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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883743585  27 WHYLFPASHLS--RDPVDGALRRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDV 104
Cdd:cd01193    88 KEELDPAEGRAgvLDPRTGVERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDL 167

                  ....*....
gi 1883743585 105 RTTQIYTHV 113
Cdd:cd01193   168 STTMIYTHV 176

integron integrase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883743585  27 WHYLFPASHLSRDPVDGALRRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRT 106
Cdd:PRK15417  229 WFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVST 308

                          90       100
                  ....*....|....*....|..
gi 1883743585 107 TQIYTHVLQNGANGVRSPLSDL 128
Cdd:PRK15417  309 TMIYTHVLKVGGAGVRSPLDAL 330

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883743585  27 WHYLFPASHLS--RDPVDGALRRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDV 104
Cdd:cd01193    88 KEELDPAEGRAgvLDPRTGVERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDL 167

                  ....*....
gi 1883743585 105 RTTQIYTHV 113
Cdd:cd01193   168 STTMIYTHV 176

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1883743585  46 RRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTHV 113
Cdd:cd00798   100 RGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHV 167

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]

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1883743585  45 LRRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTHVLQN 116
Cdd:TIGR02225 207 RRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARE 278

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]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1883743585  46 RRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTHV 113
Cdd:TIGR02224 210 RGGRLTPRGVQYRLQQLRAKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHV 277

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1883743585  46 RRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTHV 113
Cdd:COG4973   210 RGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHL 277

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1883743585  35 HLSRDPVDGALRRHHLDPTTLQKAVRATArqLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYT 111
Cdd:cd00397    93 SLYLNKLFGTKLGERLSRRTLRRIFKKAG--IEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167

site-specific tyrosine recombinase XerC; Reviewed

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883743585  50 LDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTHV 113
Cdd:PRK01287  243 LARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRV 306

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883743585  28 HYLFPASH---LSRDPVDGALRRHhldpttlqkAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDV 104
Cdd:cd01182    95 FPLFPNRRgqpLTRDGVAYILNKY---------VALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESV 165

                  ....*..
gi 1883743585 105 RTTQIYT 111
Cdd:cd01182   166 ETTQIYA 172

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883743585  30 LFPASHLSRDPVDGalRRHHLDPTTLQKAVRATARQLQLGKpVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQI 109
Cdd:cd00796    83 LKRKRGKDGFFVDG--RFFGIPIASLRRAFKKARKRAGLED-LRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMR 159

                  ...
gi 1883743585 110 YTH 112
Cdd:cd00796   160 YAH 162

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1883743585  42 DGALRRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLL-ARGADIRTVQEQLGHSDVRTTQIYTH 112
Cdd:cd01195    96 DRASRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALdAGAGLIRKVQDFSRHADLRTLQVYDD 167

integrase; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1883743585  56 QKAVRATARQLQLGKpvTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTH 112
Cdd:PHA02601  262 ERAVKRAGIDLPEGQ--ATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAH 316

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883743585  29 YLFPAShlsRDPvdgalrRHHLDPTTLQKAVRAtarqlqLG-KPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTT 107
Cdd:COG0582   296 YVFPSR---RGP------KKPMSENTLNKALRR------MGyGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKV 360

                  ....*.
gi 1883743585 108 Q-IYTH 112
Cdd:COG0582   361 RaAYNR 366

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases 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 bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1883743585  60 RATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYT----HVLQNGANGV 121
Cdd:cd00799   123 RRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYIreadRFKDNAAAKL 188

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1883743585  46 RRHHLDPTTLQKAVRATARQLQLGKPVTCHTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYT 111
Cdd:cd01197   106 RGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIYT 171

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.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1883743585  75 HTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIY 110
Cdd:cd01191   123 HSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158

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.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1883743585  75 HTLRHSFATHLLARGADIRTVQEQLGHSDVRTTQIYTH 112
Cdd:cd01187   105 HRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142

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.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1883743585  75 HTLRHSFATHLLARGADIRTVQEQLGHSDV-RTTQIYTH 112
Cdd:cd01184   142 HSFRHTFITALKRAGVPEELIAQIVGHSRGgVTHDTYGK 180