSMAY 106
Cdd:PRK00236  147 GSGLRLSELVGLDIDDLDLASGTLRvlgkGNKERtVPLGRAAREALEAYLAlrplFLPDDDALFLGARG--GRLSPRVVQ 224

                          90       100
                  ....*....|....*....|..
gi 1586009570 107 KILRAAAEYVGL-DDIGTHTLR 127
Cdd:PRK00236  225 RRVKKLGKKAGLpSHITPHKLR 246
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 26-127 4.56e-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: 37.99  E-value: 4.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRD----AKRpyFNLIEKKKRIDMTPALQREFKAYVE-------GKEDHEFLFKS-R 93
Cdd:cd01188    21 RDYAILLLLARLGLRAGDVAGLRLDDidwrSGT--ITVRQKKTGRPVELPLTEPVGEALAdylrdgrPRTDSREVFLRaR 98

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1586009570  94 EGINKPISRSMAYKILRAAAEYVGLDDI--GTHTLR 127
Cdd:cd01188    99 APYRPLSSTSQISSIVRRYLRKAGIEPShrGTHSLR 134
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 23-127 1.39e-03

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 36.48  E-value: 1.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  23 QNMRNYMLFVTGINSGLRISDILQLRVRDAK-RPYFNLIE----KKKRIDMTP-ALQREFKAYVEGKEDHEFLFKSREGI 96
Cdd:cd01193    19 TELRHRLILSLLYGAGLRISELLRLRVKDIDfERGVIRVRqgkgGKDRVVPLPeKLLEPLRRYLKSARPKEELDPAEGRA 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1586009570  97 N-----------KPISRSMAYKILRAAAEYVGLD-DIGTHTLR 127
Cdd:cd01193    99 GvldprtgverrHHISETTVQRALKKAVEQAGITkRVTPHTLR 141
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 26-127 2.79e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 35.52  E-value: 2.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRDAKRPYFNLIEKKK------RIDMTPALQREFKAYVEGK-EDHEFLFKS--REGI 96
Cdd:cd01195    21 RDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKgkkqreVVTLPPTTREALAAWLAARgEAEGPLFVSldRASR 100

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1586009570  97 NKPISRSMAYKILRAAAEYVGLDD-IGTHTLR 127
Cdd:cd01195   101 GRRLSPQAVYRIVRRLAERIGLGKrLSPHGLR 132
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 26-114 4.88e-03

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 34.95  E-value: 4.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRDAKR---PYFNLIEKKKRIDMTPaLQRE----FKAYV------EGKEDHEFLFKS 92
Cdd:cd01182    22 RDHALLLLLYDTGARVQELADLTIRDLRLddpATVRLHGKGRKERTVP-LWKEtvaaLKAYLqefhltPDPKQLFPLFPN 100

                          90       100
                  ....*....|....*....|..
gi 1586009570  93 RegINKPISRSMAYKILRAAAE 114
Cdd:cd01182   101 R--RGQPLTRDGVAYILNKYVA 120
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 26-127 7.88e-03

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: 34.22  E-value: 7.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586009570  26 RNYMLFVTGINSGLRISDILQLRVRDAKRPYfNLIE-------KKKRIDMTPALQREFKAYVEGKEDHEFLFKSREGINK 98
Cdd:cd00796    24 HLRLIVLLALYTGARRGEILSLRWDDIDLEV-GLIVlpetkngKPRTVPLSDEAIAILKELKRKRGKDGFFVDGRFFGIP 102

                          90       100
                  ....*....|....*....|....*....
gi 1586009570  99 PISRSmayKILRAAAEYVGLDDIGTHTLR 127
Cdd:cd00796   103 IASLR---RAFKKARKRAGLEDLRFHDLR 128
 
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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