site-specific integrase [Staphylococcus phage 3 AJ-2017]
Protein Classification
tyrosine-type recombinase/integrase( domain architecture ID 11471964)
tyrosine-type recombinase/integrase cleaves 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.
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| XerD | COG4974 | Site-specific recombinase XerD [Replication, recombination and repair]; |
54-330 | 1.15e-47 | |||||
Site-specific recombinase XerD [Replication, recombination and repair]; : Pssm-ID: 443999 [Multi-domain] Cd Length: 291 Bit Score: 162.47 E-value: 1.15e-47
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| Name | Accession | Description | Interval | E-value | |||||
| XerD | COG4974 | Site-specific recombinase XerD [Replication, recombination and repair]; |
54-330 | 1.15e-47 | |||||
Site-specific recombinase XerD [Replication, recombination and repair]; Pssm-ID: 443999 [Multi-domain] Cd Length: 291 Bit Score: 162.47 E-value: 1.15e-47
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| INT_ICEBs1_C_like | cd01189 | C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ... |
169-325 | 3.98e-25 | |||||
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: 98.79 E-value: 3.98e-25
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| Phage_integrase | pfam00589 | Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ... |
164-326 | 1.34e-17 | |||||
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: 78.90 E-value: 1.34e-17
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| recomb_XerD | TIGR02225 | tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ... |
74-333 | 1.73e-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: 51.81 E-value: 1.73e-07
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| xerC | PRK00236 | site-specific tyrosine recombinase XerC; Reviewed |
60-326 | 1.51e-05 | |||||
site-specific tyrosine recombinase XerC; Reviewed Pssm-ID: 234698 [Multi-domain] Cd Length: 297 Bit Score: 45.92 E-value: 1.51e-05
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| Name | Accession | Description | Interval | E-value | |||||
| XerD | COG4974 | Site-specific recombinase XerD [Replication, recombination and repair]; |
54-330 | 1.15e-47 | |||||
Site-specific recombinase XerD [Replication, recombination and repair]; Pssm-ID: 443999 [Multi-domain] Cd Length: 291 Bit Score: 162.47 E-value: 1.15e-47
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| XerC | COG4973 | Site-specific recombinase XerC [Replication, recombination and repair]; |
54-326 | 2.63e-39 | |||||
Site-specific recombinase XerC [Replication, recombination and repair]; Pssm-ID: 443998 [Multi-domain] Cd Length: 287 Bit Score: 140.48 E-value: 2.63e-39
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| FimB | COG0582 | Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ... |
54-330 | 2.10e-30 | |||||
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons]; Pssm-ID: 440347 [Multi-domain] Cd Length: 391 Bit Score: 118.99 E-value: 2.10e-30
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| INT_ICEBs1_C_like | cd01189 | C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ... |
169-325 | 3.98e-25 | |||||
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: 98.79 E-value: 3.98e-25
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| DNA_BRE_C | cd00397 | DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ... |
175-323 | 3.83e-20 | |||||
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: 85.99 E-value: 3.83e-20
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| Phage_integrase | pfam00589 | Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ... |
164-326 | 1.34e-17 | |||||
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: 78.90 E-value: 1.34e-17
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| INT_Rci_Hp1_C | cd00796 | Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ... |
186-325 | 9.32e-15 | |||||
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Pssm-ID: 271177 [Multi-domain] Cd Length: 162 Bit Score: 70.82 E-value: 9.32e-15
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| INT_tnpA_C_Tn554 | cd01186 | Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ... |
181-334 | 9.86e-12 | |||||
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: 62.82 E-value: 9.86e-12
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| INTN1_C_like | cd01185 | Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ... |
188-330 | 9.16e-10 | |||||
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: 56.89 E-value: 9.16e-10
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| INT_P4_C | cd00801 | Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ... |
184-330 | 2.53e-08 | |||||
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: 53.04 E-value: 2.53e-08
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| INT_RitA_C_like | cd01188 | C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ... |
186-323 | 1.46e-07 | |||||
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: 50.70 E-value: 1.46e-07
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| recomb_XerD | TIGR02225 | tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ... |
74-333 | 1.73e-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: 51.81 E-value: 1.73e-07
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| INT_C_like_3 | cd01192 | Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ... |
176-319 | 3.85e-07 | |||||
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: 49.60 E-value: 3.85e-07
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| INT_IntI_C | cd01193 | Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ... |
163-326 | 4.45e-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: 49.20 E-value: 4.45e-07
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| INT_RitC_C_like | cd01182 | C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ... |
188-323 | 7.17e-07 | |||||
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: 48.81 E-value: 7.17e-07
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| integrase_gron | TIGR02249 | integron integrase; Members of this family are integrases associated with integrons (and ... |
263-328 | 3.33e-06 | |||||
integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other] Pssm-ID: 131303 [Multi-domain] Cd Length: 315 Bit Score: 48.16 E-value: 3.33e-06
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| xerC | PRK00236 | site-specific tyrosine recombinase XerC; Reviewed |
60-326 | 1.51e-05 | |||||
site-specific tyrosine recombinase XerC; Reviewed Pssm-ID: 234698 [Multi-domain] Cd Length: 297 Bit Score: 45.92 E-value: 1.51e-05
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| Phage_int_SAM_5 | pfam13102 | Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ... |
55-148 | 1.52e-05 | |||||
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: 42.98 E-value: 1.52e-05
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| Phage_int_SAM_3 | pfam14659 | Phage integrase, N-terminal SAM-like domain; This domain is found in a variety of phage ... |
57-111 | 2.80e-05 | |||||
Phage integrase, N-terminal SAM-like domain; This domain is found in a variety of phage integrase proteins. Pssm-ID: 464243 [Multi-domain] Cd Length: 55 Bit Score: 40.99 E-value: 2.80e-05
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| INT_XerDC_C | cd00798 | XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ... |
284-326 | 5.90e-05 | |||||
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: 42.88 E-value: 5.90e-05
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| INT_C_like_4 | cd01194 | Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ... |
284-325 | 3.67e-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: 271194 [Multi-domain] Cd Length: 174 Bit Score: 40.82 E-value: 3.67e-04
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| PRK15417 | PRK15417 | integron integrase; |
285-328 | 5.53e-03 | |||||
integron integrase; Pssm-ID: 185315 [Multi-domain] Cd Length: 337 Bit Score: 38.10 E-value: 5.53e-03
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| xerS | PRK05084 | site-specific tyrosine recombinase XerS; Reviewed |
179-330 | 9.66e-03 | |||||
site-specific tyrosine recombinase XerS; Reviewed Pssm-ID: 235339 [Multi-domain] Cd Length: 357 Bit Score: 37.59 E-value: 9.66e-03
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