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Conserved domains on  [gi|582647714|gb|EVZ37520|]
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phage integrase [Staphylococcus aureus F19383]

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
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 ...
 2-175 3.56e-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: 113.93  E-value: 3.56e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   2 NKVEAIKFNDDIVKMYEALKIKSERDYLFFKLAIHSGLKVSELLTITVSQVK-----RLIEKCTlsemCKAHfhsliKIR 76
Cdd:cd01192    1 QIVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVTnkdklSIKEQKT----GKQK-----TFP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  77 LPETLSKELLQYIEDRSLSNEDVLFQSLR--TNQVLSRQQAYRIIHQASIEAGI-DNVGLTTLRKTFAYHAYQKGIPIPV 153
Cdd:cd01192   72 LNPTLVKALKEYIDDLDLKRNDYLFKSLKqgPEKPISRKQAYKILKKAADDLGLnYNIGTHSLRKTFGYHVYKQGKDIEL 151

                        170       180
                 ....*....|....*....|..
gi 582647714 154 IQKYLGHQSAIETLNFIGLENE 175
Cdd:cd01192  152 LMKLLNHSSPSITLRYLGIDQE 173
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 2-175 3.56e-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: 113.93  E-value: 3.56e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   2 NKVEAIKFNDDIVKMYEALKIKSERDYLFFKLAIHSGLKVSELLTITVSQVK-----RLIEKCTlsemCKAHfhsliKIR 76
Cdd:cd01192    1 QIVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVTnkdklSIKEQKT----GKQK-----TFP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  77 LPETLSKELLQYIEDRSLSNEDVLFQSLR--TNQVLSRQQAYRIIHQASIEAGI-DNVGLTTLRKTFAYHAYQKGIPIPV 153
Cdd:cd01192   72 LNPTLVKALKEYIDDLDLKRNDYLFKSLKqgPEKPISRKQAYKILKKAADDLGLnYNIGTHSLRKTFGYHVYKQGKDIEL 151

                        170       180
                 ....*....|....*....|..
gi 582647714 154 IQKYLGHQSAIETLNFIGLENE 175
Cdd:cd01192  152 LMKLLNHSSPSITLRYLGIDQE 173
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
11-166 1.91e-21

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 88.51  E-value: 1.91e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEALKIKS---ERDYLFFKLAIHSGLKVSELLTITVSQV---KRLIeKCTLSEMCKAHFhslikIRLPETLSKE 84
Cdd:COG4974  116 EEIEALLEALDTETpegLRDRALLLLLYATGLRVSELLGLKWSDIdldRGTI-RVRRGKGGKERT-----VPLSPEALEA 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  85 LLQYIEDRSLSNEDVLFQSLRTNQvLSRQQAYRIIHQASIEAGID-NVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSa 163
Cdd:COG4974  190 LREYLEERRPRDSDYLFPTRRGRP-LSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSS- 267


                 ...
gi 582647714 164 IET 166
Cdd:COG4974  268 IST 270
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 11-168 2.80e-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: 85.45  E-value: 2.80e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   11 DDIVKMYEALKIKS--ERDYLFFKLAIHSGLKVSELLTITVSQV---KRLIeKCTLSEMCKAHFHSLikirlPETLSKEL 85
Cdd:pfam00589   5 DEVERLLDAAETGPlsIRDKALLELLYATGLRISELCSLRWSDIdfeNGVI-RVHRGKGNKERTVPL-----SDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   86 LQYIEDRSLSNE--DVLFQSLRTNQvLSRQQAYRIIHQASIEAGIDNVgLT--TLRKTFAYHAYQKGIPIPVIQKYLGHQ 161
Cdd:pfam00589  79 KEWLSKRLLEAPksDYLFASKRGKP-LSRQTVRKIFKRAGKEAGLELP-LHphMLRHSFATHLLEAGVDLRVVQKLLGHS 156


                  ....*..
gi 582647714  162 SaIETLN 168
Cdd:pfam00589 157 S-ISTTQ 162
PRK09871 PRK09871
tyrosine recombinase; Provisional
 25-169 6.00e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 61.54  E-value: 6.00e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  25 ERDYLFFKLAIHSGLKVSELLTITVSQVKrLIEKCTLSEMCKAHFHSLIKIRLPETLSKELLQYIED--RSLSNEDVLFQ 102
Cdd:PRK09871  26 ARDYCLILLAYRHGMRISELLDLHYQDLD-LNEGRINIRRLKNGFSTVHPLRFDEREAVERWTQERAnwKGADRTDAIFI 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582647714 103 SLRTNQvLSRQQAYRIIHQASIEAG-IDNVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSAIETLNF 169
Cdd:PRK09871 105 SRRGSR-LSRQQAYRIIRDAGIEAGtVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRY 171
 
Name Accession Description Interval E-value
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 2-175 3.56e-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: 113.93  E-value: 3.56e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   2 NKVEAIKFNDDIVKMYEALKIKSERDYLFFKLAIHSGLKVSELLTITVSQVK-----RLIEKCTlsemCKAHfhsliKIR 76
Cdd:cd01192    1 QIVEPIKDKKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVTnkdklSIKEQKT----GKQK-----TFP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  77 LPETLSKELLQYIEDRSLSNEDVLFQSLR--TNQVLSRQQAYRIIHQASIEAGI-DNVGLTTLRKTFAYHAYQKGIPIPV 153
Cdd:cd01192   72 LNPTLVKALKEYIDDLDLKRNDYLFKSLKqgPEKPISRKQAYKILKKAADDLGLnYNIGTHSLRKTFGYHVYKQGKDIEL 151

                        170       180
                 ....*....|....*....|..
gi 582647714 154 IQKYLGHQSAIETLNFIGLENE 175
Cdd:cd01192  152 LMKLLNHSSPSITLRYLGIDQE 173
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
11-166 1.91e-21

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 88.51  E-value: 1.91e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEALKIKS---ERDYLFFKLAIHSGLKVSELLTITVSQV---KRLIeKCTLSEMCKAHFhslikIRLPETLSKE 84
Cdd:COG4974  116 EEIEALLEALDTETpegLRDRALLLLLYATGLRVSELLGLKWSDIdldRGTI-RVRRGKGGKERT-----VPLSPEALEA 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  85 LLQYIEDRSLSNEDVLFQSLRTNQvLSRQQAYRIIHQASIEAGID-NVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSa 163
Cdd:COG4974  190 LREYLEERRPRDSDYLFPTRRGRP-LSRRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSS- 267


                 ...
gi 582647714 164 IET 166
Cdd:COG4974  268 IST 270
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 11-168 2.80e-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: 85.45  E-value: 2.80e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   11 DDIVKMYEALKIKS--ERDYLFFKLAIHSGLKVSELLTITVSQV---KRLIeKCTLSEMCKAHFHSLikirlPETLSKEL 85
Cdd:pfam00589   5 DEVERLLDAAETGPlsIRDKALLELLYATGLRISELCSLRWSDIdfeNGVI-RVHRGKGNKERTVPL-----SDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714   86 LQYIEDRSLSNE--DVLFQSLRTNQvLSRQQAYRIIHQASIEAGIDNVgLT--TLRKTFAYHAYQKGIPIPVIQKYLGHQ 161
Cdd:pfam00589  79 KEWLSKRLLEAPksDYLFASKRGKP-LSRQTVRKIFKRAGKEAGLELP-LHphMLRHSFATHLLEAGVDLRVVQKLLGHS 156


                  ....*..
gi 582647714  162 SaIETLN 168
Cdd:pfam00589 157 S-ISTTQ 162
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 13-162 2.54e-17

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: 75.21  E-value: 2.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  13 IVKMYEALKIKSERDYLFFKLAIHSGLKVSELLTITVSQVKRLIEKCTLSEMcKAHFHSLIKIRLPETLSKELLQYIEDR 92
Cdd:cd00397    5 LLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGK-KTKGGKERTVPLPKELAEELKEYLKER 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582647714  93 SLSNEDVLFQSLRTNQV-------LSRQQAYRIIHQASIEAGIDnVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQS 162
Cdd:cd00397   84 RDKRGPLLKSLYLNKLFgtklgerLSRRTLRRIFKKAGIEAGRK-ITPHSLRHTFATNLLENGVDIKVVQKLLGHSS 159
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 11-162 3.42e-12

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 61.19  E-value: 3.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEAL-KIKSERDYLFFKLAIHSGLKVSELLTITVSQVKrliekctlsemckahfHSLIKIRLPET--------- 80
Cdd:cd00796    8 DEEARLLAALeESTNPHLRLIVLLALYTGARRGEILSLRWDDID----------------LEVGLIVLPETkngkprtvp 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  81 LSKELLQYIEDR-SLSNEDVLFQSLRTNqVLSRQQAYRIIHQASIEAGIDNVGLTTLRKTFAYHAYQKGIPIPVIQKYLG 159
Cdd:cd00796   72 LSDEAIAILKELkRKRGKDGFFVDGRFF-GIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILG 150


                 ...
gi 582647714 160 HQS 162
Cdd:cd00796  151 HSS 153
PRK09871 PRK09871
tyrosine recombinase; Provisional
 25-169 6.00e-12

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 61.54  E-value: 6.00e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  25 ERDYLFFKLAIHSGLKVSELLTITVSQVKrLIEKCTLSEMCKAHFHSLIKIRLPETLSKELLQYIED--RSLSNEDVLFQ 102
Cdd:PRK09871  26 ARDYCLILLAYRHGMRISELLDLHYQDLD-LNEGRINIRRLKNGFSTVHPLRFDEREAVERWTQERAnwKGADRTDAIFI 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582647714 103 SLRTNQvLSRQQAYRIIHQASIEAG-IDNVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSAIETLNF 169
Cdd:PRK09871 105 SRRGSR-LSRQQAYRIIRDAGIEAGtVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRY 171
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 24-161 2.01e-11

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 59.83  E-value: 2.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  24 SERDYLFFKLAIHSGLKVSELLTITVSQVKrLIEKCTLSEMCKAHFHSLIKIRLPETLS-KELLQYIEDRSLSNEDVLFQ 102
Cdd:cd01197   25 PARDYCLLLLAFRHGFRVSELCDLHLSDVD-LESRRLHIRRLKNGFSTTHPLRFDEREAlEAWLKERANWKGADTDWIFL 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714 103 SLRTNQvLSRQQAYRIIHQASIEAGID-NVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQ 161
Cdd:cd01197  104 SRRGGP-LSRQQAYRIIRDLGKEAGTVtQTHPHMLRHACGYALADRGADTRLIQDYLGHR 162
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 26-166 2.84e-11

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: 59.18  E-value: 2.84e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  26 RDYLFFKLAIHSGLKVSELL------------TITVSQVKRliekctlsemckahfHSLIKIRLPETLSKELLQYIED-R 92
Cdd:cd01188   21 RDYAILLLLARLGLRAGDVAglrlddidwrsgTITVRQKKT---------------GRPVELPLTEPVGEALADYLRDgR 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582647714  93 SLSNEDVLFQSLR--TNQVLSRQQAYRIIHQASIEAGIDN--VGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSAIET 166
Cdd:cd01188   86 PRTDSREVFLRARapYRPLSSTSQISSIVRRYLRKAGIEPshRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETT 163
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
11-162 9.87e-11

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 59.20  E-value: 9.87e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEALK--IKSERDYLFFKLAIHSGLKVSELLTITVSQVKrlIEKCTLSEMCKAhfHSLIKIRLPETLSKELLQY 88
Cdd:COG4973  115 DELAQLLDALAddPLAVRDRAIVELLYSTGLRLGELVGLDWEDVD--LDAGEVRVRGKT--GKSRTVPLGPKALAALREW 190

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582647714  89 IEDRSLSN---EDVLFQSlRTNQVLSRQQAYRIIHQASIEAGI-DNVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQS 162
Cdd:COG4973  191 LAVRPELAapdEGALFPS-RRGTRLSPRNVQKRLRRLAKKAGLpKHVHPHDLRHSFATHLLESGGDLRAVQELLGHAS 267
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 26-166 1.90e-10

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: 57.29  E-value: 1.90e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  26 RDYLFFKLAIHSGLKVSELLTITVSQVK-------RLIEK------CTLSEMCKAHFHSLIKIRLPETLSKELLqyiedr 92
Cdd:cd01182   22 RDHALLLLLYDTGARVQELADLTIRDLRlddpatvRLHGKgrkertVPLWKETVAALKAYLQEFHLTPDPKQLF------ 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  93 slsnedVLFQSLRTNQvLSRQQAYRIIHQASIEAGIDNVGLT------TLRKTFAYHAYQKGIPIPVIQKYLGHQSaIET 166
Cdd:cd01182   96 ------PLFPNRRGQP-LTRDGVAYILNKYVALASNRCPSLPkritphTLRHTKAMHLLQAGVDLTVIRDWLGHES-VET 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 11-162 7.39e-10

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: 55.36  E-value: 7.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEALKikSERDYLFFKLAIHSGLKVSELLTITVSQVKrliekctlSEmckahfHSLIKIR-----------LPE 79
Cdd:cd01193    9 DEVRRILGALT--ELRHRLILSLLYGAGLRISELLRLRVKDID--------FE------RGVIRVRqgkggkdrvvpLPE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  80 TLSKELLQYIE--------DRSLSNEDVLFQSLRTNQV--LSRQQAYRIIHQASIEAGIDN-VGLTTLRKTFAYHAYQKG 148
Cdd:cd01193   73 KLLEPLRRYLKsarpkeelDPAEGRAGVLDPRTGVERRhhISETTVQRALKKAVEQAGITKrVTPHTLRHSFATHLLEAG 152

                        170
                 ....*....|....
gi 582647714 149 IPIPVIQKYLGHQS 162
Cdd:cd01193  153 TDIRTIQELLGHSD 166
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 11-168 1.01e-09

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 54.49  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEALKIKSERDYLFFKLAIHSGLKVSELLTITVSQVKrlIEKCTlsemckahfhslIKIRlpETLSKELLQYIE 90
Cdd:cd01189    2 EELKKLLEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDID--FENGT------------IRIN--RTLVRKKKGGYV 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  91 DRSLSNEdvlfQSLRT----NQVLSRQQAYRIIHQASIEAGIDNVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSAIET 166
Cdd:cd01189   66 IKPPKTK----SSIRTiplpDELIELLKELKAFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTT 141


                 ..
gi 582647714 167 LN 168
Cdd:cd01189  142 LD 143
xerD PRK00283
tyrosine recombinase;
37-162 1.45e-09

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 55.97  E-value: 1.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  37 SGLKVSELLTITVSQVK------RLIEK------CTLSEMCKAHFHSLIKIRLPETLSKEllqyiedrslsNEDVLFQSL 104
Cdd:PRK00283 146 TGLRVSELVGLTLDDVSlrqgvvRVTGKgnkerlVPLGEEAVYAIERYLERGRPALLNGR-----------SSDALFPSA 214

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714 105 RTNQvLSRQQAYRIIHQASIEAGIDNVGLT--TLRKTFAYHAYQKGIPIPVIQKYLGHQS 162
Cdd:PRK00283 215 RGGQ-LTRQTFWHRIKHYAKRAGIDPKKLSphVLRHAFATHLLNHGADLRVVQELLGHSD 273
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 11-162 3.91e-08

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: 50.34  E-value: 3.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEA-LKIKSERDYL--FFKLAIHSGLKVSELLTITVSQVKRLIEKCTLS-EMCKAHfhslIKIRLPetLSKELL 86
Cdd:cd01185    1 EELKRLMALeLSDTSRLELVrdMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRyRRKKTG----KPVTVP--LLPVAR 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582647714  87 QYIEDRSLSN-EDVLFQslrtnqVLSRQQAYRIIHQASIEAGID-NVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQS 162
Cdd:cd01185   75 EILEKYKDDRsEGKLFP------VLSNQKINRYLKEIAKIAGIDkHLTFHVARHTFATLLLLKGVDIETISKLLGHSS 146
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 37-162 8.24e-07

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: 46.74  E-value: 8.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  37 SGLKVSELLTITVSQV---KRLIeKCT----------LSEMCKAHFHSLIKIRLPETLSKEllqyiedrslsNEDVLFQS 103
Cdd:cd00798   31 SGLRVSELVGLDLSDVdldEGLV-RVTgkgnkerlvpFGSYAVEALEEYLEERRPLLLKKK-----------PPDALFLN 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 582647714 104 LRTNQvLSRQQAYRIIHQASIEAGIDNvGLT--TLRKTFAYHAYQKGIPIPVIQKYLGHQS 162
Cdd:cd00798   99 KRGKR-LSRRGVWRILKKYAERAGLPK-HVSphTLRHSFATHLLEGGADLRVVQELLGHAS 157
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 28-166 1.72e-05

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: 43.45  E-value: 1.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  28 YLFFKLAIHSGLKVSELLTITVSQVKrlIEKCTLSeMCKAHFHsliKIRL-P--ETLSKELLQYIEDR----SLSNEDVL 100
Cdd:cd00797   28 ATLFGLLYATGLRVGEALRLRLEDVD--LDSGILT-IRQTKFG---KSRLvPlhPSTVGALRDYLARRdrllPSPSSSYF 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714 101 FQSLRTNQvLSRQQAYRIIHQASIEAGIDNVG------LTTLRKTFAYHA----YQKGIPI----PVIQKYLGHQSAIET 166
Cdd:cd00797  102 FVSQQGGR-LTGGGVYRVFRRLLRRIGLRGAGdgrgprLHDLRHTFAVNRltrwYREGADVerklPVLSTYLGHVNVTDT 180
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 26-167 2.85e-05

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: 42.46  E-value: 2.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  26 RDYLFFKLAIHSGLKVSELLTITVSQVKRliEKCTLSEMCKAHFHSLIkIRLPETLSKELLQYIEDRSlSNEDVLFQSLR 105
Cdd:cd01195   21 RDEALVRLLLDNALRRSEAVALDVEDLEK--EHRRLRILGKGKKQREV-VTLPPTTREALAAWLAARG-EAEGPLFVSLD 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582647714 106 TN---QVLSRQQAYRIIHQASIEAGIDN-VGLTTLRKTFAYHAYQKGIP-IPVIQKYLGHqSAIETL 167
Cdd:cd01195   97 RAsrgRRLSPQAVYRIVRRLAERIGLGKrLSPHGLRHSAITLALDAGAGlIRKVQDFSRH-ADLRTL 162
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 24-162 7.22e-05

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 42.06  E-value: 7.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  24 SERDYLFFKLAIHSGLKVSELLTITVSQVKRliEKCTLSEMCKAHfhsliKIRL-P--ETLSKELLQYIEDRSLSNED-- 98
Cdd:PRK00236 135 ALRDRAILELLYGSGLRLSELVGLDIDDLDL--ASGTLRVLGKGN-----KERTvPlgRAAREALEAYLALRPLFLPDdd 207

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 582647714  99 VLFQSLRtNQVLSRQQAYRIIHQASIEAGI-DNVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQS 162
Cdd:PRK00236 208 ALFLGAR-GGRLSPRVVQRRVKKLGKKAGLpSHITPHKLRHSFATHLLESGGDLRAVQELLGHAS 271
PRK09870 PRK09870
tyrosine recombinase; Provisional
 26-167 8.12e-05

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 41.46  E-value: 8.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  26 RDYLFFKLAIHSGLKVSELLTITVSQVKrLIEKCTLSEMCKAHF---HSLIKIRLpetlsKELLQYIEDRSL---SNEDV 99
Cdd:PRK09870  33 RNYCLTLLCFIHGFRASEICRLRISDID-LKAKCIYIHRLKKGFsttHPLLNKEI-----QALKNWLSIRTSyphAESEW 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 582647714 100 LFQSLRTNQvLSRQQAYRIIHQASIEAGID-NVGLTTLRKTFAYHAYQKGIPIPVIQKYLGHQSAIETL 167
Cdd:PRK09870 107 VFLSRKGNP-LSRQQFYHIISTSGGNAGLSlEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTV 174
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
10-47 5.82e-04

Phage integrase/recombinase [Mobilome: prophages, transposons];


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 39.31  E-value: 5.82e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 582647714  10 NDDIVKMYEALKIKSERDYLFFKLAIHSGLKVSELLTI 47
Cdd:COG4342  113 DEEIREALKYLKEKDEEVYLLYKLLLFSGLRLSEALRL 150
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 11-162 2.34e-03

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 37.71  E-value: 2.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  11 DDIVKMYEALK--IKSERDYLFFKLAIHSGLKVSELLTITVSQV---KRLI----EKctlSEMCKAHfhslikiRLPetL 81
Cdd:COG0582  209 EELPELLRALDayRGSPVTRLALRLLLLTGVRPGELRGARWSEIdleAALWtipaER---MKTRRPH-------IVP--L 276

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582647714  82 SKELLQYIED-RSLS-NEDVLFQSLRT-NQVLSRQQAYRIIHqasiEAGIDNVGLTTLRKTFAYHAYQKGIPIPVIQKYL 158
Cdd:COG0582  277 SRQALEILKElKPLTgDSEYVFPSRRGpKKPMSENTLNKALR----RMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQL 352


                 ....
gi 582647714 159 GHQS 162
Cdd:COG0582  353 AHKD 356
 
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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