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Conserved domains on  [gi|446178193|ref|WP_000256048|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Enterobacteriaceae]

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 ...
 3-143 5.74e-44

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 cd01184:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 180  Bit Score: 142.83  E-value: 5.74e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVTlDNGLVCIDINEDGDGKSVKNKHSVRLVPLTDGaygFDLTSFLSWVDMQPDEGPLF------ 76
Cdd:cd01184   35 TGARLNEICQLRVDDIKE-EDGIWCIDINDDAEGRRLKTKASRRLVPIHPR---LIELGFLDYVEALRADGKLFlfpekr 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  77 ---GMTPSAYSSWFNSRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITYDLYGK 143
Cdd:cd01184  111 dkdGKYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
 
Name Accession Description Interval E-value
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 3-143 5.74e-44

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) 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: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 142.83  E-value: 5.74e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVTlDNGLVCIDINEDGDGKSVKNKHSVRLVPLTDGaygFDLTSFLSWVDMQPDEGPLF------ 76
Cdd:cd01184   35 TGARLNEICQLRVDDIKE-EDGIWCIDINDDAEGRRLKTKASRRLVPIHPR---LIELGFLDYVEALRADGKLFlfpekr 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  77 ---GMTPSAYSSWFNSRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITYDLYGK 143
Cdd:cd01184  111 dkdGKYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
3-137 1.67e-19

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 82.35  E-value: 1.67e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVtLDNGLVCIDinedgDGKSvknkHSVRLVPLTDGAygfdLTSFLSWVDMQ--PDEGPLF---- 76
Cdd:COG4974  145 TGLRVSELLGLKWSDID-LDRGTIRVR-----RGKG----GKERTVPLSPEA----LEALREYLEERrpRDSDYLFptrr 210

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446178193  77 --GMTPSAYSSWFNSRVltEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:COG4974  211 grPLSRRAIRKILKRLA--KRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTT 271
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 3-137 8.06e-13

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: 62.34  E-value: 8.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193    3 TGARSAEVCHLTKRDIvTLDNGLVCIDInedgdgksVKNKHSvRLVPLTDGAygfdltsfLSWVDMQPDEGPLFG----- 77
Cdd:pfam00589  33 TGLRISELCSLRWSDI-DFENGVIRVHR--------GKGNKE-RTVPLSDAA--------LELLKEWLSKRLLEApksdy 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446178193   78 ---------MTPSAYSSWFNSrvLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:pfam00589  95 lfaskrgkpLSRQTVRKIFKR--AGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT 161
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 3-157 1.65e-07

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 49.12  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193    3 TGARSAEVCHLTKRDIVTLDNGLVCIdinedgdGKSVKNkhsvRLVPLTDGAygfdltsfLSWVDMQPDEG-PLFGMTPS 81
Cdd:TIGR02225 137 TGLRVSELVGLRLEDVNLDEGFVRVR-------GKGNKE----RLVPLGEEA--------IEALERYLKEArPLLLKKKV 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   82 AYSSW-FNS------------RVLTE---ALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITyDLYgkGH 145
Cdd:TIGR02225 198 KESDAlFLNrrggplsrqgvwKILKEyakRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTT-QIY--TH 274

                         170
                  ....*....|...
gi 446178193  146 -AVGRLADVLKTA 157
Cdd:TIGR02225 275 vARERLKEVHKKH 287
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 3-137 3.53e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 45.15  E-value: 3.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNGLVCIDinedgdGKSvkNKhsVRLVPLTDGAygfdltsfLSWVD--------MQPDEGP 74
Cdd:PRK00236 148 SGLRLSELVGLDIDDL-DLASGTLRVL------GKG--NK--ERTVPLGRAA--------REALEaylalrplFLPDDDA 208

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  75 LFgmtPSAYSSWFNSRV-------LTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:PRK00236 209 LF---LGARGGRLSPRVvqrrvkkLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT 275
 
Name Accession Description Interval E-value
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 3-143 5.74e-44

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) 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: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 142.83  E-value: 5.74e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVTlDNGLVCIDINEDGDGKSVKNKHSVRLVPLTDGaygFDLTSFLSWVDMQPDEGPLF------ 76
Cdd:cd01184   35 TGARLNEICQLRVDDIKE-EDGIWCIDINDDAEGRRLKTKASRRLVPIHPR---LIELGFLDYVEALRADGKLFlfpekr 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  77 ---GMTPSAYSSWFNSRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITYDLYGK 143
Cdd:cd01184  111 dkdGKYSKAASKWFNRLLRKLGIKDDERKSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
3-137 1.67e-19

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 82.35  E-value: 1.67e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVtLDNGLVCIDinedgDGKSvknkHSVRLVPLTDGAygfdLTSFLSWVDMQ--PDEGPLF---- 76
Cdd:COG4974  145 TGLRVSELLGLKWSDID-LDRGTIRVR-----RGKG----GKERTVPLSPEA----LEALREYLEERrpRDSDYLFptrr 210

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446178193  77 --GMTPSAYSSWFNSRVltEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:COG4974  211 grPLSRRAIRKILKRLA--KRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTT 271
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
3-155 2.56e-17

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 76.54  E-value: 2.56e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVtLDNGLVCIDinedgdGKSvknkHSVRLVPLTDGAygfdLTSFLSWVDMQP-----DEGPLF- 76
Cdd:COG4973  143 TGLRLGELVGLDWEDVD-LDAGEVRVR------GKT----GKSRTVPLGPKA----LAALREWLAVRPelaapDEGALFp 207

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  77 ---G--MTPSAYSSWFnsRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITYDlYGKgHAVGRLA 151
Cdd:COG4973  208 srrGtrLSPRNVQKRL--RRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQI-YTH-LDFQHLA 283


                 ....
gi 446178193 152 DVLK 155
Cdd:COG4973  284 EVYR 287
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 3-137 1.47e-16

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: 71.97  E-value: 1.47e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVtLDNGLVcidinedgDGKSVKNKHSvRLVPLTDGAYgfdltSFLSWVDMQPDE------GPLF 76
Cdd:cd00796   35 TGARRGEILSLRWDDID-LEVGLI--------VLPETKNGKP-RTVPLSDEAI-----AILKELKRKRGKdgffvdGRFF 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446178193  77 GMTPSAYSSWFNsRVLTEALGdsQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd00796  100 GIPIASLRRAFK-KARKRAGL--EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMT 157
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 3-143 1.07e-15

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: 69.51  E-value: 1.07e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNGLVCID--INEDGDGKSV----KNKHSVRLVPLTDGAYGfDLTSFLSWvdmqpdegplf 76
Cdd:cd01189   28 TGLRRGELLALTWSDI-DFENGTIRINrtLVRKKKGGYVikppKTKSSIRTIPLPDELIE-LLKELKAF----------- 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446178193  77 gmtpsaysswfnSRVLTEAlgDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITYDLYGK 143
Cdd:cd01189   95 ------------KKLLKKA--GLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYAH 147
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 3-137 1.38e-13

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: 64.42  E-value: 1.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNGlvCIDINEdgdGKSVKNKHsvRLVPLTDGAYGFdltsFLSWVDMQPDEGPLFGM---T 79
Cdd:cd00397   29 TGLRISELLALKVKDI-DLDNG--TIRVRG---KKTKGGKE--RTVPLPKELAEE----LKEYLKERRDKRGPLLKslyL 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446178193  80 PSAYSSWFNSRVLTEAL---------GDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd00397   97 NKLFGTKLGERLSRRTLrrifkkagiEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTT 163
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 3-137 8.06e-13

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: 62.34  E-value: 8.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193    3 TGARSAEVCHLTKRDIvTLDNGLVCIDInedgdgksVKNKHSvRLVPLTDGAygfdltsfLSWVDMQPDEGPLFG----- 77
Cdd:pfam00589  33 TGLRISELCSLRWSDI-DFENGVIRVHR--------GKGNKE-RTVPLSDAA--------LELLKEWLSKRLLEApksdy 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446178193   78 ---------MTPSAYSSWFNSrvLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:pfam00589  95 lfaskrgkpLSRQTVRKIFKR--AGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT 161
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 3-137 4.60e-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: 49.57  E-value: 4.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIVTLDNGLVCidinedgDGKSVKNKHSVRlVPLTDGAYgfdltSFLSWVDMQPDEGPLFGMtPSA 82
Cdd:cd01185   30 TGLRFSDLKNLTWKNIVEASGRTWI-------RYRRKKTGKPVT-VPLLPVAR-----EILEKYKDDRSEGKLFPV-LSN 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446178193  83 YSswFNS--RVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd01185   96 QK--INRylKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTT 150
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 3-137 1.58e-07

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: 48.42  E-value: 1.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNGLVCIDinedgDGKSVKNkhsvRLVPLTDGAYGfDLTSFLSWVDMQP--DEGPLFGMTP 80
Cdd:cd01193   33 AGLRISELLRLRVKDI-DFERGVIRVR-----QGKGGKD----RVVPLPEKLLE-PLRRYLKSARPKEelDPAEGRAGVL 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446178193  81 SAYSSW-----FNSRVL-------TEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd01193  102 DPRTGVerrhhISETTVqralkkaVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTT 170
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 3-157 1.65e-07

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 49.12  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193    3 TGARSAEVCHLTKRDIVTLDNGLVCIdinedgdGKSVKNkhsvRLVPLTDGAygfdltsfLSWVDMQPDEG-PLFGMTPS 81
Cdd:TIGR02225 137 TGLRVSELVGLRLEDVNLDEGFVRVR-------GKGNKE----RLVPLGEEA--------IEALERYLKEArPLLLKKKV 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   82 AYSSW-FNS------------RVLTE---ALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITyDLYgkGH 145
Cdd:TIGR02225 198 KESDAlFLNrrggplsrqgvwKILKEyakRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTT-QIY--TH 274

                         170
                  ....*....|...
gi 446178193  146 -AVGRLADVLKTA 157
Cdd:TIGR02225 275 vARERLKEVHKKH 287
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 3-137 8.48e-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: 46.35  E-value: 8.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNGLV-CIdinedgdGKsvKNKhsVRLVPLTDGA------YgfdLTSFLSWVDMQPDEGPL 75
Cdd:cd00798   31 SGLRVSELVGLDLSDV-DLDEGLVrVT-------GK--GNK--ERLVPFGSYAvealeeY---LEERRPLLLKKKPPDAL 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446178193  76 F------GMTPSaySSWFNSRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd00798   96 FlnkrgkRLSRR--GVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT 161
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 79-138 1.31e-06

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: 45.70  E-value: 1.31e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  79 TPSAYSSWFnSRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITY 138
Cdd:cd01188  106 STSQISSIV-RRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTA 164
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 1-144 1.54e-06

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: 1.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   1 MVTGARSAEVCHLTKRDIvTLDNGLVCIDinedgdGKSVKNKhSVRLVPLTDGAygfdLTSFLSWVDMQPDEGPLFgmtP 80
Cdd:COG0582  235 LLTGVRPGELRGARWSEI-DLEAALWTIP------AERMKTR-RPHIVPLSRQA----LEILKELKPLTGDSEYVF---P 299

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446178193  81 SAYSSW--FNSRVLTEALGDS--QDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITYDLYGKG 144
Cdd:COG0582  300 SRRGPKkpMSENTLNKALRRMgyGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRA 367
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 3-137 3.53e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 45.15  E-value: 3.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNGLVCIDinedgdGKSvkNKhsVRLVPLTDGAygfdltsfLSWVD--------MQPDEGP 74
Cdd:PRK00236 148 SGLRLSELVGLDIDDL-DLASGTLRVL------GKG--NK--ERTVPLGRAA--------REALEaylalrplFLPDDDA 208

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193  75 LFgmtPSAYSSWFNSRV-------LTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:PRK00236 209 LF---LGARGGRLSPRVvqrrvkkLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT 275
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 1-137 6.46e-06

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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 43.90  E-value: 6.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   1 MVT-GARSAEVCHLTKRDIVTLDNGLVcidINEDGDGKSVKNKHsVRLVPLTDGAygfdLTSFLSWVDMQPDEGPLFGMT 79
Cdd:cd01194   31 MVTeGLRTVEIVRADVGDLRQEGEGTI---LYVQGKGKTSKDDF-VYLRPDVLKA----LQAYLKARGKLDFEEPLFTSL 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446178193  80 PSAYS---------SWFNSRVLTEALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd01194  103 SNNSKgqrlttrsiRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTT 169
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 3-137 2.01e-05

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: 42.65  E-value: 2.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDIvTLDNG--LVCIdinedgdGKSVKNkhsvRLVPLTDGAygfdLTSFLSWVDMQ---PDEGPLFG 77
Cdd:cd01182   33 TGARVQELADLTIRDL-RLDDPatVRLH-------GKGRKE----RTVPLWKET----VAALKAYLQEFhltPDPKQLFP 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446178193  78 MTPSAYSSWFN----SRVLTEALGD--------SQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd01182   97 LFPNRRGQPLTrdgvAYILNKYVALasnrcpslPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETT 168
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 94-137 3.29e-05

tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 42.59  E-value: 3.29e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446178193   94 EALGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:TIGR02224 228 AKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTT 271
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 1-141 3.51e-04

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: 39.18  E-value: 3.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   1 MVTGARSAEVCHLTKRDIVtLDNGLvcIDInedgDGKSVKNKHSVRlVPLTDGAYGFdLTSFLSWvdmQPDEGPLF-GMT 79
Cdd:cd00801   29 LLTGQRIGELARARWSEID-LEEKT--WTI----PAERTKNKRPHR-VPLSDQALEI-LEELKEF---TGDSGYLFpSRR 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446178193  80 PSAYSSWFNSR--VLTEALGDSQDVSLHSLRHWLATRMKERGVN--LVDAQgiLGHSSQSI---TYDLY 141
Cdd:cd00801   97 KKKKPISENTInkALKRLGYKGKEFTPHDLRRTFSTLLNELGIDpeVIERL--LNHVLGGVvraAYNRY 163
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 3-133 5.33e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 38.96  E-value: 5.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178193   3 TGARSAEVCHLTKRDiVTLDNGLVCIDinedgDGKSVKNkhsvRLVPLTDGAygfdltsfLSWVD-----------MQPD 71
Cdd:PRK01287 169 TGIRRGELARLDLYD-VDASRGVVTVR-----QGKGNKD----RVVPVGERA--------LAWLQrylqdvrpqlaVRPD 230

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446178193  72 EGPLF------GMTPSAYSSwFNSRVLTEAlGDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSS 133
Cdd:PRK01287 231 SGALFvamdgdGLARNTLTN-MVGRYIRAA-GIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAK 296
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 102-141 3.78e-03

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 36.43  E-value: 3.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446178193 102 VSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSITyDLY 141
Cdd:PRK05084 303 LTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETT-DLY 341
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 97-137 8.86e-03

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: 34.71  E-value: 8.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 446178193  97 GDSQDVSLHSLRHWLATRMKERGVNLVDAQGILGHSSQSIT 137
Cdd:cd01187   97 GERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMT 137
 
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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