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Conserved domains on  [gi|1172330438|ref|WP_080713716|]
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Tsr25 family tyrosine-type DNA invertase [Bacteroides fragilis]

Protein Classification

site-specific integrase( domain architecture ID 10586849)

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

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 122-293 2.00e-23

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 cd01185:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 161  Bit Score: 94.25  E-value: 2.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 122 RMIRMSgCPDESASAKAVDWFvLMFMLRGIPFVDLAHLRRSNLDK----GVLTYCRHKTGQEVSITVPREAMDIINRRMa 197
Cdd:cd01185     5 RLMALE-LSDTSRLELVRDMF-LFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTGKPVTVPLLPVAREILEKYK- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 198 ENDHPSYLLPILgqprtgqrrqekvltPYQEYqcelrnlNRRLERVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVIS 277
Cdd:cd01185    82 DDRSEGKLFPVL---------------SNQKI-------NRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETIS 139

                         170
                  ....*....|....*.
gi 1172330438 278 RGLGHSSVKVTETYLK 293
Cdd:cd01185   140 KLLGHSSIKTTQIYAK 155
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 7-90 5.33e-14

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


:

Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 66.86  E-value: 5.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438   7 TLTVFMISEIERFREEGRESARRIYHNMLRLLRESAGKEEIGFEEVTPAFLGNYE-FLLLGRGLSWNTVSTYMRALRAGY 85
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGSKGTARNYKSTLKHLKKFLKKKDITFEEITVDFLEKFEeYLKKKKGLSENTISKYFRTLRAVL 80


                  ....*
gi 1172330438  86 NRGMK 90
Cdd:pfam13102  81 NKAIK 85
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 122-293 2.00e-23

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: 94.25  E-value: 2.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 122 RMIRMSgCPDESASAKAVDWFvLMFMLRGIPFVDLAHLRRSNLDK----GVLTYCRHKTGQEVSITVPREAMDIINRRMa 197
Cdd:cd01185     5 RLMALE-LSDTSRLELVRDMF-LFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTGKPVTVPLLPVAREILEKYK- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 198 ENDHPSYLLPILgqprtgqrrqekvltPYQEYqcelrnlNRRLERVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVIS 277
Cdd:cd01185    82 DDRSEGKLFPVL---------------SNQKI-------NRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETIS 139

                         170
                  ....*....|....*.
gi 1172330438 278 RGLGHSSVKVTETYLK 293
Cdd:cd01185   140 KLLGHSSIKTTQIYAK 155
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
16-293 2.72e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 96.99  E-value: 2.72e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438  16 IERFREE------GRESARRIYHNMLR-LLRESAGKEEIGFEEVTPAFLGNYEFLLLGRGLSWNTVSTYMRALRAGYNRG 88
Cdd:COG4974     7 LEAFLEElkrekgLSPNTIKAYRRDLRrFLRFLEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438  89 MKGrpGYVTG-LFDKVYTG-TRSDVKRAVDARTVGRMIRmsgCPDESASAKAVDWFVLMFMLR-GIPFVDLAHLRRSNLD 165
Cdd:COG4974    87 VRE--GLLEDnPAAKVKLPkKPRKLPRVLTEEEIEALLE---ALDTETPEGLRDRALLLLLYAtGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 166 --KGVLTYCRHKTGQEVSITVPREAMDIINRRMAENDHPS--YLLPilgqPRTGQRrqekvLTPyqeyqcelRNLNRRLE 241
Cdd:COG4974   162 ldRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRDsdYLFP----TRRGRP-----LSR--------RAIRKILK 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1172330438 242 RVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYLK 293
Cdd:COG4974   225 RLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTH 276
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 7-90 5.33e-14

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 66.86  E-value: 5.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438   7 TLTVFMISEIERFREEGRESARRIYHNMLRLLRESAGKEEIGFEEVTPAFLGNYE-FLLLGRGLSWNTVSTYMRALRAGY 85
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGSKGTARNYKSTLKHLKKFLKKKDITFEEITVDFLEKFEeYLKKKKGLSENTISKYFRTLRAVL 80


                  ....*
gi 1172330438  86 NRGMK 90
Cdd:pfam13102  81 NKAIK 85
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 131-295 1.06e-04

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: 41.92  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 131 DESASAKAVDWFVLMFMLR-GIPFVDLAHLRRSNLD--KGVLTYCRHKTGQEVSITVPREAM----DIINRRMAENDHPS 203
Cdd:pfam00589  14 AETGPLSIRDKALLELLYAtGLRISELCSLRWSDIDfeNGVIRVHRGKGNKERTVPLSDAALellkEWLSKRLLEAPKSD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 204 YLLPilgqprtGQRRQEKVLtpyqeyqcelRNLNRRLERVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHS 283
Cdd:pfam00589  94 YLFA-------SKRGKPLSR----------QTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 1172330438 284 SVKVTETYLKPF 295
Cdd:pfam00589 157 SISTTQIYTHVA 168
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 122-293 2.00e-23

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: 94.25  E-value: 2.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 122 RMIRMSgCPDESASAKAVDWFvLMFMLRGIPFVDLAHLRRSNLDK----GVLTYCRHKTGQEVSITVPREAMDIINRRMa 197
Cdd:cd01185     5 RLMALE-LSDTSRLELVRDMF-LFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTGKPVTVPLLPVAREILEKYK- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 198 ENDHPSYLLPILgqprtgqrrqekvltPYQEYqcelrnlNRRLERVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVIS 277
Cdd:cd01185    82 DDRSEGKLFPVL---------------SNQKI-------NRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETIS 139

                         170
                  ....*....|....*.
gi 1172330438 278 RGLGHSSVKVTETYLK 293
Cdd:cd01185   140 KLLGHSSIKTTQIYAK 155
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
16-293 2.72e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 96.99  E-value: 2.72e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438  16 IERFREE------GRESARRIYHNMLR-LLRESAGKEEIGFEEVTPAFLGNYEFLLLGRGLSWNTVSTYMRALRAGYNRG 88
Cdd:COG4974     7 LEAFLEElkrekgLSPNTIKAYRRDLRrFLRFLEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438  89 MKGrpGYVTG-LFDKVYTG-TRSDVKRAVDARTVGRMIRmsgCPDESASAKAVDWFVLMFMLR-GIPFVDLAHLRRSNLD 165
Cdd:COG4974    87 VRE--GLLEDnPAAKVKLPkKPRKLPRVLTEEEIEALLE---ALDTETPEGLRDRALLLLLYAtGLRVSELLGLKWSDID 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 166 --KGVLTYCRHKTGQEVSITVPREAMDIINRRMAENDHPS--YLLPilgqPRTGQRrqekvLTPyqeyqcelRNLNRRLE 241
Cdd:COG4974   162 ldRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRDsdYLFP----TRRGRP-----LSR--------RAIRKILK 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1172330438 242 RVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYLK 293
Cdd:COG4974   225 RLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTH 276
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
16-291 5.84e-17

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 79.24  E-value: 5.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438  16 IERFREEGRE-----SARRIYHNMLRLLRESAGKEEIGFEEVTPAFLGNYEFLLLGRGLSWNTVSTYMRALRAGYNRGMK 90
Cdd:COG4973     8 LEAYLEHLRErrlspKTLEAYRRDLRRLIPLLGDADLPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRSFFNWAVR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438  91 GrpGYVT-GLFDKVYTGTRSDVK-RAVDARTVGRMIRMsgcPDESASAKAVDWFVLMFMLRGIPFVDLAHLRRS--NLDK 166
Cdd:COG4973    88 E--GLLEaNPAAGVKAPKAPRKLpRALTVDELAQLLDA---LADDPLAVRDRAIVELLYSTGLRLGELVGLDWEdvDLDA 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 167 GVLTYcRHKTGQEVSITVPREAMDIINRRMAEndhpsyllpilgQPRTGQRRQEKVLTPYQEYQCELRNLNRRLERVSVD 246
Cdd:COG4973   163 GEVRV-RGKTGKSRTVPLGPKALAALREWLAV------------RPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKK 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1172330438 247 LRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETY 291
Cdd:COG4973   230 AGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIY 274
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 7-90 5.33e-14

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 66.86  E-value: 5.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438   7 TLTVFMISEIERFREEGRESARRIYHNMLRLLRESAGKEEIGFEEVTPAFLGNYE-FLLLGRGLSWNTVSTYMRALRAGY 85
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGSKGTARNYKSTLKHLKKFLKKKDITFEEITVDFLEKFEeYLKKKKGLSENTISKYFRTLRAVL 80


                  ....*
gi 1172330438  86 NRGMK 90
Cdd:pfam13102  81 NKAIK 85
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 156-291 4.57e-07

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


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 48.86  E-value: 4.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 156 LAHLRRS--NLDKGVLTYCRHKTGQEVSITVPREAMDIINRRMAEndhpsyllpilgqPRTGQRRQEKVLTPYQEYQCEl 233
Cdd:cd00796    42 ILSLRWDdiDLEVGLIVLPETKNGKPRTVPLSDEAIAILKELKRK-------------RGKDGFFVDGRFFGIPIASLR- 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1172330438 234 RNLNRRLERVSV-DLRLggrlssYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETY 291
Cdd:cd00796   108 RAFKKARKRAGLeDLRF------HDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRY 160
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 232-291 9.73e-07

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: 47.55  E-value: 9.73e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1172330438 232 ELRNLNRRLERVSVDlrlggRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVT-ETY 291
Cdd:cd01189    90 ELKAFKKLLKKAGLP-----RITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTlDVY 145
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 140-292 5.44e-06

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


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 45.93  E-value: 5.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 140 DWFVLMFMLR-GIPFVDLAHLRRSNLDKGVLtYCR-----HKTGQEVSITVPREAMDIINRRMAEndHPSYLLPILGQPR 213
Cdd:cd00397    19 DRAILLLLLEtGLRISELLALKVKDIDLDNG-TIRvrgkkTKGGKERTVPLPKELAEELKEYLKE--RRDKRGPLLKSLY 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1172330438 214 TGQRRQEKVLTPYQeyqceLRNLNRRLERVSvdLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYL 292
Cdd:cd00397    96 LNKLFGTKLGERLS-----RRTLRRIFKKAG--IEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 113-291 1.11e-05

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 46.57  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 113 RAVDARTVGRMIR-MSGCPDESASAKAVdWFVLMFMLR-GipfvDLAHLRRS--NLDKGVLTYC--RHKTGQEVSITVPR 186
Cdd:COG0582   204 PALTPEELPELLRaLDAYRGSPVTRLAL-RLLLLTGVRpG----ELRGARWSeiDLEAALWTIPaeRMKTRRPHIVPLSR 278

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 187 EAMDIINRRMAENDHPSYLLPilgqprtGQRRQEKVLTPyqeyqcelRNLNRRLERVSVDlrlggRLSSYTARHTWATIA 266
Cdd:COG0582   279 QALEILKELKPLTGDSEYVFP-------SRRGPKKPMSE--------NTLNKALRRMGYG-----RFTPHGFRHTASTLL 338

                         170       180
                  ....*....|....*....|....*.
gi 1172330438 267 FHQETPVGVISRGLGHSSV-KVTETY 291
Cdd:COG0582   339 NEAGFPPDVIERQLAHKDGnKVRAAY 364
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 148-293 1.24e-05

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: 44.93  E-value: 1.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 148 LRGIpfvDLAHLRRSNLD--KGVLTYCRHKTGQ--EVSITVP-REAM-DIINRRMAENDHPSYLLpilgqprtgqrrqeK 221
Cdd:cd01188    34 LRAG---DVAGLRLDDIDwrSGTITVRQKKTGRpvELPLTEPvGEALaDYLRDGRPRTDSREVFL--------------R 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172330438 222 VLTPYQEYQCElRNLN----RRLERVSVDLRLGGrlsSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYLK 293
Cdd:cd01188    97 ARAPYRPLSST-SQISsivrRYLRKAGIEPSHRG---THSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAK 168
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 131-295 1.06e-04

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: 41.92  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 131 DESASAKAVDWFVLMFMLR-GIPFVDLAHLRRSNLD--KGVLTYCRHKTGQEVSITVPREAM----DIINRRMAENDHPS 203
Cdd:pfam00589  14 AETGPLSIRDKALLELLYAtGLRISELCSLRWSDIDfeNGVIRVHRGKGNKERTVPLSDAALellkEWLSKRLLEAPKSD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 204 YLLPilgqprtGQRRQEKVLtpyqeyqcelRNLNRRLERVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHS 283
Cdd:pfam00589  94 YLFA-------SKRGKPLSR----------QTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 1172330438 284 SVKVTETYLKPF 295
Cdd:pfam00589 157 SISTTQIYTHVA 168
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 174-292 3.93e-04

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: 40.35  E-value: 3.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 174 HKTGQEVSI----TVPREAMDIINRRmaENDHPSYLLPILgqprtgQRRQEKVLTPYQEYqcelrnlnRRLERVSVDLRL 249
Cdd:cd01192    62 QKTGKQKTFplnpTLVKALKEYIDDL--DLKRNDYLFKSL------KQGPEKPISRKQAY--------KILKKAADDLGL 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1172330438 250 GGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYL 292
Cdd:cd01192   126 NYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYL 168
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 234-302 1.04e-03

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It 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: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 39.32  E-value: 1.04e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 234 RNLNRRLERvsvdlRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVT-ETYLKPFgDKEVDR 302
Cdd:cd01186   120 YDLVRRLKK-----RTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTlNTYGHLS-EEDIRR 183
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 158-293 1.34e-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: 38.79  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 158 HLRRSNLD--KGVLTYCRHKTGQEVSITVPREAMDIINRRMAENDHPSYLLPILG-----QPRTGQRRQEKVLTpyqeyq 230
Cdd:cd01193    42 RLRVKDIDfeRGVIRVRQGKGGKDRVVPLPEKLLEPLRRYLKSARPKEELDPAEGragvlDPRTGVERRHHISE------ 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1172330438 231 celRNLNRRLERVSVDLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYLK 293
Cdd:cd01193   116 ---TTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTH 175
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 236-294 3.19e-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: 38.03  E-value: 3.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172330438 236 LNRRLERVS-VDLRLGGRLSSYTARHTWATIAFHQETPVGVISRGLGHSSVKVTETYLKP 294
Cdd:cd01182   115 LNKYVALASnRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEA 174
 
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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