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Conserved domains on  [gi|492476429|ref|WP_005857485|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Parabacteroides]

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
SCOP:  4002347

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 ...
17-181 1.34e-28

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: 104.68  E-value: 1.34e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  17 EFLSTLEKLREDRLYWEELY------FTIAFASALRVSDIRMLKWENVLNKNSIILIEKKTKKNREVRLNDETVSIIKEL 90
Cdd:cd01192    4 EPIKDKKLIKEIKLYLKKANprnyllFIVGINTGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFPLNPTLVKALKEY 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  91 YTLMGKPSVNSYLFEGYK--NKPMGIWQINKRLKDVKDRYNLSIDhFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLNH 168
Cdd:cd01192   84 IDDLDLKRNDYLFKSLKQgpEKPISRKQAYKILKKAADDLGLNYN-IGTHSLRKTFGYHVYKQGK----DIELLMKLLNH 158
                        170
                 ....*....|...
gi 492476429 169 SNVGTTYTYIGIR 181
Cdd:cd01192  159 SSPSITLRYLGID 171
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
17-181 1.34e-28

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: 104.68  E-value: 1.34e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  17 EFLSTLEKLREDRLYWEELY------FTIAFASALRVSDIRMLKWENVLNKNSIILIEKKTKKNREVRLNDETVSIIKEL 90
Cdd:cd01192    4 EPIKDKKLIKEIKLYLKKANprnyllFIVGINTGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFPLNPTLVKALKEY 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  91 YTLMGKPSVNSYLFEGYK--NKPMGIWQINKRLKDVKDRYNLSIDhFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLNH 168
Cdd:cd01192   84 IDDLDLKRNDYLFKSLKQgpEKPISRKQAYKILKKAADDLGLNYN-IGTHSLRKTFGYHVYKQGK----DIELLMKLLNH 158
                        170
                 ....*....|...
gi 492476429 169 SNVGTTYTYIGIR 181
Cdd:cd01192  159 SSPSITLRYLGID 171
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
11-177 3.46e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 103.54  E-value: 3.46e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  11 DYLPYEEFLSTLEKLREDRLYWEELY--FTIAFASALRVSDIRMLKWENV-LNKNSIILIEKKTKKNREVRLNDETVSII 87
Cdd:COG4974  111 RVLTEEEIEALLEALDTETPEGLRDRalLLLLYATGLRVSELLGLKWSDIdLDRGTIRVRRGKGGKERTVPLSPEALEAL 190
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  88 KElYTLMGKPSVNSYLFEGYKNKPMGIWQINKRLKDVKDRYNLSiDHFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLN 167
Cdd:COG4974  191 RE-YLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIP-KRVTPHSLRHTFATHLLEAGV----DLRTVQELLG 264
                        170
                 ....*....|
gi 492476429 168 HSNVGTTYTY 177
Cdd:COG4974  265 HSSISTTQIY 274
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
15-178 1.68e-21

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: 85.83  E-value: 1.68e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429   15 YEEFLSTLEKLREDrlYWEELYFTIAFASALRVSDIRMLKWENVLNKNSIILIE-KKTKKNREVRLNDETVSIIKELYTL 93
Cdd:pfam00589   7 VERLLDAAETGPLS--IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLKEWLSK 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429   94 MGKP-SVNSYLFEGYKNKPMGIWQINKRLKDVKDRYNLSiDHFSTHSFRKTFGRYLYEAngrsQESLMMLKEVLNHSNVG 172
Cdd:pfam00589  85 RLLEaPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-LPLHPHMLRHSFATHLLEA----GVDLRVVQKLLGHSSIS 159

                  ....*.
gi 492476429  173 TTYTYI 178
Cdd:pfam00589 160 TTQIYT 165
xerD PRK00283
tyrosine recombinase;
19-178 3.29e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 40.18  E-value: 3.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  19 LSTLEKLReDRLYWEELYftiafASALRVSDIRMLKWENV-LNKNSIILIeKKTKKNREVRLNDETVSIIKElY------ 91
Cdd:PRK00283 128 IDTPLGLR-DRAMLELLY-----ATGLRVSELVGLTLDDVsLRQGVVRVT-GKGNKERLVPLGEEAVYAIER-Ylergrp 199
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  92 TLMGKPSVNsYLFEGYKNKPM---GIWQinkRLKDVKDRYNLSIDHFSTHSFRKTFGRYLYEaNGrsqESLMMLKEVLNH 168
Cdd:PRK00283 200 ALLNGRSSD-ALFPSARGGQLtrqTFWH---RIKHYAKRAGIDPKKLSPHVLRHAFATHLLN-HG---ADLRVVQELLGH 271
                        170
                 ....*....|..
gi 492476429 169 SNVGTT--YTYI 178
Cdd:PRK00283 272 SDISTTqiYTHV 283
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
17-181 1.34e-28

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: 104.68  E-value: 1.34e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  17 EFLSTLEKLREDRLYWEELY------FTIAFASALRVSDIRMLKWENVLNKNSIILIEKKTKKNREVRLNDETVSIIKEL 90
Cdd:cd01192    4 EPIKDKKLIKEIKLYLKKANprnyllFIVGINTGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFPLNPTLVKALKEY 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  91 YTLMGKPSVNSYLFEGYK--NKPMGIWQINKRLKDVKDRYNLSIDhFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLNH 168
Cdd:cd01192   84 IDDLDLKRNDYLFKSLKQgpEKPISRKQAYKILKKAADDLGLNYN-IGTHSLRKTFGYHVYKQGK----DIELLMKLLNH 158
                        170
                 ....*....|...
gi 492476429 169 SNVGTTYTYIGIR 181
Cdd:cd01192  159 SSPSITLRYLGID 171
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
11-177 3.46e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 103.54  E-value: 3.46e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  11 DYLPYEEFLSTLEKLREDRLYWEELY--FTIAFASALRVSDIRMLKWENV-LNKNSIILIEKKTKKNREVRLNDETVSII 87
Cdd:COG4974  111 RVLTEEEIEALLEALDTETPEGLRDRalLLLLYATGLRVSELLGLKWSDIdLDRGTIRVRRGKGGKERTVPLSPEALEAL 190
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  88 KElYTLMGKPSVNSYLFEGYKNKPMGIWQINKRLKDVKDRYNLSiDHFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLN 167
Cdd:COG4974  191 RE-YLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIP-KRVTPHSLRHTFATHLLEAGV----DLRTVQELLG 264
                        170
                 ....*....|
gi 492476429 168 HSNVGTTYTY 177
Cdd:COG4974  265 HSSISTTQIY 274
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
12-177 4.48e-22

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 90.02  E-value: 4.48e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  12 YLPYEEFLSTLEKLREDRLYWE-ELYFTIAFASALRVSDIRMLKWENVLNKNSIILIEKKTKKNREVRLNDETVSIIKEL 90
Cdd:COG4973  111 ALTVDELAQLLDALADDPLAVRdRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRGKTGKSRTVPLGPKALAALREW 190
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  91 YTLMG--KPSVNSYLFEGYKNKPMGIWQINKRLKDVKDRYNLSiDHFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLNH 168
Cdd:COG4973  191 LAVRPelAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLP-KHVHPHDLRHSFATHLLESGG----DLRAVQELLGH 265

                 ....*....
gi 492476429 169 SNVGTTYTY 177
Cdd:COG4973  266 ASISTTQIY 274
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
15-178 1.68e-21

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: 85.83  E-value: 1.68e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429   15 YEEFLSTLEKLREDrlYWEELYFTIAFASALRVSDIRMLKWENVLNKNSIILIE-KKTKKNREVRLNDETVSIIKELYTL 93
Cdd:pfam00589   7 VERLLDAAETGPLS--IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLKEWLSK 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429   94 MGKP-SVNSYLFEGYKNKPMGIWQINKRLKDVKDRYNLSiDHFSTHSFRKTFGRYLYEAngrsQESLMMLKEVLNHSNVG 172
Cdd:pfam00589  85 RLLEaPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-LPLHPHMLRHSFATHLLEA----GVDLRVVQKLLGHSSIS 159

                  ....*.
gi 492476429  173 TTYTYI 178
Cdd:pfam00589 160 TTQIYT 165
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
15-178 2.40e-19

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: 80.22  E-value: 2.40e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  15 YEEFLSTLEKLREDRLYWEeLYFTIAFASALRVSDIRMLKWENVLNKNSIILIEK---KTKKNREVRLNDETVSIIKELY 91
Cdd:cd00397    2 LEKLLDAIDEDKKIDLRDR-AILLLLLETGLRISELLALKVKDIDLDNGTIRVRGkktKGGKERTVPLPKELAEELKEYL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  92 T-------LMGKPSVNSYLFEGYKNKPMGIWQINKRLKDVKDRYNlsiDHFSTHSFRKTFGRYLYEANGrsqeSLMMLKE 164
Cdd:cd00397   81 KerrdkrgPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG---RKITPHSLRHTFATNLLENGV----DIKVVQK 153
                        170
                 ....*....|....
gi 492476429 165 VLNHSNVGTTYTYI 178
Cdd:cd00397  154 LLGHSSISTTQRYL 167
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
12-177 9.20e-15

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: 68.12  E-value: 9.20e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  12 YLPYEEFLSTLEKLREDRLYWEELYFTIAFASALRVSDIRMLKWENV-LNKNSIILIEKKTKKNREVRLNDETVSIIKEL 90
Cdd:cd00796    4 FLTEDEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIdLEVGLIVLPETKNGKPRTVPLSDEAIAILKEL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  91 YTLMGKPSVN-SYLFEGYKnkpmgIWQINKRLKDVKDRYNLSIDHFstHSFRKTFGRYLYEANGrsqeSLMMLKEVLNHS 169
Cdd:cd00796   84 KRKRGKDGFFvDGRFFGIP-----IASLRRAFKKARKRAGLEDLRF--HDLRHTFASRLVQAGV----PIKTVAKILGHS 152

                 ....*...
gi 492476429 170 NVGTTYTY 177
Cdd:cd00796  153 SIKMTMRY 160
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
37-181 6.49e-13

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: 63.05  E-value: 6.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  37 FTIAFASALRVSDIRMLKWENVLNKNS---IILIEKKTKKNREVRLNDETVSIIkELYTLMGKpsvNSYLFEGYKNkpmg 113
Cdd:cd01185   24 FLFSCYTGLRFSDLKNLTWKNIVEASGrtwIRYRRKKTGKPVTVPLLPVAREIL-EKYKDDRS---EGKLFPVLSN---- 95
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492476429 114 iWQINKRLKDVkdRYNLSID-HFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLNHSNVGTTYTYIGIR 181
Cdd:cd01185   96 -QKINRYLKEI--AKIAGIDkHLTFHVARHTFATLLLLKGV----DIETISKLLGHSSIKTTQIYAKIV 157
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
17-144 1.09e-12

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: 63.06  E-value: 1.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  17 EFLSTLEKLREDRLYweELYFTIAFASALRVSDIRMLKWENV-LNKNSIILIEKKTKKNRE--VRLNDETVSIIKELYTL 93
Cdd:cd00801    7 ELWRALDTANLSPPT--KLALRLLLLTGQRIGELARARWSEIdLEEKTWTIPAERTKNKRPhrVPLSDQALEILEELKEF 84
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492476429  94 MGkpsVNSYLFEG--YKNKPMGIWQINKRLKdvkdRYNLSIDHFSTHSFRKTF 144
Cdd:cd00801   85 TG---DSGYLFPSrrKKKKPISENTINKALK----RLGYKGKEFTPHDLRRTF 130
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
37-180 2.47e-12

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: 61.87  E-value: 2.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  37 FTIAFASALRVSDIRMLKWENVLNKN-SIILIEKKTKKNREVRLNDETVSIIKElYTLMGKPSVNS-YLFEGYKNkPMGI 114
Cdd:cd01188   26 LLLLARLGLRAGDVAGLRLDDIDWRSgTITVRQKKTGRPVELPLTEPVGEALAD-YLRDGRPRTDSrEVFLRARA-PYRP 103
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429 115 WQINKRLKDVKDRY----NLSIDHFSTHSFRKTFGRYLYEANGrsqeSLMMLKEVLNHSNVGTTYTYIGI 180
Cdd:cd01188  104 LSSTSQISSIVRRYlrkaGIEPSHRGTHSLRHSLATRMLRAGT----SLKVIADLLGHRSIETTAIYAKI 169
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
4-174 2.07e-11

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 61.21  E-value: 2.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429   4 KGVLTKS-----DYLPYEEFLSTLEKLREDRLYWE-ELYFTIAFASALRVSDIRMLKWENVLNKNSIILI--EK-KTKKN 74
Cdd:COG0582  192 KGALPKPkvkhhPALTPEELPELLRALDAYRGSPVtRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIpaERmKTRRP 271
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  75 REVRLNDETVSIIKELYTLMGKpsvNSYLFEGYKN--KPMGIWQINKRLKdvkdryNLSIDHFSTHSFRKTFGRYLYEAN 152
Cdd:COG0582  272 HIVPLSRQALEILKELKPLTGD---SEYVFPSRRGpkKPMSENTLNKALR------RMGYGRFTPHGFRHTASTLLNEAG 342
                        170       180
                 ....*....|....*....|..
gi 492476429 153 grsqESLMMLKEVLNHSNVGTT 174
Cdd:COG0582  343 ----FPPDVIERQLAHKDGNKV 360
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
37-178 1.06e-04

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 40.49  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  37 FTIAFASALRVSDIRMLKWENVLNKNSI-------ILIEKKTKKNREVRLNDETVSIIKelytlmgkpsvnsylfegykn 109
Cdd:cd01187   19 VQAAVFTGARASELATLKFGCLHAQTSDdgtflywLKWENKGGKQLDIPISKKVAELIK--------------------- 77
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492476429 110 kpmgiwQINKRLKDVKDRYNLS-----IDHFSTHSFRKTFGRYLyeANGRsqESLMMLKEVLNHSNVGTTYTYI 178
Cdd:cd01187   78 ------TINWTLNELSELKNISddhgeRFRFHTHRFRHTVATRL--ANSG--MGILVLQQLLGHSSPEMTLRYA 141
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
37-178 2.80e-04

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: 39.98  E-value: 2.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  37 FTIAFASALRVSDIRMLKWENVLNKNSIILI-EKKTKKNREVRLNDETVSIIKELYTLMGKPSVN---SYLFEGYKNKPM 112
Cdd:cd00797   31 FGLLYATGLRVGEALRLRLEDVDLDSGILTIrQTKFGKSRLVPLHPSTVGALRDYLARRDRLLPSpssSYFFVSQQGGRL 110
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492476429 113 -------GIWQINKR--LKDVKDRYNLSIdhfstHSFRKTFG-RYL---YEANGRSQESLMMLKEVLNHSNVGTTYTYI 178
Cdd:cd00797  111 tgggvyrVFRRLLRRigLRGAGDGRGPRL-----HDLRHTFAvNRLtrwYREGADVERKLPVLSTYLGHVNVTDTYWYL 184
xerD PRK00283
tyrosine recombinase;
19-178 3.29e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 40.18  E-value: 3.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  19 LSTLEKLReDRLYWEELYftiafASALRVSDIRMLKWENV-LNKNSIILIeKKTKKNREVRLNDETVSIIKElY------ 91
Cdd:PRK00283 128 IDTPLGLR-DRAMLELLY-----ATGLRVSELVGLTLDDVsLRQGVVRVT-GKGNKERLVPLGEEAVYAIER-Ylergrp 199
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  92 TLMGKPSVNsYLFEGYKNKPM---GIWQinkRLKDVKDRYNLSIDHFSTHSFRKTFGRYLYEaNGrsqESLMMLKEVLNH 168
Cdd:PRK00283 200 ALLNGRSSD-ALFPSARGGQLtrqTFWH---RIKHYAKRAGIDPKKLSPHVLRHAFATHLLN-HG---ADLRVVQELLGH 271
                        170
                 ....*....|..
gi 492476429 169 SNVGTT--YTYI 178
Cdd:PRK00283 272 SDISTTqiYTHV 283
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
6-178 1.66e-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: 37.40  E-value: 1.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429   6 VLTKSDYlpyeEFLSTLEKlREDRLYWeelYFTIAF--ASALRVSDIRMLKWENVlNKNSIILIEKKTKKNR---EVRLN 80
Cdd:cd01191    1 VISNADY----NFLKKCLK-KDGNLEW---YFVVRFlaATGARVSELIKIKVEHV-ELGYFDIYSKGGKLRRlyiPKKLR 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492476429  81 DETVSIIKELYTLMGkpsvnsYLFEGYKNKPMGIWQINKRLKDVKDRYNLSIDHFSTHSFRKTFGRYLYEangrSQESLM 160
Cdd:cd01191   72 NEALEWLKSTNRKSG------YIFLNRFGERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLE----KYNDIA 141
                        170
                 ....*....|....*...
gi 492476429 161 MLKEVLNHSNVGTTYTYI 178
Cdd:cd01191  142 LLADLMGHESIETTRIYL 159
 
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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