PaperBLAST

PaperBLAST Hits for tr|A0A098G9Q8|A0A098G9Q8_9GAMM Resolvase OS=Legionella fallonii LLAP-10 OX=1212491 GN=LFA_pA0076 PE=4 SV=1 (140 a.a., MNDGLKYGYA...)

Show query sequence

>tr|A0A098G9Q8|A0A098G9Q8_9GAMM Resolvase OS=Legionella fallonii LLAP-10 OX=1212491 GN=LFA_pA0076 PE=4 SV=1
MNDGLKYGYARVSTKEQNLDLQVDALTKAGCHKIFREVAKGAKTDRPKLNELLSVLKSGD
TLIIWKLDRMGRSLQHLITTFNELIKKGIGIISIQDPIDGCFYRNGANATKTTCFCHQFN
HFKLNLKIYLLNNFTGSRLS

Running BLASTp...

Found 165 similar proteins in the literature:

tnpR / AAB03401.1 resolvase from Xanthomonas campestris (see paper)
tnpR / CAA97956.1 resolvase from Xanthomonas campestris (see paper)
59% identity, 31% coverage

IAU57_09125 recombinase family protein from Pseudomonas aeruginosa
54% identity, 31% coverage

• Complete Genome Sequence of Pseudomonas aeruginosa CMC-097, Isolated from a Ventilator-Associated Pneumonia Patient, Containing a Novel Carbapenem Resistance Class 1 Integron
  Rao, Microbiology resource announcements 2021
  • “...IRR: aatgatgacctcaagccggttctggtcg Type II toxin-antitoxin system IAU57_09120 Invertase Recombinase family protein; DNA invertase Pin-like protein IAU57_09125 tnpR IRL: aatgttctccgtggcccgcttccggccg TnpR resolvase protein 3-PA0981 d DR: accccAATAA IAU57_09130 Hypothetical protein a A novel integron was identified in this study. b DR, direct repeat; IRL, left inverted repeat;...”

IAU57_09120 recombinase family protein from Pseudomonas aeruginosa
53% identity, 48% coverage

• Complete Genome Sequence of Pseudomonas aeruginosa CMC-097, Isolated from a Ventilator-Associated Pneumonia Patient, Containing a Novel Carbapenem Resistance Class 1 Integron
  Rao, Microbiology resource announcements 2021
  • “...Class 1 integron integrase IntI1 IS Psy42 IAU57_09115 yafQ IRR: aatgatgacctcaagccggttctggtcg Type II toxin-antitoxin system IAU57_09120 Invertase Recombinase family protein; DNA invertase Pin-like protein IAU57_09125 tnpR IRL: aatgttctccgtggcccgcttccggccg TnpR resolvase protein 3-PA0981 d DR: accccAATAA IAU57_09130 Hypothetical protein a A novel integron was identified in this...”

t3437 DNA-invertase from Salmonella enterica subsp. enterica serovar Typhi Ty2
53% identity, 49% coverage

• Staphylococcus aureus Isolated From Retail Meat and Meat Products in China: Incidence, Antibiotic Resistance and Genetic Diversity
  Wu, Frontiers in microbiology 2018
  • “...t085 (3), t2616 (4), t289 (3)t10370 (3), t7568 (4), t10332 (1), t3932 (2), t605 (2), t3437 (2), t1689 (1), t304 (1), t3092 (1), t8927 (1), t1685 (1), t127 (1) ST943 (14) t091 (11), t002 (1), t250 (1), t289 (1) ST4440 * (1) t091 (1) ST4466 *...”

Q8Z339 DNA-invertase from Salmonella typhi
STY3695 DNA-invertase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
53% identity, 49% coverage

• Analysis of Salmonella typhimurium Protein-Targeting in the Nucleus of Host Cells and the Implications in Colon Cancer: An in-silico Approach
  Li, Infection and drug resistance 2020
  • “...protein RepA (Accession No. Q934T6), putative DNA-binding protein (Accession No. Q934Z5, Q8Z752), DNA-invertase (Accession No. Q8Z339), RNA polymerase-binding transcription factor DksA (Accession No. P0A1G6), RNA polymerase sigma factor RpoD (Accession No. P0A2E4), ATP-dependent RNA helicase (Accession No. Q8Z877), DNA topoisomerase III (Accession No. Q8Z6F5), topoisomerase IV...”
• Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials
  Dyson, PLoS neglected tropical diseases 2022
  • “...tail fibre assembly chaperone (STY3692), alternate tail fibre tips (STY3693 and STY3694), a site-specific invertase (STY3695), and major tail tube filament structural gene (STY3696)[ 50 ]. The inversion, likely mediated by the site-specific invertase (STY3695), appears to have resulted in the formation of an alternative tail...”
• Selective capture of Salmonella enterica serovar typhi genes expressed in macrophages that are absent from the Salmonella enterica serovar Typhimurium genome
  Faucher, Infection and immunity 2005
  • “...STY2005 STY2016 STY2020 STY2022 STY2026 STY3663 STY3695 Putative bacteriophage protein min DNA invertase Conserved hypothetical protein Putative bacteriophage...”
  • “...five remaining genes (STY0207, STY1635, STY2026, STY2732, and STY3695) did not correspond to the three main hybridization profiles. SPIs and prophages. Among...”

lpg2573 transposase (resolvase, DNA invertase) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
51% identity, 52% coverage

• Legionella pneumophila Excludes Autophagy Adaptors from the Ubiquitin-Labeled Vacuole in Which It Resides
  Omotade, Infection and immunity 2020 (secret)

BN49_RS11400 recombinase family protein from Klebsiella pneumoniae
53% identity, 49% coverage

• The Acquisition of Colistin Resistance Is Associated to the Amplification of a Large Chromosomal Region in Klebsiella pneumoniae kp52145
  Sánchez, International journal of molecular sciences 2021
  • “...protein 39 BN49_RS11395 2037760 2038207 448 IS1 family transposase (Pseudo: partial start) DDE_Tnp_IS1 superfamily 40 BN49_RS11400 2038403 2038969 + 567 DNA invertase 41 BN49_RS11405 2039112 2040284 + 1173 Major tail sheath protein 42 BN49_RS11410 2040294 2040809 + 516 Phage major tail tube protein 43 BN49_RS11415 2040864...”

Fphi_1744 invertase/recombinase like protein from Francisella philomiragia subsp. philomiragia ATCC 25017
55% identity, 47% coverage

• Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources
  Siddaramappa, BMC genomics 2012
  • “...family transposase (Fphi_1742, 238 aa), a transposase-like protein (Fphi_1743, 137 aa), and an invertase/recombinase/resolvase-like protein (Fphi_1744, 189 aa). These genes were absent in all other publicly available complete Francisella genomes, including strain TX07-7308. Several genes encoding putative phage integrases were also identified in the genomes of...”
  • “...C are: Fphi_1740, transposase X; Fphi_1741 and 1750, integrase catalytic subunit; Fphi_1742, transposase; Fphi_1743, transposase; Fphi_1744, invertase/recombinase-like protein; Fphi_1745, truncated ArsB arsenite/antimonite exporter; Fphi_1746, arsenate reductase; Fphi_1747, sulfate transporter; Fphi_1748, hypothetical protein; Fphi_1749, mechanosensitive ion channel family protein; Fphi_1817, ArsR family transcriptional regulator; Fphi_1818, ArsB arsenite/antimonite...”

LM6179_p0035 recombinase family protein from Listeria monocytogenes 6179
52% identity, 51% coverage

• Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France
  Palma, BMC genomics 2020
  • “...Hypothetical protein CXL08_07455 yes group_1208 Tn3 transposase DDE domain protein LM6179_p0036 no hin DNA-invertase hin LM6179_p0035 no cadC Cd-resistance transcriptional regulatory protein CadC LM6179_p0034 no cadA1 Putative Cd-transporting ATPase LM6179_p0033 no group_1212 Hypothetical protein CXL08_07450 yes group_1213 Helix-turn-helix domain DNA-binding protein CXL08_07445 yes xerC_1 Site-specific tyrosine...”

4m6fA / P03015 Dimer of the g-segment invertase bound to a DNA substrate (see paper)
53% identity, 49% coverage

• Ligand: dna (4m6fA)

t1346 DNA-invertase from Salmonella enterica subsp. enterica serovar Typhi Ty2
STY1643 DNA-invertase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
53% identity, 50% coverage

• The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022
  European, EFSA journal. European Food Safety Authority 2024
  • “...t843 130 a 2021 Bovine meat (1) 1 t898 121 2021 Bovine meat (1) 1 t1346 8 2021 Bovine meat (1) 1 t1422 692 a 2022 Turkey meat (5) 5 t1430 9 a 2022 Broiler meat (1), Turkey meat (6) 7 2021 Bovine meat (1), Pig...”
• The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021
  European, EFSA journal. European Food Safety Authority 2023
  • “...* 2021 0 Bovine meat (1) 1 t1154 5 2020 0 Sheep meat (1) 1 t1346 8 2021 0 Bovine meat (1) 1 t1430 9 * 2021 0 Bovine meat (1), pig meat (3) 4 t2112 97 * 0 Bovine meat (1) 1 t15010 97 2020...”
  • “...(AT, 2020): spa types: t011 (4 isolates) t034 (4). Bovine meat (DE, 2021): spa types: t1346 (1 isolate), t002 (2), t008 (2), t311 (2), t2112 (1), t174 ST41110 (1), t011 (4), t034 (4), t359 (1), t559 (1), t843 mec C positive (1), t899 (1), t1430 (1),...”
• Staphylococcus aureus Isolated From Retail Meat and Meat Products in China: Incidence, Antibiotic Resistance and Genetic Diversity
  Wu, Frontiers in microbiology 2018
  • “...(4) t2524 (3), t2091 (1) ST1301 (1) t2524 (1) CC72 (19) ST72 (18) t3092 (14), t1346 (4) ST4436 * (1) t148 (1) CC395 (2) ST4434 * (1) t16984 * (1) ST395 (1) t17624 * (1) CC97 (10) ST97 (9) t730 (3), t237 (2), t359 (2), t4682...”
• Selective capture of Salmonella enterica serovar typhi genes expressed in macrophages that are absent from the Salmonella enterica serovar Typhimurium genome
  Faucher, Infection and immunity 2005
  • “...STY4821-STY4853 (33) Ty, Pa Ty, Pa, Jae STY1635 STY1643 STY2005 STY2016 STY2020 STY2022 STY2026 STY3663 STY3695 Putative bacteriophage protein min DNA invertase...”
• Cloning and sequencing of a genomic island found in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius
  McGillivary, Infection and immunity 2005
  • “...an integrase, whereas the predicted protein produced from STY1643 is most similar to an invertase/recombinase. In contrast, no such invertible sequences and...”
  • “...(24) showed that the entire locus from STY1600 to STY1643 was unique to the enteropathogens serovar Typhi CT18 and S. enterica Ty2, an observation that suggests...”

GIN_BPMU / P03015 Serine recombinase gin; G-segment invertase; Gin; Gene product 53; gp53; EC 3.1.22.-; EC 6.5.1.- from Escherichia phage Mu (Bacteriophage Mu) (see 6 papers)
NP_050655 DNA invertase from Escherichia phage Mu
53% identity, 48% coverage

• function: Performs inversion of a viral 3 kp segment (G-segment) that encodes two alternate pairs of tail fiber proteins thereby modifying the host specificity of the virus. Binds as a dimer to the viral gix sites which are 34-bp palindromic sequences that flank the invertible G-segment. Catalyzes site-specific recombination in the presence of the host factor Fis. Gin dimers bound to each of the gix sites and host factor Fis bound to the enhancer come together to form the synaptic complex. Each Gin monomer introduces a nick and becomes covalently attached to the 5'-phosphate of the DNA, resulting in double-stranded staggered breaks at both recombination sites. A 180 degrees rotation of one of the two Gin dimers followed by religation of the DNA leads to the inversion of the G-segment (G+ or G- orientation).
  subunit: Homodimer. During inversion, two dimers associate to form a homotetramer.
• Exploiting large non-isomorphous differences for phase determination of a G-segment invertase-DNA complex.
  Ritacco, Acta crystallographica. Section D, Biological crystallography 2014
  • GeneRIF: Conformation of the G-segment invertase-bound substrate DNA duplex significantly differs from those of substrates bound in other serine recombinase-DNA complexes.

STM2702 Fels-2 prophage: similar to te-specific recombinases, DNA invertase Pin homolog from Salmonella typhimurium LT2
ITP16_13610 serine-type DNA invertase Fin from Salmonella enterica subsp. enterica serovar Typhimurium
51% identity, 51% coverage

• Complete Annotated Genome Sequence of the Salmonella enterica Serovar Typhimurium LT7 Strain STK003, Historically Used in Gene Transfer Studies
  Zaworski, Microbiology resource announcements 2021
  • “...of Mauve [ 15 ]) likely was mediated by pin homolog ITP16_13610 (LT2 locus tag STM2702) ( 16 ). Alternative host ranges are conferred by similar inversions mediated by cin of phage P1 and gin of phage Mu ( 17 ) and possibly pin of the...”
  • “...that are open boxes labeled with locus tags of predicted coding DNA sequences (CDS). CDS STM2702 of LT2 (GenBank accession number AE006468 ) and its identical homolog, ITP16_13610 ( fin ) of LT7 ( CP064263 ), adjoin the inversion. Alternative C-terminal segments are fused to identical...”
• Two DNA invertases contribute to flagellar phase variation in Salmonella enterica serovar Typhimurium strain LT2
  Kutsukake, Journal of bacteriology 2006
  • “...of serovar Typhimurium, revealed that it contains another gene (STM2702) that is highly homologous to the hin gene (28). This gene locates just adjacent to a...”
• Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray
  Reen, Applied and environmental microbiology 2005
  • “...strains appeared to have lost the central regions (STM2702 to STM2730). Gifsy-2 (STM1005 to STM1056) (region X) was present in all serovar Typhimurium strains...”
• Complete Annotated Genome Sequence of the Salmonella enterica Serovar Typhimurium LT7 Strain STK003, Historically Used in Gene Transfer Studies
  Zaworski, Microbiology resource announcements 2021
  • “...from the Geneious_Prime_2020.2.4 implementation of Mauve [ 15 ]) likely was mediated by pin homolog ITP16_13610 (LT2 locus tag STM2702) ( 16 ). Alternative host ranges are conferred by similar inversions mediated by cin of phage P1 and gin of phage Mu ( 17 ) and...”
  • “...sequences (CDS). CDS STM2702 of LT2 (GenBank accession number AE006468 ) and its identical homolog, ITP16_13610 ( fin ) of LT7 ( CP064263 ), adjoin the inversion. Alternative C-terminal segments are fused to identical N termini for STM2703 and ITP16_13615; similarly, identical N termini of STM2706...”

P06693 Transposon Tn917 resolvase from Enterococcus faecalis
52% identity, 51% coverage

• Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates.
  Tansirichaiya, Microbiology spectrum 2022
  • “...genes from Tn 552 , Tn 917 , and Tn 2501 (accession numbers P18358 , P06693 , and P05823 ), with percent identities of 42.33%, 35.64%, and 29.10%, respectively. The region of Tn 7350 that was not present in Tn 7351 was also flanked by the...”

PinE / b1158 e14 prophage; site-specific DNA recombinase from Escherichia coli K-12 substr. MG1655 (see 7 papers)
pinE / P03014 e14 prophage; site-specific DNA recombinase from Escherichia coli (strain K12) (see 6 papers)
b1158 e14 prophage; site-specific DNA recombinase from Escherichia coli str. K-12 substr. MG1655
P03014 Serine recombinase PinE from Escherichia coli (strain K12)
52% identity, 50% coverage

• Positively charged specificity site in cyclin B1 is essential for mitotic fidelity
  Mayer, 2024
• Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes
  Strittmatter, Applied and environmental microbiology 2023 (secret)
• Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome
  Mehta, BMC microbiology 2004
  • “...protein family that includes phage T4 gene 38 and Mu gene 50 proteins. The pin (b1158) protein is a site-specific DNA invertase like the Min invertase of p15B, Gin of phage Mu, Hin of S. enterica , and Cin of phages P1 and P7, as well...”
  • “...IPR003458 tail fibre assembly StfE b1157 1291113411 166 (-) 0.47 - side tail fibre PinE b1158 1347714031 184 (+) 0.49 PF00239, PF02796, PS00397, PS00398 DNA invertase catalyses the inversion of 1800 bp P-region (+) McrA b1159 1413814971 277 (+) 0.38 SM00507, IPR002711, IPR003615 Modified cytosine restriction...”
• Transcriptional profile of the Escherichia coli response to the antimicrobial insect peptide cecropin A
  Hong, Antimicrobial agents and chemotherapy 2003
  • “...ybiX (b0804) -- (b0817) -- (b0872) csgD (b1040) pin (b1158) ychK (b1234) -- (b1364) ydbA 1(b1401) ydcF (b1414) fdnH (b1475) ynhA (b1679) -- (b1973) hisC (b2021)...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b1035 b4162 b3986 b3316 b3985 b3313 b3314 b0719 b3317 b3315 b3318 b1158 b3319 b2667 b3320 b2185 b3312 b3321 b2607 9.7 8.3 6.9 6.3 5.8 5.7 5.6 5.4 5.4 5.2 5.1...”
• Past, Present, and Future of Genome Modification in Escherichia coli
  Mori, Microorganisms 2022
  • “...ECK2152 nfo 2,244,868 2,245,725 EG10651 P0A6C1 endonuclease IV nuclease ECK1144 pinE pin 1,205,690 1,206,244 EG10737 P03014 Site-specific DNA recombinase of e14 prophage. recombinase e14 prophage ECK1538 pinQ ydfL 1,628,428 1,629,018 G6819 P77170 Predicted recombinase PinQ recombinase Qin prophage ECK1369 pinR ynaD 1,427,890 1,428,480 C G6697 P0ADI0...”

PA3867 probable DNA invertase from Pseudomonas aeruginosa PAO1
50% identity, 48% coverage

• Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14
  Lee, mSystems 2023
  • “...and D ). Differences in genomic context were observed for PA0982, PA2520 ( czcA ), PA3867, PA2226 ( qsrO ), and PA3507 ( 52 ). Overall, this analysis suggests that a change in the genome location was not the primary driver of instability in these least...”
• Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2022
  • “...P+ 26755 PA4914 LysR family transcriptional regulator AmaR 0.69 1.10 TR 1,186,255 4.00 P 05685 PA3867 recombinase family protein 1.49 1.00 DRRMR 1,186,255 4.00 P+ 05690 PA3866 pyocin protein S4 2.04 1.09 AP; SF 4,470,329 17.53 gb+ 21130 PA0958 outer membrane porin OprD 0.70 1.00 TSM...”
• Integrated whole-genome screening for Pseudomonas aeruginosa virulence genes using multiple disease models reveals that pathogenicity is host specific
  Dubern, Environmental microbiology 2015
  • “...of small molecules + + + + PA3799 Unknown + + + + + + PA3867 DNA replication, recombination, modification and repair + + + + + + PA3950 Transcription, RNA processing and degradation + + PA4000 rlpA Unknown + + + + PA4059 Unknown +...”
  • “...PA5548) were conserved in five genomes, one (TufA) in four genomes and two (PA0823 and PA3867) only in three genomes. Ten targets were highly conserved in B.cenocepacia J2315, with an identity higher than 60%, whereas 41 had no or poor (<40%) identity. Analysis against the E.coli...”

CIN_BPP1 / P10311 DNA-invertase; Site-specific recombinase from Escherichia phage P1 (Bacteriophage P1) (see paper)
P1_gp029 DNA invertase from Escherichia phage P1
52% identity, 49% coverage

• function: Performs inversion of a viral 3 kp segment (C-segment) that encodes two alternate pairs of tail fiber proteins thereby modifying the host specificity of the virus.
• Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages
  Piya, PLoS biology 2023
  • “...[123,124] P1_gp027 lydA holin 1.2E-01 2.4E-03 NE NE [123,124] P1_gp028 lydC holin 1.1E+00 1.2E-01 NE P1_gp029 cin site-specific recombinase 1.4E+00 9.5E-01 NE NE [125] P1_gp001 Sv prime C-terminal moiety of tail fiber gpS 5.3E-01 3.2E-01 NE NE [126] P1_gp030 U prime structural protein gpU prime of...”

EfmE4452_1558, EfmE4453_1842 recombinase family protein from Enterococcus faecium E4453
50% identity, 48% coverage

• Hospital and community ampicillin-resistant Enterococcus faecium are evolutionarily closely linked but have diversified through niche adaptation
  de, PloS one 2012
  • “...EfmE4453_1800 hypothetical protein EfmE4452_1556 EfmE4453_1844 putative ATP-binding protein EfmE4452_1557 EfmE4453_1843 related to integrase of Tn552 EfmE4452_1558 EfmE4453_1842 Resolvase/integrase Bin EfmE4452_1560 EfmE4453_1840 toxin-antitoxin system, toxin component, MazF family EfmE4452_1561 EfmE4453_1839 D-xylulose kinase EfmE4452_1563 EfmE4453_1837 transporter permease EfmE4452_1564 EfmE4453_1836 ABC transporter EfmE4452_1565 EfmE4453_1835 beta-1,4-xylosidase EfmE4452_1566 EfmE4453_1834 xylose isomerase...”
  • “...hypothetical protein EfmE4452_1556 EfmE4453_1844 putative ATP-binding protein EfmE4452_1557 EfmE4453_1843 related to integrase of Tn552 EfmE4452_1558 EfmE4453_1842 Resolvase/integrase Bin EfmE4452_1560 EfmE4453_1840 toxin-antitoxin system, toxin component, MazF family EfmE4452_1561 EfmE4453_1839 D-xylulose kinase EfmE4452_1563 EfmE4453_1837 transporter permease EfmE4452_1564 EfmE4453_1836 ABC transporter EfmE4452_1565 EfmE4453_1835 beta-1,4-xylosidase EfmE4452_1566 EfmE4453_1834 xylose isomerase EfmE4452_1567...”

Z0318 DNA invertase from prophage CP-933H from Escherichia coli O157:H7 EDL933
51% identity, 47% coverage

• Genomic instability in regions adjacent to a highly conserved pch prophage in Escherichia coli O157:H7 generates diversity in expression patterns of the LEE pathogenicity island
  Yang, Journal of bacteriology 2009
  • “...(hemL) Z0268 to Z2069 (open reading frames in Rhs element) Z0318 (pinH from CP-933H); same as RDOBGS 7 Z196 to Z1204 (perC-like region of TAI) Z1961 (prrA) to...”

ECs0284 DNA-invertase from Escherichia coli O157:H7 str. Sakai
51% identity, 50% coverage

• Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot
  Gao, PloS one 2018
  • “...did have functional annotations (n = 6) were all involved in genetic information processing: DNA-invertase (ECs0284), transcriptional activator (ECs1588), and recombinase (ECs1933), restriction alleviation and modification enhancement protein (ECs1932), single-stranded DNA binding protein (ECs1587), and Icd-like protein (ECs1577). 10.1371/journal.pone.0202775.t001 Table 1 Genes enriched for SNVs from...”
  • “...coli O157:H7. Gene ID Description Length SNV density (Counts/1000 bases) ECs0281 hypothetical protein 593 16.86 ECs0284 DNA-invertase 554 18.05 ECs1395 hypothetical protein 872 17.20 ECs1577 Icd-like protein 197 20.30 ECs1581 hypothetical protein 299 20.07 ECs1587 putative single stranded DNA-binding protein 410 21.95 ECs1588 putative transcriptional activator...”
• Genomic regions conserved in lineage II Escherichia coli O157:H7 strains
  Steele, Applied and environmental microbiology 2009
  • “...encoding baseplate assembly proteins E. coli Sakai (14) ORF ECs0284 (88% homology over 338 nt), encoding a DNA invertase, adjacent to 213 nt of DNA sequence,...”
• Identification of Escherichia coli O157:H7 genomic regions conserved in strains with a genotype associated with human infection
  Steele, Applied and environmental microbiology 2007
  • “...0 0 5 No Yes Yes No 16 ECs0270 ECs0271 and -2 ECs0276 ECS0281 ECs0282 and -3 ECs0284 10 10 10 10 10 10 10 0 0 0 10 10 5 5 3 5 5 5 5 0 0 0 5 5 No Yes Yes Yes No...”

E0Z06_RS15195 recombinase family protein from Rheinheimera sp. D18
49% identity, 49% coverage

• Novel Mobilizable Genomic Island GEI-D18A Mediates Conjugational Transfer of Antibiotic Resistance Genes in the Multidrug-Resistant Strain Rheinheimera sp. D18
  Fu, Frontiers in microbiology 2020
  • “...further suggested that the integration of GEI-D18A occurred within the intergenic sequence between E0Z06_RS15010 and E0Z06_RS15195 and that it resulted in the 12-bp direct repeat (DR) GATCTGCANNAA flanking GEI-D18A. Thirty-six ORFs were identified in GEI-D18A by genomic annotation, including night ARGs associated with tetracycline [ tetR...”
  • “...encoding genes, E0Z06_RS15085 and E0Z06_RS15165; one DDE-type integrase/transposase/recombinase encoding gene E0Z06_RS15015; one recombinase encoding gene E0Z06_RS15195; one resolvase encoding gene E0Z06_RS15010; and two ATP-binding protein TniB (involved in transposition) encoding genes, E0Z06_RS15020 and E0Z06_RS15105, were identified in GEI-D18A, suggesting that GEI-D18A can potentially transfer into other...”

PFLU5282A putative DNA invertase from Pseudomonas fluorescens SBW25
48% identity, 45% coverage

• Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment
  Gómez, Biology letters 2022
  • “...transcriptional regulator transcription 0 0 0 0 1 0 0 0 0 0 0 0 PFLU5282A putative DNA invertase cytoplasmic site-specific recombinases, DNA invertase Pin homologues replication, recombination and repair 0 0 0 0 1 0 0 0 0 0 0 0 codA cytosine deaminase cytoplasmic...”

Krad_4707 Resolvase domain from Kineococcus radiotolerans SRS30216
48% identity, 48% coverage

• Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216
  Bagwell, PloS one 2008
  • “...of plasmid monomers. PepA DR_0717 Rv2213 Krad_3276 Krad_1149 PinR Putative recombinase PinR DR_C0005 No homologs Krad_4707 Krad_4374 PolA DNA polymerase I PolA DR_1707 No homologs Krad_2951 PolB DNA polymerase II PolB No homologs No homologs No homologs PriA Putative primosomal protein n' (replication factor Y) PriA...”

G5574_10530 recombinase family protein from Pantoea stewartii
49% identity, 48% coverage

• A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris)
  White, Microbial genomics 2023
  • “...a phage tail sheath protein (locus tag: G5574_10520) and a recombinase family protein (locus tag: G5574_10530). Caution should be exercised when interpreting the presence or similarity of ZJ-FGZX1 prophage 6 with regions in C10109_Jinnung, because the corresponding region in C10109_Jinnung is fragmented across three contigs of...”

SH1761 DNA-invertase in Staphylococcus aureus transposon Tn552 from Staphylococcus haemolyticus JCSC1435
47% identity, 48% coverage

• Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis
  Méric, Genome biology and evolution 2015
  • “...protein 181 142 0.979 2,482,195 SERP1588 Mobile element protein 139 139 0.971 1,617,610 SAR1828 tnpR SH1761 ( S. haemolyticus ) DNA-invertase transposon Tn552 121 75 0.960 1,911,329 SAR0374 SA1829, SACOL0896 Hypothetical SAV0790 homolog in superantigen-encoding pathogenicity islands SaPI 84 47 0.957 414,760 SERP1579 Mobile element protein...”

P19241 Transposon Tn552 DNA-invertase BinR from Staphylococcus aureus
48% identity, 49% coverage

• Redesigning Recombinase Specificity for Safe Harbor Sites in the Human Genome.
  Wallen, PloS one 2015
  • “...plasmid was verified by sequence analysis. Recombination assays The genes encoding the Bin (UniProt ID: P19241) and Tn21 (UniProt ID: P04130) recombinase catalytic domains were synthesized (GeneArt) and fused to the H1 zinc-finger protein by overlap PCR (Table B in S1 Document ), as previously described...”
• Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis
  Berry, Applied and environmental microbiology 2002
  • “...to Staphylococcus aureus DNA invertase BinR SW:BINR_STAAU (P19241) (65.02 in 183 aa) Similar to Shigella flexneri Tn501 transposition transposase TnpA...”

AWC34_RS01870 recombinase family protein from Staphylococcus equorum
47% identity, 49% coverage

• Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses
  Heo, Scientific reports 2022
  • “...transposase 0.28 0.69 0.89 L Chromosome AWC34_RS01805 Antibiotic biosynthesis monooxygenase 0.62 0.06 0.39 S Chromosome AWC34_RS01870 HTH domain-containing protein 1.25 0.93 0.03 L Chromosome AWC34_RS01875 Hypothetical protein 1.10 0.44 0.64 PR Chromosome AWC34_RS01880 Hypothetical protein 1.63 0.30 0.52 SPO Chromosome AWC34_RS01885 Metal-sensitive transcriptional regulator 3.18 2.78...”

HMPREF0769_11633 recombinase family protein from Staphylococcus aureus subsp. aureus MN8
SAR0719 putative resolvase from Staphylococcus aureus subsp. aureus MRSA252
47% identity, 49% coverage

• Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
  Tsuchiya, The Biochemical journal 2018
  • “...the identified peptides are marked by asterisks. Gene name Protein name MW (kDa) Sequence Score HMPREF0769_11633 Resolvase, N-terminal domain protein 21.845 LNAYGC*EK 72.531 MW2460 MW2460 protein 63.757 LC*EDVAVYNHQIEK 97.291 ybaK Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase 17.89 GGC*SPVGMK 41.689 pyrE Orotate phosphoribosyltransferase 22.057 SPIYC*DNR 105.25 binL BinL protein 22.491 LNTHGC*EK...”
• Genetic variation in spatio-temporal confined USA300 community-associated MRSA isolates: a shift from clonal dispersion to genetic evolution?
  Carpaij, PloS one 2011
  • “...+ + + + + + + + - + + + + + Resolvase SAR0719 MGE + - + + + + + + + + + + + + - + Serine protease-like C SAR1906 Chromosome - + - + + + - +...”
  • “...) (SAR1902), serine protease-like C protein ( splC ) (SAR1906); a resolvase ( tnpR ) (SAR0719), a putative DNA repair protein (SAR0617), the exported protein gene SAR2565, a gene encoding a membrane protein (SAR2132), two genes encoding phage proteins (SAR1554 and SAR2066) and two genes encoding...”

SAR1828 resolvase from Staphylococcus aureus subsp. aureus MRSA252
47% identity, 48% coverage

• Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis
  Méric, Genome biology and evolution 2015
  • “...FIG01108158: hypothetical protein 181 142 0.979 2,482,195 SERP1588 Mobile element protein 139 139 0.971 1,617,610 SAR1828 tnpR SH1761 ( S. haemolyticus ) DNA-invertase transposon Tn552 121 75 0.960 1,911,329 SAR0374 SA1829, SACOL0896 Hypothetical SAV0790 homolog in superantigen-encoding pathogenicity islands SaPI 84 47 0.957 414,760 SERP1579 Mobile...”

BINL_STAAU / P18358 Transposon Tn552 resolvase from Staphylococcus aureus (see paper)
46% identity, 48% coverage

• function: Resolvase catalyzes the resolution (a site-specific recombination) of the cointegrated replicon to yield the final transposition products.
• Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates.
  Tansirichaiya, Microbiology spectrum 2022
  • “...the resolvase genes from Tn 552 , Tn 917 , and Tn 2501 (accession numbers P18358 , P06693 , and P05823 ), with percent identities of 42.33%, 35.64%, and 29.10%, respectively. The region of Tn 7350 that was not present in Tn 7351 was also flanked...”

YP_001174712 TnpR from Lactococcus lactis
47% identity, 51% coverage

• The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment
  Flórez, PloS one 2015
  • “...36 (580) YP_006998456 orf9 12,172 12,726 37.0 184 Resolvase/integrase (pGdh442_04 Lactococcus lactis ) 99 (184) YP_001174712 orf10 13,493 12,807 37.6 228 Tnp A2 transposase (pCV56C Lactococcus lactis ) 99 (228) YP_005867383 orf11 13,918 13,619 27.3 99 Hypothetical protein (pK214_p03 Lactococcus lactis ) 99 (99) YP_001429517 orf12...”

ZMO0888 Resolvase domain protein from Zymomonas mobilis subsp. mobilis ZM4
45% identity, 52% coverage

• Transcriptome profiling of Zymomonas mobilis under ethanol stress
  He, Biotechnology for biofuels 2012
  • “...1.02~1.99-fold change in this array, such as topA (ZMO1193), ZMO1401, dnaZX (ZMO086), ZMO1582, intZ (ZMO1930), ZMO0888, holA (ZMO1433), xerD (ZMO0598), mutS (ZMO1907), ZMO1194, mutM (ZMO1187), parC (ZMO1054), recF (ZMO1584), ZMO1185, recR (ZMO0812). However, transcripts encoding the others genes related to DNA replication, recombination and repair were...”

SPSF3K_02221 recombinase family protein from Streptococcus parauberis
46% identity, 51% coverage

• Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum
  Lee, PloS one 2021
  • “...protein 4.47 1.70 0.71 / SPSF3K_02220 Relaxase/mobilization nuclease domain containing protein 4.97 1.56 - mobC SPSF3K_02221 Plasmid mobilization relaxosome protein MobC 5.11 1.09 - / SPSF3K_02222 IS6 family transposase 0.93 - -0.80 / SPSF3K_02223 GNAT family N-acetyltransferase 2.06 0.67 - / SPSF3K_02224 Recombinase family protein 2.50...”

LLKF_p0016 resolvase from Lactococcus lactis subsp. lactis KF147
46% identity, 51% coverage

• Molecular characterization of a novel mosaic tet(S/M) gene encoding tetracycline resistance in foodborne strains of Streptococcus bovis
  Barile, Microbiology (Reading, England) 2012
  • “...1216 transposase A portion (77152 aa) Transposase 90 96 X92946 Perreten et al. (1997) 4 LLKF_p0016 Resolvase Resolvase 92 97 CP001835 Siezen et al. (2010) 5 LLKF_p0022 IS 1068 transposase (C terminus) Transposase 99 98 CP001835 Siezen et al. (2010) 6 LLKF_p0021 IS 1068 transposase (N...”

MAB_p04c putative resolvase/invertase/recombinase from Mycobacterium abscessus ATCC 19977
47% identity, 46% coverage

• Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus
  Ripoll, PloS one 2009
  • “...map. The plasmid carries a mercury resistance operon flanked by two genes encoding site-specific recombinases (MAB_p04c and MAB_p10, orange); it also encodes a relaxase/helicase that may function in conjugation or mobilization (MAB_p15c, yellow). 10.1371/journal.pone.0005660.t001 Table 1 General features of the M. abscessus genome and comparison with...”

JJB81_13890 flagellar phase variation DNA invertase Hin from Salmonella enterica subsp. enterica serovar Typhimurium
47% identity, 48% coverage

• Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium
  Zaworski, G3 (Bethesda, Md.) 2021
  • “...is not present in Abony serovar isolates, consistent with the present configuration. hin gene, STM2772, JJB81_13890 The Hin protein mediates inversion of a segment including its own gene and a promoter of fliC (H2, phase 2) and the fljA [repressor of fliC (H1, phase 1)] (...”

STM2772 H inversion: regulation of flagellar gene expression by site-specific inversion of DNA from Salmonella typhimurium LT2
NP_461699 H inversion protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
P03013 DNA-invertase hin from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
47% identity, 48% coverage

• Evidence of international transmission of mobile colistin resistant monophasic Salmonella Typhimurium ST34
  Supa-Amornkul, Scientific reports 2023
  • “...fljAB region revealed that all had the deletion of fljA-fljB ( STM2770-2771 ) and hin (STM2772) with the conservation of iroB (Supplementary Fig.1b). However, the 5 ends of the deletions were distinct except for two pairs of isolates, which also had relatively small SNV distances. The...”
• Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium
  Zaworski, G3 (Bethesda, Md.) 2021
  • “...Fels-2 is not present in Abony serovar isolates, consistent with the present configuration. hin gene, STM2772, JJB81_13890 The Hin protein mediates inversion of a segment including its own gene and a promoter of fliC (H2, phase 2) and the fljA [repressor of fliC (H1, phase 1)]...”
• Genotyping Study of Salmonella 4,[5],12:i:- Monophasic Variant of Serovar Typhimurium and Characterization of the Second-Phase Flagellar Deletion by Whole Genome Sequencing
  Arrieta-Gisasola, Microorganisms 2020
  • “...States (US), in 2009 [ 10 ]. These isolates lacked 77 genes from STM2692 to STM2772 and harbored a 7 kb fragment insertion composed of two partial Fels-2 genes (STM2704 and STM2706) and three genes homologous to STM1054, STM1053 and STM1997 ( umuC ), which encode...”
• Molecular identification in monophasic and nonmotile variants of Salmonella enterica serovar Typhimurium
  Bugarel, MicrobiologyOpen 2012
  • “...hixL and hixR , between which site-specific recombination occurs carried out by the invertase Hin (STM2772). Monophasic variant lacking second flagellar phase S . 1 ,4,[5],12:i:- emerged worldwide a few years ago ( Switt et al. 2009 ) and have since become one of the most...”
• Salmonella enterica serotype 4,5,12:i:-, an emerging Salmonella serotype that represents multiple distinct clones
  Soyer, Journal of clinical microbiology 2009
  • “...located in the 3 end of cluster V, including STM2772 (hin, encodes a recombinase that regulates the regulation of flagellar gene expression) and STM2773 (iroB,...”
• Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray
  Reen, Applied and environmental microbiology 2005
  • “...of the Fels-2 prophage, region XIX (STM2740 to STM2772), which encoded another PTS transport system and contained a sugar metabolism gene cluster, was absent...”
  • “...along with the highly conserved regulatory hin gene (STM2772) involved in flagellar phase switching. The absence of the hin gene results in monophasic isolates...”
• The genome of Salmonella enterica serovar gallinarum: distinct insertions/deletions and rare rearrangements
  Wu, Journal of bacteriology 2005
  • “...Fels-1 (STM893 to STM929), and Fels-2 (STM2694 to STM2772). (The genes of serovar Typhimurium LT2 are numbered consecutively on the genome from STM1 [35].)...”
• Host gene expression changes and DNA amplification during temperate phage induction
  Frye, Journal of bacteriology 2005
  • “...was previously mapped near centisome 60 (close to the STM2772 gene) (6, 7, 10, 17, 18). A small region of genome amplification was observed in SL1344 around...”
• Pathoadaptive mutations in Salmonella enterica isolated after serial passage in mice.
  Koskiniemi, PloS one 2013
  • GeneRIF: Combination of the flagellum cassette inversion mediated by Hin recombinase and the stpA mutation increased Salmonella typhimurium competitive indexes grown in mice up to 20-fold.
• Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion.
  McLean, eLife 2013
  • GeneRIF: Hin is a member of the DNA invertase subclass of serine recombinases that are regulated by a remote recombinational enhancer element containing two binding sites for the protein Fis.
• Colon cancer and cell transformation by clinicalSalmonellastrains are associated with bacterial virulence and intracellular fitness
  Stévenin, 2023
• Co-integrate Col3m bla NDM-1-harboring plasmids in clinical Providencia rettgeri isolates from Argentina.
  De, Microbiology spectrum 2023
  • “...98 kb sequence was flanked by two copies of a DNA-invertase ( hin ; UniProt P03013, last entry 18 January 2023) and the transposon Tn As2 . Third, we analyzed the plasmids in PreM15758, finding only one copy of hin -Tn As2 in p15758C_98 and p15758B_210...”
• Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence.
  Daeschel, BMC genomics 2022
  • “...QAC efflux gene (n/2490) Positive isolates without a QAC efflux gene (n/2479) hin DNA invertase P03013 2175 2 ebrB Multidrug efflux pump P0CW83 2283 2 copY Transcriptional repressor in response to copper Q47839 1138 17 slmA Nucleoid occlusion factor P0C093 2281 1 nucH Thermonuclease P43270 1051...”
  • “...190 1 cueR Transcriptional regulator involved in copper response P0A9G4 193 2 hin DNA invertase P03013 187 1 merA Resistance to mercury P17239 191 2 For the targeted BlastN search we drew from a list of environmental stress response genes curated by Pasquali et al. [...”

SA083 recombinase family protein from Escherichia coli
48% identity, 46% coverage

• <i>Bacillus velezensis</i> HBXN2020 alleviates <i>Salmonella</i> Typhimurium infection in mice by improving intestinal barrier integrity and reducing inflammation
  Wang, eLife 2024
  • “...are S. aureus S18+; ( C ) and ( G ) indicator bacteria are Salmonella SA083 ( S . Enteritidis SE006); ( D ) and ( H ) indicator bacteria are Escherichia coli EC16 ( E. coli EC016). FS: fermentation supernatant; BL: bacteria liquid. Figure 1figure...”
• Development and evaluation of an indirect enzyme-linked immunosorbent assay based on a recombinant SifA protein to detect Salmonella infection in poultry
  Gao, Poultry science 2023
  • “...pathogens . MATERIALS AND METHODS Bacterial Strains and Cloning Vector S. Pullorum SA023, S. Enteritidis SA083, S. Typhimurium SA014, E. coli ACN001, Bordetella avium P8, and Pasteurella multocida C48-1 were isolated and identified from internal organs of poultry suffering from systemic infections by Veterinary Diagnostic Laboratory,...”
• Oral or intranasal immunization with recombinant Lactobacillus plantarum displaying head domain of Swine Influenza A virus hemagglutinin protects mice from H1N1 virus
  Zhang, Microbial cell factories 2022
  • “...Salmonella SS , Salmonella SE , Salmonella SO , Salmonella pullorum SA023 , Salmonella enteritidis SA083 , Salmonella typhimurium SA014 , Riemerella anatipestifer 2,020,008 , Riemerella anatipestifer 2,020,014 , Pasteurella multocida 2,018,133 , Clostridium perfringens 22 , Staphylococcus sp 1 , Staphylococcus sp 2 , Staphylococcus...”
  • “...Salmonella ST, Salmonella SH, Salmonella SS, Salmonella SE, Salmonella SO, Salmonella typhimurium SA014, Salmonella enteritidis SA083, Salmonella pullorum SA023, Escherichia coli (ATCC 35,150), Escherichia coli XT-13, Escherichia coli AV006, Escherichia coli GS-1, Riemerella anatipestifer 2,020,008, Riemerella anatipestifer 2,020,014, Pasteurella multocida 2,018,133, Clostridium perfringens 22, Staphylococcus sp...”

WP_195767670 recombinase family protein from Klebsiella pneumoniae
47% identity, 50% coverage

• Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates
  Tansirichaiya, Microbiology spectrum 2022
  • “...strains Tet-11 Tn 7350 cI repressor (2874) 5,812 99.12 HF955507 Recombinase family protein 570 99 WP_195767670 Hypothetical protein 849 91 SAP93263 RepB family plasmid replication initiator protein 720 99 WP_087871684 Transcriptional regulator ardK 342 100 ACI63129 Zinc metalloproteinase Mpr 465 99 CDF32051 IS Sbo1 1,709 96...”

Dshi_3683 Resolvase domain from Dinoroseobacter shibae DFL 12
49% identity, 39% coverage

• The Influence of Genes on the "Killer Plasmid" of Dinoroseobacter shibae on Its Symbiosis With the Dinoflagellate Prorocentrum minimum
  Mansky, Frontiers in microbiology 2021
  • “...three tested transposon mutants (Dshi_3684, Dshi_3685, Dshi_3686) this operon also contains the gene Dshi_3687 and Dshi_3683, for which no transposon mutants was available. Dshi_3687 is annotated as a cobalt/nickel transport protein, EcfT, which is a conserved part of uptake systems ( Rodionov et al., 2006 ;...”

AWC34_RS13220 recombinase family protein from Staphylococcus equorum
42% identity, 54% coverage

• Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses
  Heo, Scientific reports 2022
  • “...deacetylase 0.45 1.79 0.07 E Plasmid2 AWC34_RS13215 LysE family translocator 1.69 1.67 1.85 E Plasmid2 AWC34_RS13220 Recombinase family protein 0.68 0.61 0.23 L Plasmid2 AWC34_RS13280 Threonine/serine exporter 0.14 1.05 0.58 S Plasmid2 AWC34_RS13285 Threonine/serine exporter 0.25 0.66 0.03 S Plasmid2 AWC34_RS13295 Protein rep 2.60 0.86 1.10...”

SAP031A_026 recombinase family protein from Staphylococcus aureus
43% identity, 53% coverage

• The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia
  Al-Trad, Antibiotics (Basel, Switzerland) 2023
  • “...which mainly encodes hypothetical proteins except for a resolvase-like protein of the serine recombinase superfamily (SAP031A_026, nts. 16,42416,978 of pWBG749) ( Figure 5 ). pSauR23-1 also encodes a type II toxin-antitoxin (TA) system comprising an endoribonuclease toxin of the RelE/ParE family that was paired with an...”

PP_5490 recombinase family protein from Pseudomonas putida KT2440
43% identity, 49% coverage

• Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440
  Wirth, mBio 2023
  • “...have been sequenced ( 28 ) and further contains three additional mobile genetic elements (i.e., PP_5490; a site-specific DNA recombinase of the Tn 3 family; PP_1931, an IS 1182 -like element of the IS Ppu 16 family transposase; and PP_1960, a site-specific integrase)which may indicate horizontal...”

pRPA5 resolvase from Rhodopseudomonas palustris CGA009
42% identity, 49% coverage

• Genetic and physical map of the structural genes (nifH,D,K) coding for the nitrogenase complex of Rhodopseudomonas capsulata
  Avtges, Journal of bacteriology 1983
  • “...,ug of tetracycline per ml in R. capsulata. Plasmid pRPA5 is pRK292 with an 11.8-kilobase-pair (kbp) Hindlll fragment of R. capsulata DNA homologous to the K....”
  • “...in preparation). The procedure used for TnS mutagenesis of pRPA5 was as described by Berg (2). The presence of two HindIII sties in TnS, symmetrically located...”

HA1_01897 recombinase family protein from Clostridium perfringens F262
46% identity, 50% coverage

• Genome sequencing and analysis of a type A Clostridium perfringens isolate from a case of bovine clostridial abomasitis
  Nowell, PloS one 2012
  • “...(53 ORFs) and Contig_6 (32 ORFs). Sequences unique to C. perfringens F262 included site-specific recombinases (HA1_01897, HA1_06197, HA1_00723, HA1_07162), unique phage-like proteins (HA1_08482, many in Contig_14, HA1_08347, HA1_13167, HA1_13212, HA1_13597), unique sigma factors (HA1_06057, HA1_13097) and unique predicted transcriptional regulators (HA1_06282, HA1_13192, HA1_13197, HA1_07182). The two...”

Mpop_5457 hypothetical protein from Methylobacterium populi BJ001
48% identity, 47% coverage

• Comparative Analysis of Xenorhabdus koppenhoeferi Gene Expression during Symbiotic Persistence in the Host Nematode
  An, PloS one 2016
  • “.... bovienii , XBJ1_1339) 79/91 116 7e-25 XK_scots25 (-) -Hypothetical protein ( Methylobacterium populi , Mpop_5457) 71/81 147 3e-17 XK_scots26 (-) -No similarity to known genes XK_scots27 (-) -No similarity to known genes XK_scots28 (-) -No similarity to known genes XK_scots29 (-) -No similarity to known...”

AWC34_RS12845 recombinase family protein from Staphylococcus equorum
53% identity, 40% coverage

• Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses
  Heo, Scientific reports 2022
  • “...protein L33 0.12 0.75 0.09 S Chromosome AWC34_RS13395 Hypothetical protein 1.03 0.02 0.44 S Chromosome AWC34_RS12845 Recombinase family protein 2.18 0.54 0.17 L Plasmid1 AWC34_RS12865 Putative sulfate exporter family transporter 0.26 1.82 0.37 S Plasmid1 AWC34_RS12925 Hypothetical protein 0.22 1.06 1.01 S Plasmid1 AWC34_RS12980 Hypothetical protein...”

GRD74_15810 recombinase family protein from Clavibacter michiganensis subsp. michiganensis
42% identity, 47% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...in plasmid pMSF1 (GRD74_15975 and GRD74_16015) and two are present in plasmid pMSF2 (GRD74_15630 and GRD74_15810), whereas an integrase-encoding gene (GRD74_15815) is located downstream of the GRD74_15810 gene in plasmid pMSF2. The hybrid assembly of strain OP3 resulted in a draft genome comprised of five contigs....”

GRD61_16000 recombinase family protein from Clavibacter michiganensis subsp. michiganensis
42% identity, 47% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...with the function of plasmids were identified in these sequences. Two resolvase-encoding genes (GRD61_15865 and GRD61_16000) and an integrase-encoding gene (GRD61_16005) were detected, located in plasmid pVL2 of strain VL527. Genes encoding a relaxase (GRD61_15780) and the ParB protein (GRD61_15830) were identified in the plasmid pVL2....”

D739_p1006 recombinase family protein from Serratia marcescens
48% identity, 41% coverage

• Diversity and Global Distribution of IncL/M Plasmids Enabling Horizontal Dissemination of β-Lactam Resistance Genes among the Enterobacteriaceae
  Adamczuk, BioMed research international 2015
  • “...exc1 /KPC4_0057 [exclusion protein 1] pOXA-48a 0 R830b 15 tniQ /D739_p1005 [transposase helper protein TniQ]; D739_p1006 [resolvase/integrase]; D739_p1010 [organomercurial lyase]; D739_p1020 [putative reverse transcriptase]; D739_p1024 [hypothetical protein]; D739_p1025 [Il-IS_2, transposase]; D739_p1026 [lipoprotein signal peptidase]; D739_p1027 [cobalt-zinc-cadmium resistance protein CzcD]; D739_p1028 [Cd(II)/Pb(II)-responsive transcriptional regulator]; D739_p1029 [hypothetical protein];...”

GQ603_16215, GRD74_15975 recombinase family protein from Clavibacter michiganensis subsp. michiganensis
42% identity, 47% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...and a TraM relaxosome protein-encoding gene (GQ603_16005) in contig three; two resolvase-encoding genes (GQ603_16175 and GQ603_16215) in contig four; and a resolvase gene (GQ603_16365) in contig five. These results suggest that strain OP3 possesses three plasmids, pOP1 (contig five), pOP2 (contig three) and pOP3 (contig four)....”
  • “...in pMSF2) were identified in strain MSF322. Two resolvase-encoding genes are present in plasmid pMSF1 (GRD74_15975 and GRD74_16015) and two are present in plasmid pMSF2 (GRD74_15630 and GRD74_15810), whereas an integrase-encoding gene (GRD74_15815) is located downstream of the GRD74_15810 gene in plasmid pMSF2. The hybrid assembly...”

tniR / AAA98330.1 resolvase from Xanthomonas sp. W17 (see 2 papers)
47% identity, 41% coverage

LSEI_0344 Site-specific recombinase, DNA invertase Pin related protein from Lactobacillus casei ATCC 334
45% identity, 46% coverage

• Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution
  Cai, Genome biology and evolution 2009
  • “...LSEI_0036 Hypothetical protein 39 1 LSEI_0038 Hypothetical protein 39 1 LSEI_0039 Hypothetical protein 44 4 LSEI_0344 DNA integration/recombination/inversion protein 38 4 LSEI_0345 Transposase 44 4 LSEI_0346 Multidrug resistance protein B 41 4 LSEI_0357 Hypothetical protein 53 -- LSEI_0554 Hypothetical protein 41 5 LSEI_0568 Hypothetical protein 44...”

RSP_2482 TonB-dependent receptor protein from Rhodobacter sphaeroides 2.4.1
45% identity, 31% coverage

• Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1
  Peters, BMC research notes 2012
  • “...0.4721 0.0369 N/A N/A RSP_3624 RSP_3792 Hypothetical CII/CII 238 8 0.0318 0.8434 0.0377 0.7706 0.9452 RSP_2482 RSP_4189 Receptor PC/PD 294 6 0.0270 0.5608 0.0481 0.9162 0.9250 RSP_2064 RSP_6012 Hypothetical CI/CI 126 11 0.0485 0.9247 0.0525 N/A N/A RSP_4252 RSP_3907 Hypothetical PD/PA 163 2 0.0050 0.0757 0.0658...”

Q9WW47 DNA invertase-like protein from Pediococcus pentosaceus
43% identity, 47% coverage

• Functional analysis of three plasmids from Lactobacillus plantarum
  van, Applied and environmental microbiology 2005
  • “...No hits Resolvase-like protein pMD136 (Pediococcus pentosus, Q9WW47) No hits No hits ArsR-like protein pL1100 (Listeria innocua, Q926M3) ArsD-like protein...”

LACR_D08 Site-specific recombinase, DNA invertase Pin related protein from Lactococcus lactis subsp. cremoris SK11
41% identity, 45% coverage

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...positive 2.3 LACR_2381 secY preprotein translocase subunit SecY negative 21.0 LACR_2340 hypothetical protein positive 1.7 LACR_D08 site-specific recombinase, DNA invertase Pin related protein negative 11.5 LACR_1260 hypothetical protein positive 1.4 LACR_1122 deoxyuridine 5'-triphosphate nucleotidohydrolase negative 6.4 LACR_1079 hypothetical protein positive 1.5 LACR_2118 deoxyuridine 5'-triphosphate nucleotidohydrolase negative...”

RSP_4189 TonB-dependent receptor protein from Rhodobacter sphaeroides 2.4.1
43% identity, 31% coverage

• Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1
  Peters, BMC research notes 2012
  • “...0.0369 N/A N/A RSP_3624 RSP_3792 Hypothetical CII/CII 238 8 0.0318 0.8434 0.0377 0.7706 0.9452 RSP_2482 RSP_4189 Receptor PC/PD 294 6 0.0270 0.5608 0.0481 0.9162 0.9250 RSP_2064 RSP_6012 Hypothetical CI/CI 126 11 0.0485 0.9247 0.0525 N/A N/A RSP_4252 RSP_3907 Hypothetical PD/PA 163 2 0.0050 0.0757 0.0658 N/A...”

CU052_00025 recombinase family protein from Vibrio harveyi
39% identity, 50% coverage

• Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis
  Deng, BMC genomics 2019
  • “...gene encoding a thermolabile hemolysin (TLH) was on ChII. In addition, four virulence genes (CU052_28670, CU052_00025, CU052_00190, and CU052_00400) were on plasmid with CU052_28670 on p345185, and CU052_00025, CU052_00190, and CU052_00400 on p34567. Table 3 Virulence factors predicted with VFDB database Virulence factor Annotation Chromosome Identity...”

YP_001429515 resolvase from Lactococcus lactis subsp. lactis
46% identity, 46% coverage

• The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment
  Flórez, PloS one 2015
  • “...14,782 29 190 Site-specific recombinase, DNA invertase Pin-like protein (pK214_01 Lactococcus lactis ) 97 (190) YP_001429515 orf 16,783 16,935 34 51 IS1216, transposase family protein ( Enterococcus faecium ) (177 aa) 100 (51) WP_002349406 orf14 17,004 17,462 41 152 Transposase IS 240 ( Enterococcus faecium )...”

SMc02287 PUTATIVE DNA-INVERTASE PROTEIN from Sinorhizobium meliloti 1021
41% identity, 54% coverage

• Transcriptome profiling reveals the importance of plasmid pSymB for osmoadaptation of Sinorhizobium meliloti
  Domínguez-Ferreras, Journal of bacteriology 2006
  • “...polymerase-related protein (SMb21448), a putative DNA invertase (SMc02287), and a probable exodeoxyribonuclease III (xthA1). Slight induction of the rpo-like...”

cinH / CAC80898.1 CinH resolvase from Acinetobacter sp. ED23-35 (see paper)
40% identity, 51% coverage

YP_001220603 resolvase from Aeromonas bestiarum
43% identity, 47% coverage

• Identification of novel genes in the carotenogenic and oleaginous yeast Rhodotorula toruloides through genome-wide insertional mutagenesis
  Liu, BMC microbiology 2018
  • “...Streptomyces sp. 47% RTM5 Genic sequence ZP_07628725.1 putative lipoprotein Prevotella amnii 45% RTM6 Genic sequence YP_001220603.1 resolvase site-specific recombinase Aeromonas bestiarum 94% RAM1 Genic sequence XP_003032296 Riboflavin transporter MCH5 Schizophyllum commune 52% RAM2 Upstream-0.5kb YP_001220603 resolvase Aeromonas bestiarum 95% RAM3 Genic sequence XP_571856 hexose transport-related protein...”

MMP0766 Site-specific recombinase from Methanococcus maripaludis S2
42% identity, 48% coverage

• Insertion sequence diversity in archaea
  Filée, Microbiology and molecular biology reviews : MMBR 2007
  • “...1 Halobacterium sp. M. burtonii 6 3 Others Ta1443 MMP0766 NC_002578 NC_005791 17 X T. acidophium M. maripaludis a Where no accession number is given, the genome...”

LSA0076 Putative DNA invertase (Plasmidic Resolvase) from Lactobacillus sakei subsp. sakei 23K
49% identity, 47% coverage

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...lsa1788 Putative phage-related 1,4-beta-N-acetyl muramidase (cell wall hydrolase) -1.0 D D DNA recombination and repair LSA0076 lsa0076 Putative DNA invertase (plasmidic resolvase) -1.1 -1.5 -1.4 LSA0366 ruvA Holliday junction DNA helicase RuvA -0.5 LSA0382 dinP DNA-damage-inducible protein P -0.5 LSA0487 recA DNA recombinase A -0.8 -1.1...”

AAur_pTC10225 resolvase, N terminal domain from Arthrobacter aurescens TC1
45% identity, 37% coverage

• Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
  Mongodin, PLoS genetics 2006
  • “...83.3%100%, seems to be limited to the region delimited by 17 pTC1-encoded ORFS (AAur_pTC10202 through AAur_pTC10225; Table S4 ) containing the atrazine degradation genes atzB and atzC and several transposases ( Figure 4 ). Outside this region, there were 14 additional genes showing more limited similarity...”

PSLT045 putative resolvase from Salmonella typhimurium LT2
SL1344_P1_0062 recombinase family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
41% identity, 50% coverage

• Insights into the Evolution of IncR Plasmids Found in the Southern European Clone of the Monophasic Variant of Salmonella enterica Serovar Typhimurium
  Vázquez, Antibiotics (Basel, Switzerland) 2024
  • “...by an additional copy of IS 26 . The first block (42.7 kb) spans between PSLT045 (following the annotation used in NC_003277; 5-end) and traH and is inverted with respect to the equivalent region found in pLSP 40/12 and flanked by oppositely-oriented copies of IS 26...”
  • “...orientation at the conventional 3-end of the two IS (iTSD: CGATATAC/TSD: GTATATCG, originally present in PSLT045). The second block (16.6 kb) extends between PSLT045 (3-end) and ccdA . Except for PSLT045, which is intact in pSLP 40/12 and disrupted in pLSP 40/13-1, all other pSLT genes...”
• Genomic analysis and phylogenetic position of the complex IncC plasmid found in the Spanish monophasic clone of Salmonella enterica serovar Typhimurium
  Vázquez, Scientific reports 2021
  • “...the tetR and tet (A) for tetracycline resistance (Fig. 1 ). The pSLT DNA (from pSLT045 to pSLT025) comprises the spv region, which encodes the main virulence factors associated with serovar-specific virulence plasmids in S. enterica 22 , as well as the toxin-antitoxin ccdAB genes, which...”
• Genetic characterisation of variants of the virulence plasmid, pSLT, in Salmonella enterica serovar Typhimurium provides evidence of a variety of evolutionary directions consistent with vertical rather than horizontal transmission
  Hiley, PloS one 2019
  • “...) at 100% identity. Another contig, B, spanned LT2 pSLT genes from within PSLT104 to PSLT045 with one SNP difference. Another contig, C, contained sulII , strA and strB resistance genes as part of a resistance cassette and another contig, D, contained a bla -TEM-1 gene....”
  • “...of LT2 pSLT AE006471. The antibiotic resistance cassette is shown as an insert in gene PSLT045 and another IS 26 is shown inserted into the traD gene. Figure drawn using GenomeVx http://wolfe.ucd.ie/GenomeVx/ [ 17 ]. The isolate missing STTR10pl but with the AMP STR SUL resistance...”
• Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome
  Izumiya, Antimicrobial agents and chemotherapy 2011
  • “...the putative resolvase corresponding to ORF PSLT045 in pSLT. The composite transposon included a possible aminoglycoside-(3)-N-acetyltransferase AAC(3) gene...”
• Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium
  Vivero, Journal of bacteriology 2008
  • “...pSLT genes rcK srgA orf7 pefI orf6 orf5 pefA repA2 PSLT025 PSLT045 PSLT046 tlpA psiB psiA traA traL traK traP traC trbI traU trbC traF trbB traG 11.04 5.58 8.08...”
• Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm
  Hawkey, BMC genomics 2013
  • “...clone from those of STm4 and STm10 (non-synonymous G->T in codon 49 of putative resolvase SL1344_P1_0062). The STm4 and STm12 plasmids also harboured one unique SNP each, both of which were non-synonymous (SL1344_P1_0091, SL1344_P1_0064). No differences in virulence plasmid gene content were identified, amongst the S...”

O3K_25807 recombinase family protein from Escherichia coli O104:H4 str. 2011C-3493
43% identity, 50% coverage

• High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4
  Yamaichi, Nucleic acids research 2015
  • “...Transposase1 0.44 0.56 0.00 47743 47961 O3K_25802 Transposase Transposase2 0.98 0.02 0.00 48125 48682 + O3K_25807 Tn3 resolvase TnpR 1.00 0.00 0.00 48865 49725 + O3K_25812 Beta-lactamase TEM Bla-TEM 1.00 0.00 0.00 49994 50296 O3K_25817 Hypothetical protein Hp7 0.20 0.80 0.00 50293 50826 O3K_25822 Type II...”

A4Y1U2 Resolvase, N-terminal domain from Shewanella putrefaciens (strain CN-32 / ATCC BAA-453)
38% identity, 46% coverage

• TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
  Seoane, PeerJ 2019
  • “...905 55 K1-Pdp11-R GGAGATGTTTTTGTGTCGTGTT 59.1 Q6ZYR2 R2- Pdp11-F TGAGCCAACCCAATCTATCC 59.8 1,085 55 R2-Pdp11-R GTGGCAACCTCTTCTTGTCC 60.0 A4Y1U2 U2-Pdp11-F ACACCAGTTGGGCGATAAAA 60.0 873 54 U2-Pdp11-R ATCGGCAAGGTTTAAAAGCA 59.7 A4Y11U5 U5-Pdp11-F CCAGTCACCACACTCATTGG 60.0 1,932 55 U5-Pdp11-R GCTTATGAACGCACCCGTAT 59.9 A1KQX7 X7-Pdp11-F TACCTGGATGAAATGCGTCA 55.1 500 57 X7-Pdp11-R TCGTGTTTCGATAAGGCTGA 55.1 A4Y11U4 U4-Pdp11-F TCGACGATCATCATCTGAGAA 59.8...”
  • “...Since all amplicons showed the expected size, only six of them (E6XG15, E6XG14, Q8GJK1, Q6ZYR2, A4Y1U2 and E6XLE5) were randomly selected for sequencing. The resulting sequence was compared to the Pdp11 genome by means of BLASTN, obtaining an identity minimum of 78.41 % and maximum of...”

mlr6326 putative DNA invertase from Mesorhizobium loti MAFF303099
39% identity, 53% coverage

• Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis
  Deng, BMC genomics 2019
  • “...vscJ, vscK, vscL, vscN, vscO, vscQ, vscR, vscS, vscT, vsxU, vscX, vscY, vscC hopAJ2, hopJ1, mlr6326, ati2, ati1 Other T3SS I, II Pseudomonas, Mesorhizobium, Aeromonas lpg2936, trwD, virB1, virB10, CbuK_1823, CbuG_0575, T4SS I, II Legionella, Bartonella, Brucella, Coxiella CbuG_1738, COXBURSA331_A0369 PFLU6009, Psyr_2628, clpV1, pppA, clpV1, Psyr_2628,...”

SAAV_c04 putative resolvase from Staphylococcus aureus subsp. aureus ED98
49% identity, 40% coverage

• Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus
  Murray, Genome biology and evolution 2017
  • “...Lowder etal. 2009 ). Nine poultry associated genes were mapped to pAVX ( SAAV_C01, SAAV_C03, SAAV_C04, aurT, scpB, SAAV_C12, SAAV_C15, SAAV_C18 , and the pemK -like SAAV_20 ). Many of the 80 genes located on the reference genome clustered into three distinct genomic regions ( fig....”

WP_107106295 recombinase family protein from Lactococcus petauri
40% identity, 47% coverage

• Garvicins AG1 and AG2: Two Novel Class IId Bacteriocins of Lactococcus garvieae Lg-Granada
  Maldonado-Barragán, International journal of molecular sciences 2022
  • “...was identical to a recombinase family protein with a helixturnhelix (HTH) domain of Lactococcus garvieae (WP_107106295). This protein is a serine recombinase similar to Escherichia coli transposon gammadelta resolvase that catalyses the site-specific recombination of the transposon and also regulates its frequency of transposition (domain architecture...”

B7L32_24595 recombinase family protein from Serratia marcescens
40% identity, 66% coverage

• In vitro Trypanocidal Activity, Genomic Analysis of Isolates, and in vivo Transcription of Type VI Secretion System of Serratia marcescens Belonging to the Microbiota of Rhodnius prolixus Digestive Tract
  da, Frontiers in microbiology 2018
  • “...genome (locus tag prefix B7L62_). Plasmidial CDSs were found in both genomes, RPA1 (B7L32_24230 to B7L32_24595, B7L32_25505 to B7L32_25515 and B7L32_25585) and RPH1 (B7L62_23970 to B7L62_24190, B7L62_24560 to B7L62_24710 and B7L62_24795). Plasmid stability is probably maintained due to some RelE toxin genes found in the chromosome...”

NP_608306 resolvase from Klebsiella pneumoniae
40% identity, 50% coverage

• Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements
  Soler, PloS one 2008
  • “...NP_608307 37 37,56537,008 54.3 185 Resolvase [pJHCMW1, Tn1331 , Klebsiella pneumoniae ] * 2e-95 99/100 NP_608306 38 37,69440,732 51.8 1015 Transposase [pJHCMW1, Tn1331 , Klebsiella pneumoniae ] * 0.0 100/100 NP_608305 39 41,22340,942 52.7 93 Predicted transcriptional regulator [pCRY, Yersinia pestis biovar Microtus str. 91001] 7e-37...”

YP_001899048 Resolvase domain from Ralstonia pickettii 12J
42% identity, 47% coverage

• Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone
  Sen, Plasmid 2010
  • “...tnpR 53458 54051 198 66 Tn3 family resolvase Resolvase, N-terminal domain [ Ralstonia pickettii 12J] YP_001899048 100 61 orf61 54290 54568 93 + 63 putative antitoxin protein Hypothetical protein [Uncultured bacterium, pB8] YP_358814 100 62 relE 54565 54849 95 + 62 toxin protein ParE [Uncultured bacterium,...”

1gdtA / P03012 Crystal structure of a site-specific recombinase, gamma-delta resolvase complexed with a 34 bp cleavage site (see paper)
41% identity, 50% coverage

• Ligand: dna (1gdtA)

mlr9024 resolvase/INTEGRASE from Mesorhizobium loti MAFF303099
40% identity, 30% coverage

• Plasmid pCAR3 contains multiple gene sets involved in the conversion of carbazole to anthranilate
  Urata, Applied and environmental microbiology 2006
  • “...CarAcII CamB Saro02000237 FdrII 40 38 32 64 59 mlr9024 TnpA CarAaI CarAa CarBaI CarBa CarBbI CarBb CarCI CarC CarAcI CamB CarRI CarR TnpR CarRII CarR CarAaII...”

H375_RS03980 recombinase family protein from Rickettsia prowazekii str. Breinl
48% identity, 58% coverage

• Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions
  Schroeder, Ticks and tick-borne diseases 2017
  • “...H375_RS01895 ), protease modulator hflC ( H375_RS02485 ), ferredoxin-NADP(+) reductase ( H375_RS00510 ), resolvase ( H375_RS03980 ), and two hypothetical proteins ( H375_RS02580 and H375_RS03250 ) may be regulated by at least two sRNAs. In addition, several other key genes, including multidrug transporter ( H375_RS00115 ),...”

SCO4351 DNA invertase from Streptomyces coelicolor A3(2)
47% identity, 41% coverage

• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...putative mutT-like protein 0.021035 0.435471 0.479161 0.28423 SCO4272 putative mutT-like protein 0.1352 0.016206 0.32968 0.527274 SCO4351 putative DNA invertase 1.26688 0.78144 1.29284 0.68489 SCO4495 putative DNA polymerase related protein 0.09624 0.75937 0.582419 0.316259 SCO4577 putative helicase 0.726962 0.053196 1.044155 0.09189 SCO4797 putative ATP-dependent DNA helicase II...”

PSYTB_15650 recombinase family protein from Pseudomonas amygdali pv. tabaci str. ATCC 11528
39% identity, 50% coverage

• N-acylhomoserine lactone-regulation of genes mediating motility and pathogenicity in Pseudomonas syringae pathovar tabaci 11528
  Cheng, MicrobiologyOpen 2017
  • “...Chemotaxis protein 2.37 PSYTB_15370 Chemotaxis protein 3.51 PSYTB_15375 Chemotaxis protein 3.05 PSYTB_15640 Chemotaxis protein 4.00 PSYTB_15650 Chemotaxis protein 3.32 PSYTB_15680 Chemotaxis protein 3.63 PSYTB_15685 Chemotaxis protein 4.02 PSYTB_15690 Chemotaxis protein 3.43 PSYTB_15700 Chemotaxis protein 3.24 PSYTB_15805 Chemotaxis protein 2.36 PSYTB_16125 Chemotaxis protein 3.39 PSYTB_16140 Methylaccepting chemotaxis...”

slr8029 resolvase from Synechocystis sp. PCC 6803
45% identity, 44% coverage

• Expression of tardigrade disordered proteins impacts the tolerance to biofuels in a model cyanobacterium Synechocystis sp. PCC 6803
  Zhang, Frontiers in microbiology 2022
  • “...tRNA-Val. Several TFs or TF related genes such as HATPase_c ( sll0790 ), Resolvase ( slr8029 ), cNMP-binding ( slr0607 ), Radical_SAM ( sll1876 ), and DUF559 ( SGL_RS19135 ). Table 4 Top20 up-regulated and down-regulated DEGs in 1321DP8. Regulation Gene ID log2FoldChange Value of p...”
  • “...SGL_RS20165 2.234 0.030 Hypothetical protein sll1160 2.128 0.044 Hypothetical protein slr1920 1.975 0.014 Hypothetical protein slr8029 1.958 0.025 Recombinase family protein Resolvase slr0607 1.933 0.004 Cyclic nucleotide-binding domain-containing protein cNMP_binding slr1052 1.908 0.001 Tetratricopeptide repeat protein slr1452 1.895 0.000 Sulfate ABC transporter substrate-binding protein sll0419 1.880...”

resIP / AAA73395.1 resolvase protein from Streptococcus agalactiae (see paper)
42% identity, 40% coverage

CJD_1891 resolvase/recombinase from Clostridium perfringens D str. JGS1721
42% identity, 42% coverage

• Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum
  Marshall, PloS one 2010
  • “...pCP13, PCP34, 31/74 (41%) 171 1445314968 pCLL_0040 Resolvase/recombinase Resolvase/Recombinase, C. perfringens D str. JGS 1721, CJD_1891, 78/210 (37%) 210 3346234094 pCLL_0042 Site-specific recombinase resolvase family DNA-invertase, C.perfringens CPE str. F4969, AC5_A0225, 80/191 (41%) 181 3426534810 pCLL_0045 Replication protein Replication protein, C. perfringens B str. ATCC 3626,...”

Q9AKZ9 Resolvase from Enterococcus faecalis
BO233_15550 recombinase family protein from Enterococcus faecium
42% identity, 45% coverage

• Tn1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages
  Sletvold, The Journal of antimicrobial chemotherapy 2010
  • “...319 pHKK701 IS 1252 transposase (AAB42161) 99 23 res 190 pRE25 orf53 resolvase, E. faecalis (Q9AKZ9) 100 24 fic 201 pRE25 orf52 cell filament protein, Fic, E. faecalis (Q9AL00) 100 25 Integrase 215 Integrase, Enterococcus faecium DO (Q3Y1H6) 81 26 hcp 214 Plasmid2 hypothetical protein, Nitrosomonas...”
• Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks
  Lisotto, Frontiers in microbiology 2021
  • “...Chromosome B22 ST117/CT24 VRE rectal swab 13-1-2017 BO233_RS09450 Chromosome C1 ST117/CT24 VRE rectal swab 28-10-2015 BO233_15550 Plasmid C2 ST117/CT24 VRE blood 18-3-2012 BO233_14905 Plasmid C3 ST117/CT24 VRE rectal swab 28-2-2011 BO233_14905 Plasmid C4 ST117/CT24 VRE rectal swab 28-2-2011 BO233_RS12430 Chromosome C5 ST117/CT24 VRE rectal swab 12-3-2013...”
  • “...transposon integration point was located in the plasmid DNA invertase Pin gene (GenBank locus taq: BO233_15550), and their transposons differed by 101 and 260 SNPs from the reference, respectively; (ii) in one single isolate from 2012 (C6), the transposon integrated into a peptidoglycan-binding protein gene (GenBank...”

res / GB|CAA68600.1 resolvase from Clostridium perfringens (see paper)
42% identity, 47% coverage

SYNPCC7002_G0039 resolvase/recombinase from Synechococcus sp. PCC 7002
38% identity, 49% coverage

• Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA
  Ludwig, Frontiers in microbiology 2011
  • “...low levels; there were only a 12 ORFs (SYNPCC7002_A2187, A2712, A2746, SYNPCC7002_D0029, D0030, SYNPCC7002_F0015, F0016, SYNPCC7002_G0039, G0040, G0050, G0051, and G0052) with no mapped cDNA sequences under standard growth conditions; for two of those (SYNPCC7002_A2187 and A2746) transcripts were found under at least one of the...”

pYV0017 putative resolvase from Yersinia pseudotuberculosis IP 32953
YPCD1.91 putative resolvase from Yersinia pestis CO92
39% identity, 50% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...1.344 (0.165) pYV0020 YPCD1.95c sycH SycH, putative yopH targeting protein 5.088 (< 0.001) 2.029 (0.002) pYV0017 YPCD1.91 putative resolvase 0.341 (< 0.001) 1.152 (0.705) pYV0075 YPCD1.48 virG VirG; putative Yop targeting lipoprotein 1.957 (0.015) 1.544 (0.023) pYV0055 YPCD1.29c yopB YopB, putative Yop targeting protein 2.816 (<...”
  • “...protein 13.528 (< 0.001) 1.577 (0.046) pYV0014 pCD1-AAC62595 possible transposase remnant 1.789 (0.025) 1.884 (0.016) pYV0017 pCD1-tnpR putative resolvase 0.341 (< 0.001) pYV0020 pCD1-sycH putative YopH targeting protein 5.088 (< 0.001) 2.715 (< 0.001) pYV0024 pCD1-sycE putative YopE chaperone 5.781 (< 0.001) 2.403 (0.005) pYV0040 pCD1-yopK/yopQ...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.165) pYV0020 YPCD1.95c sycH SycH, putative yopH targeting protein 5.088 (< 0.001) 2.029 (0.002) pYV0017 YPCD1.91 putative resolvase 0.341 (< 0.001) 1.152 (0.705) pYV0075 YPCD1.48 virG VirG; putative Yop targeting lipoprotein 1.957 (0.015) 1.544 (0.023) pYV0055 YPCD1.29c yopB YopB, putative Yop targeting protein 2.816 (< 0.001)...”

AC3_0180 resolvase/recombinase from Clostridium perfringens E str. JGS1987
41% identity, 42% coverage

• Comparative genomics of VirR regulons in Clostridium perfringens strains
  Frandi, BMC microbiology 2010
  • “...hypothetical protein AC3_A0725 AC3_A0725 1.04 119 JGS1987 conserved hypothetical protein AC3_A0081 1.11 180 JGS1987 resolvase/recombinase AC3_0180 1.15 264 JGS1987 put. lipid A export ATP-binding/permease (MsbA) AC3_0181 1.15 124 JGS1987 hypothetical protein AC3_A0587 AC3_A0587 1.34 227 JGS1987 hypothetical protein AC3_0277 AC3_0277 1.18 112 JGS1987 hypothetical protein AC3_A0194...”
  • “...seven genes code for proteins of unknown function. One of them corresponds to a resolvase/recombinase (AC3_0180) suggesting a possible scenario in which host invasion is linked to gene mobilization. The other two genes with assigned function in the putative regulon of strain JGS1987 include a 2-keto-3-deoxygluconate...”

GQY01_RS11410 recombinase family protein from Staphylococcus epidermidis
41% identity, 45% coverage

• Genotypic and Phenotypic Characterization of Fecal Staphylococcus epidermidis Isolates Suggests Plasticity to Adapt to Different Human Body Sites
  Garcia-Gutierrez, Frontiers in microbiology 2020
  • “...100 100 GQY01_RS11405 mntA_2 0.01329 zinc ABC transporter substrate-binding protein [ Staphylococcus ] 100 100 GQY01_RS11410 group_12447 0.01329 recombinase family protein [ Staphylococcus ] 100 100 GQY01_RS11415 group_13561 0.00155 hypothetical protein [ Staphylococcus ] 99.85 100 GQY01_RS11420 group_13560 0.00155 hypothetical protein [ Staphylococcus ] 100 100...”

lr2094 recombinase from Lactobacillus reuteri
lr2094 recombinase family protein from Limosilactobacillus reuteri
42% identity, 43% coverage

• Removal of antibiotic resistance gene-carrying plasmids from Lactobacillus reuteri ATCC 55730 and characterization of the resulting daughter strain, L. reuteri DSM 17938
  Rosander, Applied and environmental microbiology 2008
  • “...ArsR Plasmid-associated protein Replication initiator protein pLR585 lr2094 lr2095 lr2096 lr2097 ACC61202 ACC61203 DQ857862 DQ857863 lr2098 lr2099 lr2100 lr2101...”

Aasi_0545 hypothetical protein from Candidatus Amoebophilus asiaticus 5a2
38% identity, 49% coverage

• A bacterial genome in transition--an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus
  Schmitz-Esser, BMC evolutionary biology 2011
  • “...transposases belong to the IS110 family (Aasi_1379 and Aasi_1284); and to the Tn3 family (Aasi_0096, Aasi_0545); one belongs to the IS3 family (probably consisting of the two consecutive ORFs Aasi_1748 and Aasi_0907); and two belong to the YhgA-like family of putative transposases (Aasi_0894, Aasi_1306; PFAM-family PF04754)....”

YP_003601011 Resolvase from Lactobacillus crispatus ST1
42% identity, 43% coverage

• Identification of pOENI-1 and related plasmids in Oenococcus oeni strains performing the malolactic fermentation in wine
  Favier, PloS one 2012
  • “...TauE L. mali , ZP_09449472 99 9 7365-7952 41,8 Res 195 Resolvase L. crispatus , YP_003601011 99 10 9124-8192 35,3 LysR 310 Transcriptional regulator, LysR O. oeni , ZP_01543901 100 11 9267-10448 42,1 Oye 393 NADH: flavin oxidoreductase O. oeni , ZP_01543900 100 12 11258-10575 45,5...”

KJR89_15010, KJS00_15145 recombinase family protein from Listeria monocytogenes
LMOh7858_pLM80_0080 site-specific recombinase, resolvase family from Listeria monocytogenes str. 4b H7858
39% identity, 47% coverage

• Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs
  Anast, MicrobiologyOpen 2022
  • “...2.5 2.6 KJS00_15455 KJR89_15140 Hypothetical protein 2.3 2.2 KJS00_15480 KJR89_15080 Hypothetical protein 2.1 1.1 KJS00_15145 KJR89_15010 Sitespecific recombinase, resolvase family 2.1 1.5 KJS00_15325 KJR89_15415 Twocomponent transcriptional response regulator 2.1 2.3 KJS00_15475 KJR89_15085 Hypothetical protein 2.0 1.0 KJS00_15460 KJR89_15135 Hypothetical protein 1.8 1.9 KJS00_15300 KJR89_15440 Putative coppertranslocating...”
  • “...kinase 2.5 2.6 KJS00_15455 KJR89_15140 Hypothetical protein 2.3 2.2 KJS00_15480 KJR89_15080 Hypothetical protein 2.1 1.1 KJS00_15145 KJR89_15010 Sitespecific recombinase, resolvase family 2.1 1.5 KJS00_15325 KJR89_15415 Twocomponent transcriptional response regulator 2.1 2.3 KJS00_15475 KJR89_15085 Hypothetical protein 2.0 1.0 KJS00_15460 KJR89_15135 Hypothetical protein 1.8 1.9 KJS00_15300 KJR89_15440 Putative...”
• Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs
  Anast, MicrobiologyOpen 2022
  • “...Hypothetical protein 5.3 1.8 LMOh7858_pLM80_0016 Hypothetical protein 4.2 2.0 LMOh7858_pLM80_0078 DNA transpositionlike protein 1.0 0.6 LMOh7858_pLM80_0080 Sitespecific recombinase, resolvase family 1.2 0.9 LMOh7858_pLM80_0081 Sitespecific recombinase, resolvase family 1.1 0.9 LMOh7858_pLM80_0083 Cadmiumtransporting ATPase CadA2 (EC 3.6.3.3) 0.7 0.7 LMOh7858_pLM80_0092 Replicationassociated protein/ParA family protein 0.6 1.1 LMOh7858_pLM80_0093 RepA...”

NM221_06205 recombinase family protein from Parvimonas micra
40% identity, 46% coverage

• Parvimonas micra can translocate from the subgingival sulcus of the human oral cavity to colorectal adenocarcinoma
  Conde-Pérez, Molecular oncology 2024
  • “...and 2. Consensus product Average length (bp) Cluster Locus tag Recombinase family protein 621 41 NM221_06205 SpaA isopeptideforming pilinrelated protein 2271 41 NM221_06200 Pseudouridine5phosphate glycosidase 546 42 NM221_06515 ABC transporter ATPbinding protein/permease 1560 42 NM221_06510 EXLDI protein 369 43 NM221_01675 Transposonencoded TnpW family protein 231 43...”

Sez_1116 resolvase/integrase from Streptococcus equi subsp. zooepidemicus MGCS10565
40% identity, 43% coverage

• Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens
  Holden, PLoS pathogens 2009
  • “...this protein (SEQ1307a) and lacks an adjacent gene predicted to encode a recombinase (SZO08550 and Sez_1116). SZO08560 and Sez_1114 share sequence similarity with hypothetical proteins of S. suis strain 05ZYH33 (SSU05_0473) and S. agalactiae strain COH1 (SAN_1519) and contain four Listeria-Bacteroides repeat Pfam domains (PF09479). The...”
  • “...contains an IS element between the inverted repeats bordering the Sez_1114 promoter and the recombinase (Sez_1116), the consequences of this on transcription of Sez_1114 are not yet known. 10.1371/journal.ppat.1000346.g005 Figure 5 Diagram of the SZO08560 invertible promoter in Sz H70. The promoter region of SZO08560 (170...”

5cy1A / P0ADI2 Tn3 resolvase - site iii complex crystal form i
39% identity, 50% coverage

• Ligand: dna (5cy1A)

DRC0005, DR_C0005 resolvase from Deinococcus radiodurans R1
36% identity, 49% coverage

• Metabolic Engineering of Extremophilic Bacterium Deinococcus radiodurans for the Production of the Novel Carotenoid Deinoxanthin
  Jeong, Microorganisms 2020
  • “...of dxs was also constructed. Approximately 1 kb of upstream/downstream DNA fragments containing drC0004 and drc0005 was amplified using drc04-1/drc04-2 and drc05-1/drc05-2 primer sets, respectively. The PCR fragments were ligated into the pAM1 plasmid at the Kpn I/ Pst I and BamH I/ Sph I sites...”
  • “...-lox71 This study Pdrc4-dxs pAM1 containing two homology arms (the partial sequences of drC0004 and drc0005 ) and P groE - dxs - lox66-km r -lox71 This study...”
• Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216
  Bagwell, PloS one 2008
  • “...required for maintenance of plasmid monomers. PepA DR_0717 Rv2213 Krad_3276 Krad_1149 PinR Putative recombinase PinR DR_C0005 No homologs Krad_4707 Krad_4374 PolA DNA polymerase I PolA DR_1707 No homologs Krad_2951 PolB DNA polymerase II PolB No homologs No homologs No homologs PriA Putative primosomal protein n' (replication...”

GQ603_15820 recombinase family protein from Clavibacter michiganensis subsp. michiganensis
40% identity, 44% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...S2B ). Plasmid-associated genes are present in contigs three, four and five: three relaxase-encoding genes (GQ603_15820, GQ603_15960, GQ603_15995) and a TraM relaxosome protein-encoding gene (GQ603_16005) in contig three; two resolvase-encoding genes (GQ603_16175 and GQ603_16215) in contig four; and a resolvase gene (GQ603_16365) in contig five. These...”

BruAb1_0287 site-specific recombinase, resolvase family from Brucella abortus biovar 1 str. 9-941
41% identity, 41% coverage

• Genomic Characterization Provides New Insights for Detailed Phage- Resistant Mechanism for Brucella abortus
  Li, Frontiers in microbiology 2019
  • “...1,767 100.00 % Phage integrase family site specific recombinase BruAb1_0286 195 100.00 % Hypothetical protein BruAb1_0287 618 100.00 % Resolvase family site-specific recombinase BruAb1_0289 228 100.00 % Hypothetical protein BruAb1_0290 285 100.00 % Hypothetical protein BruAb1_0291 261 100.00 % Hypothetical protein BruAb1_0292 390 100.00 % Hypothetical...”
  • “...% l -2-hydroxyglutarate oxidase Eight genes, BruAb1_0284-0292 , were located in RD1 region. BruAb1_0284 and BruAb1_0287 are specific recombinases, belonging to phage integrase and resolvase families, respectively. BruAb1_0285 and BruAb1_0288 were annotated as pseudo genes and the others were labeled hypothetical proteins. In addition, we further...”

BR0260 site-specific recombinase, resolvase family from Brucella suis 1330
41% identity, 41% coverage

• The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
  Paulsen, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...integrated phage remnants in B. suis (BR1083-BR1078 and BR0260- BR0256), including phage integrase genes, are also located adjacent to tRNAs and are present in...”

BMEI0901 RESOLVASE from Brucella melitensis 16M
41% identity, 41% coverage

• Comparative genomic analysis of Brucella melitensis vaccine strain M5 provides insights into virulence attenuation
  Jiang, PloS one 2013
  • “...also found in 16 M, where another copy was also found. RI2 contained two ORFs, BMEI0901 and BMEI0902. BMEI0901 encodes a resolvase similar to phage Mu DNA invertase Pin homologs, whereas BMEI0902 encodes a site-specific recombinase similar to an anti-repressor ( ant ) gene. This gene...”
• Comparative whole-genome hybridization reveals genomic islands in Brucella species
  Rajashekara, Journal of bacteriology 2004
  • “...in Brucella spp. BME_IDa Species Chromosome I BMEI0200 BMEI0901 BMEI1192 BMEI1201-1221 BMEI1815 B. B. B. B. B. Chromosome II BMEII0445 BMEII0718 BMEII0867 B....”

PCP15 resolvase from Clostridium perfringens str. 13
40% identity, 47% coverage

• Analysis of the complete genome sequences of Clostridium perfringens strains harbouring the binary enterotoxin BEC gene and comparative genomics of pCP13-like family plasmids
  Ueda, BMC genomics 2022
  • “...ABC transporter permease ( FtsX) 8* 63237006 684(+) ABC transporter ATP-binding protein 9 72707842 573(+) PCP15 resP Serine recombinase/resolvase (ResP) 10* 82138971 759(+) Hypothetical 11* 89869861 876(+) Hypothetical 12 992610,570 645() PCP18 Hypothetical 13 10,58210,896 315() PCP19 PadR family transcriptional regulator 14 11,45611,659 204(+) PCP24 Hypothetical...”
• Functional identification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens
  Bannam, Journal of bacteriology 2006
  • “...ORF8, 54/150 (36%); C. perfringens pCP13, PCP15, 50/150 (33%), resolvase pfam00239\ Hypothetical protein Hypothetical protein Transcriptional regulator B,...”
• Use of the integration elements encoded by the temperate lactococcal bacteriophage TP901-1 to obtain chromosomal single-copy transcriptional fusions in Lactococcus lactis
  Brøndsted, Applied and environmental microbiology 1999
  • “...pBF17b::4.1-kb HindIII-SalI pCP22 pBF17b::4.1-kb HindIII-SalI pCP15 pBF17b::4.9-kb HindIII-SalI pJM334 pGhost8::1.9-kb EcoRI-SalI pLB61 pMOSBlue::333-bp PCR...”
  • “...Berkeley pMOSBlue pUC7,erm pCI372 pGhost8 pAK80 pNZ273 pTRKH2 pCP15 pCP22 pJM334 pAB201 pLB45 pLB61 pLB65 pLB85 pLB86 pLB87 pLB88 pLB89 pLB95 pBF12 pBF17a...”

AC5_A0225 recombinase family protein from Clostridium perfringens CPE str. F4969
42% identity, 44% coverage

• Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum
  Marshall, PloS one 2010
  • “...CJD_1891, 78/210 (37%) 210 3346234094 pCLL_0042 Site-specific recombinase resolvase family DNA-invertase, C.perfringens CPE str. F4969, AC5_A0225, 80/191 (41%) 181 3426534810 pCLL_0045 Replication protein Replication protein, C. perfringens B str. ATCC 3626, AC1_A0161, 164/388 (42%) 446 3598037320 pCLL_0047 Putative ATPase Putative ATPase, C. perfringens E str. JGS1987,...”

GQ603_16175, GRD74_16015 recombinase family protein from Clavibacter michiganensis subsp. michiganensis
42% identity, 40% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...GQ603_15960, GQ603_15995) and a TraM relaxosome protein-encoding gene (GQ603_16005) in contig three; two resolvase-encoding genes (GQ603_16175 and GQ603_16215) in contig four; and a resolvase gene (GQ603_16365) in contig five. These results suggest that strain OP3 possesses three plasmids, pOP1 (contig five), pOP2 (contig three) and pOP3...”
  • “...were identified in strain MSF322. Two resolvase-encoding genes are present in plasmid pMSF1 (GRD74_15975 and GRD74_16015) and two are present in plasmid pMSF2 (GRD74_15630 and GRD74_15810), whereas an integrase-encoding gene (GRD74_15815) is located downstream of the GRD74_15810 gene in plasmid pMSF2. The hybrid assembly of strain...”

Aasi_0096 Resolvase domain from Candidatus Amoebophilus asiaticus 5a2
39% identity, 46% coverage

• A bacterial genome in transition--an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus
  Schmitz-Esser, BMC evolutionary biology 2011
  • “...two transposases belong to the IS110 family (Aasi_1379 and Aasi_1284); and to the Tn3 family (Aasi_0096, Aasi_0545); one belongs to the IS3 family (probably consisting of the two consecutive ORFs Aasi_1748 and Aasi_0907); and two belong to the YhgA-like family of putative transposases (Aasi_0894, Aasi_1306; PFAM-family...”

GQ603_16365 recombinase family protein from Clavibacter michiganensis subsp. michiganensis
37% identity, 47% coverage

• Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants
  Méndez, Microorganisms 2020
  • “...contig three; two resolvase-encoding genes (GQ603_16175 and GQ603_16215) in contig four; and a resolvase gene (GQ603_16365) in contig five. These results suggest that strain OP3 possesses three plasmids, pOP1 (contig five), pOP2 (contig three) and pOP3 (contig four). Moreover, contigs three, four and five of the...”

Rmet_6187 resolvase-like protein from Ralstonia metallidurans CH34
33% identity, 51% coverage

• Loss of Mobile Genomic Islands in Metal-Resistant, Hydrogen-Oxidizing Cupriavidus metallidurans
  Große, Applied and environmental microbiology 2022 (secret)

NE0836 Site-specific recombinase from Nitrosomonas europaea ATCC 19718
32% identity, 51% coverage

• Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals
  Park, Applied and environmental microbiology 2008
  • “...gatA gatB rnpA* DNA replication, recombination, repair NE0835 NE0836 NE0837* NE2207 tnpA tnpR Transcription NE2324 NE1035 NE0854 NE0951 Amino acid transport and...”
  • “...by tnpA (NE0835) and the resolvase encoded by tnpR (NE0836) were upregulated under Cd2 (31fold) and Hg2 (54-fold) stress but not under Zn2 and Cu2 DISCUSSION...”

WP_176453834 recombinase family protein from Cutibacterium acnes
37% identity, 46% coverage

• First Report of Plasmid-Mediated Macrolide-Clindamycin-Tetracycline Resistance in a High Virulent Isolate of Cutibacterium acnes ST115
  Rana, Pathogens (Basel, Switzerland) 2023
  • “...1036611142 258 nucleotidyl transferase AbiEii/AbiGii toxin 100 WP_176453835 11 1113911723 194 recombinase family protein 100 WP_176453834 12 1263212979 115 plasmid mobilization relaxosome protein MobC 100 WP_176453832 13 1297914685 569 relaxase of type IV secretion system (plasmid) 100 BBJ25226 14 1468715277 205 DUF3801 domain-containing protein 100 WP_176453830...”

VP0638 putative resolvase from Vibrio parahaemolyticus RIMD 2210633
36% identity, 43% coverage

• Genomic Features of Environmental and Clinical Vibrio parahaemolyticus Isolates Lacking Recognized Virulence Factors Are Dissimilar
  Ronholm, Applied and environmental microbiology 2016
  • “...VP1088 to VP1094 ISF-77-01 RM-14-5 VP0635 to VP0636, VP0638 to VP0643 VP0635, VP0636 VP0635, VP0636 ISF-54-12 VP1088 to VP1094 VP0635, VP0636 VP0380, VP0398 to...”

tnpR / BAB59050.1 resolvase from Pseudomonas putida (see paper)
34% identity, 47% coverage

P20384 Putative transposon Tn552 DNA-invertase bin3 from Staphylococcus aureus
37% identity, 45% coverage

• Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence.
  Daeschel, BMC genomics 2022
  • “...ravA ATPase possibly involved in cadmium stress response P31473 1192 0 bin Tn522 DNA invertase P20384 1264 120 qacC Multidrug efflux pump P14319 2290 1 cwlO Peptidoglycan endopeptidase P40767 1044 14 qorB Quinone oxidoreductase P39315 1390 5 cadA Cadmium transporting ATPase P20021 1212 141 cadC Cadmium...”
• Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov.
  Tambong, Frontiers in microbiology 2021
  • “...identified in strain 23L3C is distinct. Protein sequences in cluster 1 matched the Swiss-protein # P20384, a putative transposon Tn552 DNA-invertase bin3 that facilitates horizontal transfer and recombination events related to multidrug resistance ( Shore et al., 2010 ; Abriouel et al., 2015 ). This disproportionately...”
• Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis
  Berry, Applied and environmental microbiology 2002
  • “...to S. aureus potential DNA invertase Bin3 SW:BIN3_STAAU (P20384) (32.51 in 203 aa) No significant matches Similar to B. subtilis spore coat-associated protein N...”

EF_B0058 site-specific recombinase, resolvase family from Enterococcus faecalis V583
39% identity, 38% coverage

• An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense
  Bullen, Nature communications 2024
  • “...strains V583 ( D ) and V19 ( E ) in which the genes encoding EF_B0058 or EF_B0059 on pTEF2 are deleted. Data represent means.d. of two technical replicates. F Schematic of the EF_B0058 and EF_B0059 genes. G Reverse transcription-PCR analysis of the EF_B0058 and EF_B0059...”
  • “...sets used to probe the structure of the EF_B0058-EF_B0059 transcriptional operon are shown in red (EF_B0058 specific), green (intergenic) and blue (EF_B0059 specific). H Growth curves of E. coli expressing EF_B0059, the indicated active site mutants, or empty vector. Arrow indicates when protein expression was induced....”

RPPX_RS27515 recombinase family protein from Pseudomonas putida S12
34% identity, 47% coverage

• Comparative analysis reveals the modular functional structure of conjugative megaplasmid pTTS12 of Pseudomonas putida S12: A paradigm for transferable traits, plasmid stability, and inheritance?
  Kusumawardhani, Frontiers in microbiology 2022
  • “...highest similarity to Tn 5563 ( Figure 3A ). Tn 3-I is an identical transposase (RPPX_RS27515, tnpR and RPPX_RS27515, tnpA ) to Tn 4656 encoded on pWW53 plasmid from P. putida MT53. Moreover, the 39-bps inverted repeat (IR) sequences found on both ends of these two...”

AAur_pTC10243 DNA-invertase (Site-specific recombinase resolvase family) from Arthrobacter aurescens TC1
40% identity, 49% coverage

• Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
  Mongodin, PLoS genetics 2006
  • “...endodes a putative Soj/ParA family protein, AAur_pTC10124 (51%), which encodes a putative ParB-partitioning protein, and AAur_pTC10243 (70%), which encodes a DNA-invertase (a site-specific recombinase/resolvase family protein). This suggests that genes involved in plasmid partitioning in pTC1 and pAO1 most likely share a common ancestor. A. aurescens...”

Rmet_4599 recombinase family protein from Cupriavidus metallidurans CH34
34% identity, 47% coverage

• Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans
  Große, Microbiology spectrum 2022
  • “...+ czcC2B2 474 bp upstr. Rmet_4596 TSS_1221261-3 317 65 tnpRA -anti. czcB2 25 bp upstr. Rmet_4599 czc2 part 2 TSS_1061603+3 27 5 + czcR2S2 - ubiG -anti. czcA2B2 - uspA11 - sulP 55 bp upstr. Rmet_4465 TSS_1061540+3 41 9 + czcR2S2-ubiG -anti- czcA2B2 - uspA11 -...”

pc1469 probable resolvase from Parachlamydia sp. UWE25
33% identity, 51% coverage

• A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system
  Greub, BMC microbiology 2004
  • “...Probable DNA double-strand break repair ATPase pc1467 17420791744181 Putative transposase pc1468 17446341745023 Probable resolvase a pc1469 17453981745955 Probable transposases, partial length a pc1470-1471 17458071746692 Probable Doc (death on cure) protein, bacteriophage P1 a pc1473 17471351747512 Phage-related protein c pc1474 17476181747809 Direct repeat - 17479151747925 a ,...”

HCM1.168 resolvase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
34% identity, 46% coverage

• Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever
  Wain, Antimicrobial agents and chemotherapy 2003
  • “...region immediately to the left of dfrA14 (HCM1.166 to HCM1.168) represents a 5 conserved sequence typical of class 1 integrons (16), there is no 3 conserved...”

P30739 Resolvase/recombinase from Pseudomonas putida
35% identity, 51% coverage

• Relatedness of chromosomal and plasmid DNAs of Erwinia pyrifoliae and Erwinia amylovora
  McGhee, Applied and environmental microbiology 2002 (secret)

CD3578 putative resolvase from Clostridium difficile 630
CDR20291_3416 putative resolvase from Clostridium difficile R20291
39% identity, 45% coverage

• Identification of a Bile Acid-Binding Transcription Factor in Clostridioides difficile Using Chemical Proteomics
  Forster, ACS chemical biology 2022
  • “...symporter, respectively. While genome-wide transcription start site (TSS) mapping in C. difficile predicts promoters at cd3578 and cd3571 , no TSSs were reported for mdeA-cd3572 58 ( Figure 5B ), although in our experience these genome-wide analyses do not capture all TSSs. Because cd3573-cd3575 approached significance...”
• A novel genetic switch controls phase variable expression of CwpV, a Clostridium difficile cell wall protein
  Emerson, Molecular microbiology 2009
  • “...inversion of the cwpV switch. Genes for seven recombinases ( CD1932, CD1905, CD2066, CD1822, CD1167, CD3578 and CD1222 ) were cloned into pACYCDuet-1 and co-transformed into E. coli BL21DE3 with pUC19 plasmids carrying the cwpV switch in either the ON or OFF orientations (pCBR026 or pCBR027)....”
  • “...CD1882 This study pCBR049 pACYC-Duet1 containing CD1167 ( recV ) This study pCBR050 pACYC-Duet1 containing CD3578 This study pCBR051 pACYC-Duet1 containing CD1222 This study a pCBR035043 have the pMTL960 backbone and were constructed by insertion of Acc65I-BamHI fragments from pCBR024 to pCBR032 which have a pUC19...”
• Genome-wide detection of conservative site-specific recombination in bacteria
  Sekulovic, PLoS genetics 2018
  • “...recombinase in its vicinity. It is therefore possible that inversion of Cdi7 is catalyzed by CDR20291_3416, which is located next to the inversion site. Additional cellular factors or cis -acting elements might also participate in the DNA inversion process as was recently demonstrated for the fim...”

2r0qC / P20384 Crystal structure of a serine recombinase- DNA regulatory complex (see paper)
36% identity, 47% coverage

• Ligand: dna (2r0qC)

FAD_0665 recombinase family protein from Ferroplasma acidiphilum
37% identity, 46% coverage

• Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y^T
  Golyshina, Scientific reports 2017
  • “...Mismatch repair and recombination Recombination and mismatch repair proteins were represented by the DNA resolvase (FAD_0665) exhibiting a relatively low similarity to its counterparts from methanogens and bacteria. DNA-repair helicase FAD_1466 was similar to archaeal Rad25 proteins, FAD_1503 exhibited 30% identity with Sulfolobales XPD/Rad3-related DNA helicases...”

P04130 Transposon Tn21 resolvase from Escherichia coli
33% identity, 47% coverage

• Redesigning Recombinase Specificity for Safe Harbor Sites in the Human Genome.
  Wallen, PloS one 2015
  • “...analysis. Recombination assays The genes encoding the Bin (UniProt ID: P19241) and Tn21 (UniProt ID: P04130) recombinase catalytic domains were synthesized (GeneArt) and fused to the H1 zinc-finger protein by overlap PCR (Table B in S1 Document ), as previously described [ 51 ]. PCR products...”
• Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes
  Luck, Infection and immunity 2001
  • “...P39376 P03813 P04539 P04826 P13661 P09999 P04162 P04130 BAA78805.1 P00483 BAA78832.1 AF162223 P04483 P02980 BAA78836 BAA78837 AAD34405, AB011549 AF134403,...”

WP_002294320 recombinase family protein from Enterococcus faecium
35% identity, 48% coverage

• Genome Analysis of the Enterococcus faecium Entfac.YE Prophage
  Elahi, Avicenna journal of medical biotechnology 2022
  • “...Hypothetical protein N/A 599 LC606224 PWT87042 36 55.5 45 Recombinase family protein RR 581 LC600466 WP_002294320 99 100 46 HK97 family phage prohead protease PS 569 LC602694 WP_002349220 99 100 47 Phi13 family phage major tail protein PS 560 LC606178 WP_002332434 99 100 48 Hypothetical protein...”

cg1929 recombinase from Corynebacterium glutamicum ATCC 13032
27% identity, 59% coverage

• Methanol-Essential Growth of Corynebacterium glutamicum: Adaptive Laboratory Evolution Overcomes Limitation due to Methanethiol Assimilation Pathway
  Hennig, International journal of molecular sciences 2020
  • “...DNA repair 15 bp deletion within coding sequence (CDS) cg1806 metK MDS2T8 S-adenosylmethionine synthetase S288N cg1929 res MDS2T8 Site-specific recombinase R91H cg1801 rpe MDS2T14 Ribulose-5-phosphate epimerase Insertion of a 1.4 kb transposon ijms-21-03617-t002_Table 2 Table 2 Bacterial strains used in this study. Strain Relevant Characteristics Reference...”
• Silencing of cryptic prophages in Corynebacterium glutamicum
  Pfeifer, Nucleic acids research 2016
  • “...the corresponding adaptor protein ( alpAC , cg1890 and cg1891 ( 34 )), a resolvase (cg1929), a prophage primase (cg1959), a putative phage lysin (cg1974) and a phage integrase (cg2071), which are spread across the cryptic prophage element. In addition to regions within CGP3, CgpS target...”
• Population Heterogeneity in Corynebacterium glutamicum ATCC 13032 caused by prophage CGP3
  Frunzke, Journal of bacteriology 2008
  • “...of California, Berkeley cg1893 cg1903 cg1904 cg1907 cg1929 cg1930 cg1932 cg1935 cg1950 cg1951 cg1956 cg1959 cg1961 cg1963 cg1965 cg1974 Gene integrated...”

PSPPH_4221 hypothetical protein from Pseudomonas syringae pv. phaseolicola 1448A
35% identity, 45% coverage

• Transcriptional profile of P. syringae pv. phaseolicola NPS3121 at low temperature: physiology of phytopathogenic bacteria
  Arvizu-Gómez, BMC microbiology 2013
  • “...0.52 PSPPH_3558 aconitate hydratase 2 0.61 PSPPH_3782 porin D 0.42 PSPPH_3985 3-oxoacyl-[acyl-carrier protein] reductase 0.54 PSPPH_4221 unnamed protein product 0.44 PSPPH_4654 smtA protein 0.47 PSPPH_4703 coenzyme PQQ biosynthesis protein PqqF 0.32 PSPPH_4805 oxidoreductase FAD-binding domain/oxidoreductase NAD-binding domain/2Fe-2S iron-sulfur cluster binding domain protein 0.55 PSPPH_4833 Rhs family...”

DET0063 resolvase domain protein from Dehalococcoides ethenogenes 195
30% identity, 17% coverage

• Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit
  Mansfeldt, Applied and environmental microbiology 2014
  • “...-1109, -1112, and -1464) and virus-related gene transcripts (DET0063, -0068, -0072, -0323, -1085, -1086, -1091, -1092, -1475, and -1476). A detailed list of...”
• Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
  West, Applied and environmental microbiology 2008
  • “...IE I II III IV V VI VII VIII IX Locus tags DET0063 DET0155 DET0251 DET0273 DET0875 DET0884 DET1066 DET1472 DET1552 to to to to to to to to to -0091 -0169 -0272...”

Plano_2675 recombinase family protein from Planococcus sp. PAMC 21323
35% identity, 40% coverage

• Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants
  Jung, Standards in genomic sciences 2018
  • “...region contained five transposase-encoding genes (Plano_0544, 0548, 0556, 0557, and 0566), and four transposase-encoding genes (Plano_2675, 2678, 2683, and 2688) were present in the GI-II region (Fig. 3 ). Three GI regions account for 1.6% of total chromosomal DNA and include 52 protein coding sequences (Additional...”

DET1552 resolvase domain protein from Dehalococcoides ethenogenes 195
30% identity, 16% coverage

• Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
  West, Applied and environmental microbiology 2008
  • “...Locus tags DET0063 DET0155 DET0251 DET0273 DET0875 DET0884 DET1066 DET1472 DET1552 to to to to to to to to to -0091 -0169 -0272 -0295 -0883 -0905 -1118 -1478...”

Q9T193 Putative integrase from Listeria phage A118
NP_463492 integrase from Listeria phage A118
33% identity, 20% coverage

• Serine integrase chimeras with activity in E. coli and HeLa cells.
  Farruggio, Biology open 2014
  • “...five character word size. Because the smallest characterized serine integrases (A118 and U153, accession numbers Q9T193 and Q8LTD8, respectively) are both 452 residues in length, we estimate that there are at least 4,000 unique putative large serine recombinases in the InterPro database as of February 14,...”
• Control of Recombination Directionality by the Listeria Phage A118 Protein Gp44 and the Coiled-Coil Motif of Its Serine Integrase.
  Mandali, Journal of bacteriology 2017
  • GeneRIF: Gp44 activates the A118 integrase for excision and inhibits integration.

P22996 Resolvase from Escherichia coli
42% identity, 29% coverage

• Relationship between the Tsh autotransporter and pathogenicity of avian Escherichia coli and localization and analysis of the Tsh genetic region
  Dozois, Infection and immunity 2000 (secret)

VCA0795 resolvase, putative from Vibrio cholerae O1 biovar eltor str. N16961
38% identity, 29% coverage

• Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains
  Miller, Applied and environmental microbiology 2007
  • “...encode transposases (VCA0198 to VCA0200 and VCA0790 to VCA0795). The genes that are completely absent from the California isolates are distributed around the...”

int / CAD10283.1 U153 integrase from Listeria phage U153 (see paper)
Q8LTD8 U153 integrase from Listeria phage U153
33% identity, 20% coverage

• Serine integrase chimeras with activity in E. coli and HeLa cells.
  Farruggio, Biology open 2014
  • “...word size. Because the smallest characterized serine integrases (A118 and U153, accession numbers Q9T193 and Q8LTD8, respectively) are both 452 residues in length, we estimate that there are at least 4,000 unique putative large serine recombinases in the InterPro database as of February 14, 2014. Despite...”

LMOf6854_2391 site-specific recombinase, resolvase family, putative from Listeria monocytogenes str. 1/2a F6854
lmo2332 putative integrase [Bacteriophage A118] from Listeria monocytogenes EGD-e
LMRG_01511 hypothetical protein from Listeria monocytogenes 10403S
33% identity, 20% coverage

• Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
  Nelson, Nucleic acids research 2004
  • “...LMOh7858_2410 LMOh7858_2475 LMOf6854_0126 LMOf6854_0142 LMOf6854_2344 LMOf6854_2391 LMOf6854_2652 LMOf6854_2703 lmo0113lmo0129 EGD-e Prophage 2 402 413 2 360...”
• Listeria phage and phage tail induction triggered by components of bacterial growth media (phosphate, LiCl, nalidixic acid, and acriflavine)
  Lemaître, Applied and environmental microbiology 2015
  • “...EGD-e revealed one putative prophage (EGD-e.2; lmo2271 to lmo2332) and one putative phage tail (EGD-e.1; lmo0113 to lmo0129) (23). The laboratory strain L....”
• Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs
  Behrens, PloS one 2014
  • “...a p-value of 0.064. L. monocytogenes harbors a prophage locus with genes from lmo2271 until lmo2332 [28] , which at the very end contains weak, but consistent expression of an antisense RNA. It covers parts of the genes lmo2330 and lmo2331 and stretches from near the...”
  • “...can be found in the L. monocytogenes EGD-e genome inserted between the genes lmo2271 and lmo2332 [22] . At the very end of this prophage region, covering the 3 end of lmo2331 and the 5 end of lmo2330 we identified another down-regulated asRNA (see Fig. 5...”
• Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic variations underlying differences in pathogenicity
  Bécavin, mBio 2014
  • “...). A118 is integrated in the second half of the EGD-e genome (between lmo2271 and lmo2332 ) and the 10403S genome (between LMRG_01560 and LMRG_01510 ). Conservation of sRNAs. In the past decade, noncoding RNAs in Listeria have been studied in detail ( 33 42 )....”
• A dual-function phage regulator controls the response of cohabiting phage elements via regulation of the bacterial SOS response
  Azulay, Cell reports 2022
  • “...overexpressing LMRG_02920 (pPL2- 2920 ), and a mutant deleted of the 10403S integrase gene ( LMRG_01511, integrase ) as a control. Virions obtained from MC-treated bacterial cultures (6h after MC treatment) were tested on the indicator Lm strain Mack861 for plaque formation (numerated PFUs). The error...”
• Active Lysogeny in Listeria Monocytogenes Is a Bacteria-Phage Adaptive Response in the Mammalian Environment
  Pasechnek, Cell reports 2020
  • “...As expected, the phage CI-like repressor and its downstream genes, including the integrase gene ( LMRG_01511 or int ), were expressed under lysogeny ( Figure2 B). Under lytic conditions (i.e., UV irradiation), the phage early and late genes, including the cro -like gene, were activated, whereas...”
  • “...controlling its expression ( Rabinovich etal., 2012 ). We previously demonstrated that the phage integrase (LMRG_01511 or Int) mediates prophage excision, yet many aspects of this process remain unclear, particularly whether the phage-DNA replicates after excision and which factors, if any, facilitate its re-integration into comK...”
• Coordination of cohabiting phage elements supports bacteria-phage cooperation
  Argov, Nature communications 2019
  • “...assay of WT Lm and a mutant deleted for the 10403S integrase gene, int ( LMRG_01511 ) with MC treatment (+MC). Virions obtained from MC treated bacterial cultures (4h post MC treatment) or from bacteria grown to exponential phase (3h, OD 600 0.5) without MC treatment...”
• Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict
  Croucher, PLoS biology 2016
  • “...identical with that of the prophage inserted into the comK competence gene in Listeria monocytogenes (LMRG_01511). A different example was observed in Streptococcus equi [ 108 ], in which a prophage inserted into the comFA gene. Orthologues of this distinct integrase were identified in other species...”
  • “...comFA . The prophages identified in Bacillus thuringiensis and Bacillus cereus have integrases similar to LMRG_01511 (and are 80.9% identical to one another), and both insert at orthologous, but nonidentical, sites within the comFA codon alignment. However, the prophage inserted into comFA in Streptococcus suis has...”

Q06237 Transposon Tn1546 resolvase from Enterococcus faecium
33% identity, 48% coverage

• Tn1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages
  Sletvold, The Journal of antimicrobial chemotherapy 2010
  • “...1546 988 pIP816 Tn 1546 transposase (Q06238) 100 2 res Tn 1546 191 pIP816 resolvase (Q06237) 100 3 vanR 231 pIP816 VanR protein (Q06239) 100 4 vanS 384 pIP816 VanS protein (Q06240) 100 5 vanH 322 pIP816 VanH protein (Q05709) 100 6 vanA 343 pIP816 VanA...”
  • “...1546 988 pIP816 Tn 1546 transposase (Q06238) 100 6 res Tn 1546 191 pIP816 resolvase (Q06237) 100 7 vanR 231 pIP816 VanR protein (Q06239) 100 8 vans 384 pIP816 VanS protein (Q06240) 100 9 vanH 322 pIP816 VanH protein (Q05709) 100 10 vanA 343 pIP816 VanA...”
• Comparative DNA analysis of two vanA plasmids from Enterococcus faecium strains isolated from poultry and a poultry farmer in Norway
  Sletvold, Antimicrobial agents and chemotherapy 2007
  • “...vanS (Q06240) pIP816 vanR (Q06239) pIP816 resolvase (Q06237) pIP816 Tn1546 transposase (Q06238) C-terminal part of pS194 streptomycin resistance protein, S....”
• Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis
  Berry, Applied and environmental microbiology 2002
  • “...Similar to E. faecium transposon Tn1546 resolvase SW:TNR6_ENTFC (Q06237) (76.72 in 189 aa) Weakly similar in N terminus to B. halodurans BH0264 protein...”
• Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes
  Okinaka, Journal of bacteriology 1999
  • “...in Bacillus subtilis Resolvase (191 aa), Tn1546-like; Enterococcus faecium (Q06237); 125/185 aa positive (67%) a Each ORF is defined by a start and stop site...”

YdfL / b1545 Qin prophage; putative recombinase PinQ from Escherichia coli K-12 substr. MG1655 (see paper)
P77170 Serine recombinase PinQ from Escherichia coli (strain K12)
b1545 Qin prophage; predicted site-specific recombinase from Escherichia coli str. K-12 substr. MG1655
35% identity, 43% coverage

• Past, Present, and Future of Genome Modification in Escherichia coli
  Mori, Microorganisms 2022
  • “...Site-specific DNA recombinase of e14 prophage. recombinase e14 prophage ECK1538 pinQ ydfL 1,628,428 1,629,018 G6819 P77170 Predicted recombinase PinQ recombinase Qin prophage ECK1369 pinR ynaD 1,427,890 1,428,480 C G6697 P0ADI0 Predicted site-specific recombinase recombinase Rac prophage ECK3855 polA resA 4,040,875 4,043,661 EG10746 P00582 DNA polymerase I...”
• Construction of an Escherichia coli Strain Lacking Fimbriae by Deleting 64 Genes and Its Application for Efficient Production of Poly(3-Hydroxybutyrate) and l-Threonine
  Qiao, Applied and environmental microbiology 2021
  • “...NAD binding Downregulated b4009 rrlE 15.6541 23S ribosomal RNA b1544 ydfK 9.85026 Cold shock protein b1545 pinQ 9.77538 DNA integration b3971 rrfB 9.73643 5S ribosomal RNA b3275 rrlD 9.64158 23S ribosomal RNA b4010 rrfE 9.37997 5S ribosomal RNA b1375 ynaE 9.37997 Cold shock protein b3274 rrfD...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Transcriptional profiling of colicin-induced cell death of Escherichia coli MG1655 identifies potential mechanisms by which bacteriocins promote bacterial diversity
  Walker, Journal of bacteriology 2004
  • “...invertases, and recombinases (e.g., ybcK, b1345, b1374, and b1545). It is notable that other laterally acquired elements such as the insertion sequence IS1...”
• Global impact of sdiA amplification revealed by comprehensive gene expression profiling of Escherichia coli
  Wei, Journal of bacteriology 2001
  • “...3.2 b1545 ........................................................................................... 4.4 b1601...”

YnaD / b1374 Rac prophage; putative site-specific recombinase from Escherichia coli K-12 substr. MG1655 (see 2 papers)
pinR / MB|P0ADI0 putative DNA-invertase from lambdoid prophage Rac from Escherichia coli K12 (see paper)
P0ADI0 Serine recombinase PinR from Escherichia coli (strain K12)
b1374 Rac prophage; predicted site-specific recombinase from Escherichia coli str. K-12 substr. MG1655
35% identity, 43% coverage

• Past, Present, and Future of Genome Modification in Escherichia coli
  Mori, Microorganisms 2022
  • “...G6819 P77170 Predicted recombinase PinQ recombinase Qin prophage ECK1369 pinR ynaD 1,427,890 1,428,480 C G6697 P0ADI0 Predicted site-specific recombinase recombinase Rac prophage ECK3855 polA resA 4,040,875 4,043,661 EG10746 P00582 DNA polymerase I polymerase ECK0061 polB dinA 63,429 65,780 C EG10747 P21189 DNA polymerase II polymerase ECK1348...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
  Faith, PLoS biology 2007
  • “...YnaE regulon ( Table S2 ). Also present are rhsE, a stationary-phase survival-related protein, and b1374, a putative transposon resolvase. In the compendium, ynaE was highly expressed when Lon protease or YoeB toxin was genetically up-regulated, and when either norfloxacin antibiotic or mussel defensin protein was...”
• Genome-wide localization of mobile elements: experimental, statistical and biological considerations
  Martinez-Vaz, BMC genomics 2005
  • “...4. b1328, b1329, b1330, yi52_4, b1332, fnr 5. b1361, b1362, trkG, b1368, yi52_5, b1371, b1372, b1374 6. motB, motA, flhC, flhD, yecG, otsA, otsB 7. nac, cobT, cobs, cobU, yi52_6, b1995, yi22_3 8. b2028, gnd, yi52_7, yefJ, yefI, yefH, yefG 9. yejM, yejO, b2191, yi52_8, narP,...”
• Transcriptional profiling of colicin-induced cell death of Escherichia coli MG1655 identifies potential mechanisms by which bacteriocins promote bacterial diversity
  Walker, Journal of bacteriology 2004
  • “...DNA integrases, invertases, and recombinases (e.g., ybcK, b1345, b1374, and b1545). It is notable that other laterally acquired elements such as the insertion...”

AVM72_16420 recombinase family protein from Piscirickettsia salmonis
42% identity, 30% coverage

• Isolation, Functional Characterization and Transmissibility of p3PS10, a Multidrug Resistance Plasmid of the Fish Pathogen Piscirickettsia salmonis
  Saavedra, Frontiers in microbiology 2018
  • “...AVM72_16410 HigA family addiction module antidote protein 24 AVM72_16415 traX Conjugal transfer protein TraX 25 AVM72_16420 Resolvase 26 AVM72_16425 traN Conjugal transfer protein TraN 27 AVM72_16430 Hypothetical protein 28 AVM72_16435 Hypothetical protein 29 AVM72_16440 traL Conjugal transfer protein TraL 30 AVM72_16445 Hypothetical protein 31 AVM72_16450 topA...”

alr1459 fdxN element site-specific recombinase from Nostoc sp. PCC 7120
31% identity, 18% coverage

• Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria
  Pérez, 2024

SC060 resolvase from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
40% identity, 26% coverage

• An evolutionarily conserved family of virion tail needles related to bacteriophage P22 gp26: correlation between structural stability and length of the alpha-helical trimeric coiled coil
  Bhardwaj, Journal of molecular biology 2009
  • “...212 1b 8 1b S. enterica ParaC3 SPC_1303 212 1b 8 1b S. enterica Scho1 SC060 212 1b 8 1b S. enterica ST64T 1 26 212 1b 8 1b S. enterica L 1 26 212 1b 8 1b S. enterica Para1 4 212 1b 8 1b...”

E0Z06_RS12520 recombinase family protein from Rheinheimera sp. D18
40% identity, 26% coverage

• A Novel Mobile Element ICERspD18B in Rheinheimera sp. D18 Contributes to Antibiotic and Arsenic Resistance
  Fu, Frontiers in microbiology 2020
  • “...four genes associated with DNA replication or partitioning ( repC , repA , E0Z06_RS12575, and E0Z06_RS12520); and genes encoding a site-specific integrase ( int ) and its transcriptional regulator (E0Z06_RS12590). Sequence examination further indicated that the GI was bordered by a 20-bp direct repeat (DR; 5'-ACAATNGAGTGGGAATNNTT-3')...”

XAC2433 resolvase from Xanthomonas axonopodis pv. citri str. 306
41% identity, 21% coverage

• Asymmetric chromosome segregation in Xanthomonas citri ssp. citri
  Ucci, MicrobiologyOpen 2014
  • “...least five parA -like open reading frames (ORFs) with the following designations: XAC0192, XAC1907, XAC2205, XAC2433, and XAC3905. The last one, XAC3905, was found in a small operon ( parAB ) with XAC3906, which was identified as a chromosomal parB homologue (da Silva etal. 2002 )....”
  • “...2012 ). However, Xac carries at least four parA -like ORFs (XAC0192, XAC1907, XAC2205, and XAC2433) that could have a mipZ function, which we shall investigate experimentally soon. Another possibility would be that Xac utilizes other protein factors for septum site selection. Noteworthy, the genome of...”

Z5885 putative resolvase from Escherichia coli O157:H7 EDL933
ECs5249 putative resolvase from Escherichia coli O157:H7 str. Sakai
34% identity, 45% coverage

• An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7
  Xu, PloS one 2013
  • “...(ORFs) including two putative integrases (Z5878 and Z5890), one putative tansposase (Z5880), one putative resolvase (Z5885), several putative helicases including a DEAH box RNA helicase (Z5898), and 17 genes of unknown function. The putative DEAH box RNA helicase, Z5898, is of particular interest. The DEAH box...”
  • “...(ORFs) including two putative integrases (Z5878 and Z5890), one putative tansposase (Z5880), one putative resolvase (Z5885), 4 putative helicases (Z5898, Z5899, Z5901 and Z5902), and 17 genes of unknown function ( Figure 1 ). The OI-172 is adjacent to a leu-tRNA locus with a G+C content...”
• Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting
  Laing, Applied and environmental microbiology 2008
  • “...NA Z2186 Z2311-Z2312 Z2322 Z2969 Z4092 Z5885 ECs2126 ECs2016-ECs2017 ECs2007 ECs2620 ECs3637 ECs5249 NA OI#66/S-loop#98 OI#67/S-loop#95 OI#76/S-loop#119...”
• Genome evolution in major Escherichia coli O157:H7 lineages
  Zhang, BMC genomics 2007
  • “...hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5248 (Z5884) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5249 (Z5885) putative resolvase 80% 100% 0% S-loop#286/OI#172 ECs5250 (Z5886) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5251 (Z5887) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5252 (Z5888) putative transcription regulator 80% 100% 0%...”
• Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting
  Laing, Applied and environmental microbiology 2008
  • “...ECs2126 ECs2016-ECs2017 ECs2007 ECs2620 ECs3637 ECs5249 NA OI#66/S-loop#98 OI#67/S-loop#95 OI#76/S-loop#119 OI#112/S-loop#194 OI#172/S-loop#286 a b Putative...”
• Genome evolution in major Escherichia coli O157:H7 lineages
  Zhang, BMC genomics 2007
  • “...ECs5247 hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5248 (Z5884) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5249 (Z5885) putative resolvase 80% 100% 0% S-loop#286/OI#172 ECs5250 (Z5886) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5251 (Z5887) hypothetical protein 80% 100% 0% S-loop#286/OI#172 ECs5252 (Z5888) putative transcription regulator 80% 100%...”

DET0155 resolvase domain protein from Dehalococcoides ethenogenes 195
30% identity, 18% coverage

• Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
  West, Applied and environmental microbiology 2008
  • “...II III IV V VI VII VIII IX Locus tags DET0063 DET0155 DET0251 DET0273 DET0875 DET0884 DET1066 DET1472 DET1552 to to to to to to to to to -0091 -0169 -0272 -0295...”

CDR20291_3416 recombinase family protein from Clostridioides difficile R20291
37% identity, 41% coverage

• Genome-wide detection of conservative site-specific recombination in bacteria
  Sekulovic, PLoS genetics 2018
  • “...recombinase in its vicinity. It is therefore possible that inversion of Cdi7 is catalyzed by CDR20291_3416, which is located next to the inversion site. Additional cellular factors or cis -acting elements might also participate in the DNA inversion process as was recently demonstrated for the fim...”

ELQ88_00005 recombinase family protein from Pseudomonas sp. MPC6
35% identity, 44% coverage

• In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential
  Orellana-Saez, Frontiers in microbiology 2019
  • “...repB homolog likely involved in plasmid replication (ELQ88_00015), a gene encoding a putative serine recombinase (ELQ88_00005), and two hypothetical proteins with no predicted function. Phylogenetic Relationships Among Pseudomonas sp. MPC6 and Other Members of This Genus We exploited the genomic information to phylogenetically classify Pseudomonas sp....”

plpl0043 hypothetical protein from Legionella pneumophila str. Lens
29% identity, 49% coverage

• Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species
  Mazzamurro, PLoS biology 2024
  • “...to preserve the mobile element (e.g. an anti-restriction protein, a toxin-antitoxin system), and an integrase (plpl0043). As rocRp is shared with ICEs in other Legionella species (where chromosomal curing is a valid reason for carrying the RNA), it may be that this is a gene cluster...”

P05823 Transposon Tn2501 resolvase from Escherichia coli
33% identity, 44% coverage

• Intracellular Transposition and Capture of Mobile Genetic Elements following Intercellular Conjugation of Multidrug Resistance Conjugative Plasmids from Clinical Enterobacteriaceae Isolates
  Tansirichaiya, Microbiology spectrum 2022
  • “...552 , Tn 917 , and Tn 2501 (accession numbers P18358 , P06693 , and P05823 ), with percent identities of 42.33%, 35.64%, and 29.10%, respectively. The region of Tn 7350 that was not present in Tn 7351 was also flanked by the direct repeat GAAC...”

CBC4_RS15105 recombinase family protein from Clostridium botulinum BKT015925
36% identity, 39% coverage

• Extensive Genome Exploration of Clostridium botulinum Group III Field Strains
  Fillo, Microorganisms 2021
  • “...p5BKT015925 (the plasmid of class PG7 belonging to the reference genome BKT015925-a.n. NC_015419) CBC4_RS15070, CBC4_RS15100, CBC4_RS15105, CBC4_RS15120, and CBC4_RS15125 ( Figure S2 ). The presence or absence of these newly discovered plasmid was specific for the different C. novyi sensu lato clusters ( Table S3sheet 1...”

EF0534 site-specific recombinase, resolvase family from Enterococcus faecalis V583
36% identity, 40% coverage

• Occurrence of putative pathogenicity islands in enterococci from distinct species and of differing origins
  Semedo-Lemsaddek, Applied and environmental microbiology 2009
  • “...cylLs cylM cylB cylA cylI esp araC (ef0530) ef0534 ef0539 ef0543 ef0551 xylA (ef0556) ef0571 ef0590 gls24-like (ef0604) ef0609 ef0617 ef0628 * Corresponding...”
  • “...in four PAI regions: one included cylM, araC, and ef0534 and was also previously described for E. faecalis V583 (15); the second included ef0530 and ef0534; the...”
• Molecular characterization of a widespread, pathogenic, and antibiotic resistance-receptive Enterococcus faecalis lineage and dissemination of its putative pathogenicity island
  Nallapareddy, Journal of bacteriology 2005
  • “...Reverse espa Forward Reverse 500 araC (ef0530) Forward ef0534 Forward Reverse 1,038 Reverse 1,199 ef0539 Forward ef0543 Forward Reverse 1,045 550 a Gene coding...”
  • “...deletions localized to three regions, one including ef0530 and ef0534, a second in the middle (ef0571), and the third including ef0604 and ef0609 (Fig. 4C)....”

WP_005855789 master DNA invertase Mpi family serine-type recombinase from Parabacteroides sp.
32% identity, 43% coverage

• Phase-variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem.
  Fletcher, Proceedings of the National Academy of Sciences of the United States of America 2007
  • GeneRIF: Also known as gfi, this gene encodes a glycoprotein family invertase gene, controlling the promoter orientation of multiple S-layer protein genes

WP_015060246 recombinase family protein from Acinetobacter sp. C_3_1
35% identity, 39% coverage

• Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania
  Kumburu, The Journal of antimicrobial chemotherapy 2019
  • “...(E) -msr (E) gene pair was found, together with a predicted resolvase/recombinase product (similar to WP_015060246), in 4219 and 4300bp regions, respectively, flanked by p dif sites. The novel plasmid carried by isolate 28 additionally encoded a putative cmlA/floR chloramphenicol efflux system, located directly upstream of...”

BMEI1661 RECOMBINASE from Brucella melitensis 16M
29% identity, 36% coverage

• Rapid and Specific Detection of B. melitensis Targeting BMEI1661 Gene Using Loop-mediated Isothermal Amplification (LAMP) Combined With Lateral Flow immunoassay (LFIA)
  Ashmi, Current microbiology 2023 (PubMed)
  • “...of B. melitensis Targeting BMEI1661 Gene Using Loopmediated Isothermal Amplification (LAMP) Combined With Lateral Flow immunoassay (LFIA) Marcia Ashmi1 * Bablu...”
  • “...and Specific Detection of B. melitensis Targeting BMEI1661 Gene Using Loopmediated... Designing and Custom Synthesis of Primer LAMP assay primers, targeting...”
• Development of a labelled-LFIA coupled with LAMP for the rapid and specific detection of B. melitensis targeting BMEI1661 gene
  Ashmi, 2022
• Comparative genomic analysis of Brucella melitensis vaccine strain M5 provides insights into virulence attenuation
  Jiang, PloS one 2013
  • “...0.89 ATPases with chaperone activity, ATP-binding subunit RD4 342 BMEI0407 39.24 Unknown function RD5 883 BMEI1661 74.97 Site-specific recombinases, DNA invertase Pin homologs RD5 883 BMEI1662 73.89 Hypothetical protein BMEI1662 II >2,<1 RD6 306 BMEII0253 29.91 Murein endopeptidase RD7 330 BMEII0289 23.76 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit...”
  • “...This region is a candidate for multi-locus variable-number tandem-repeat analysis detection. RD5 contained 2 ORFs, BMEI1661 and BMEI1662. BMEI1661 is part of an operon, whereas BMEI1661 belongs to the resolvase family ( Fig S1 ). Notably, BMEI0902 in chromosome I of 16 M also belongs to...”
• Molecular targets for rapid identification of Brucella spp
  Ratushna, BMC microbiology 2006
  • “...is replicating in an intracellular environment such as macrophages. Site-specific recombinases An apparent recombinase homologue (BMEI1661) was identified as the sole unique gene for B. melitensis , and our RT-PCR results indicated that it is transcribed. There are two resolvase family genes (BME1661/BMEI0902) in the B....”
  • “...These two genes share homology over a 180 bp consensus sequence. However, one putative recombinase (BMEI1661) is much larger than the other (747 bp vs. 231 bp). They may be considered paralogous, but BME1661 contains more than 500 bp not present in any other species. In...”
• Molecular characterization of Brucella abortus chromosome II recombination
  Tsoktouridis, Journal of bacteriology 2003
  • “...BMEI0943 BMEI0971 BMEI1055 BMEI1125 BMEI1331 BMEI1380 BMEI1661 BMEI1661 BMEI1919 BMEI1921 BMEI1921 BMEII0292 BMEII0717 BMEII0722 BMEII0827 BMEII0828 BMEII0829...”

WP_050203932 recombinase family protein from Streptococcus pneumoniae
34% identity, 19% coverage

• Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement
  Martín-Galiano, Frontiers in cellular and infection microbiology 2021
  • “...W_050203801, and WP_050221901), PPH080 (WP_000266839, WP_000266847, and WP_000266854)]; and 2) serine Ints [PPH100 (WP_024478469, WP_044812715, WP_050203932, WP_050226267, WP_050230313, and WP_050974546)]. These data strongly suggest that PPH integration into lytA Spn does not require a specific interaction between attB, attP , and the Int, and that some...”

WP_024478469 recombinase family protein from Streptococcus pneumoniae
34% identity, 19% coverage

• Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement
  Martín-Galiano, Frontiers in cellular and infection microbiology 2021
  • “...is boldface. The accession numbers for the other serine integrases studied are: PPH085, WP_050199652; PPH100, WP_024478469; PPH120, WP_130892475; and PPH125, WP_023396450. Table3 Sequence similarities among tyrosine and serine integrases of PPHs a . Integrases 2 3 4 5 6 7 8 9 10 11 12 13...”
  • “...WP_054368747 56 115 (16) WP_001866671 Serine integrases 085 (1) WP_050199652 170 146 180 100 (2) WP_024478469 179 171 120 (3) WP_130892475 148 125 (4) WP_023396450 a Figures correspond to Log 10 E values calculated by pairwise alignments. NS, not significant. PPH Endolysins Endolysins encoded by virulent...”

SP670_2190 recombinase family protein from Streptococcus pneumoniae 670-6B
34% identity, 19% coverage

• Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict
  Croucher, PLoS biology 2016
  • “...with the protein that drives integration into the orthologous gene in S . pneumoniae 670-6B (SP670_2190). ( B ) Comparison between Streptococcus agalactiae isolates COH1 and FSL S3-277, the latter of which has a prophage inserted into the cas3 gene of the S . agalactiae CRISPR2...”
  • “...integrases similar to that found in the prophage disrupting comYC in S . pneumoniae 670-6B (SP670_2190). ( A ) Comparison of Streptococcus mutans isolates UA159 and NLML9, the latter of which has a prophage inserted into the comYC gene encoding the major structural component of the...”

BF2765 serinr type site-specific recombinase Mpi from Bacteroides fragilis YCH46
30% identity, 52% coverage

• Identification of the site-specific DNA invertase responsible for the phase variation of SusC/SusD family outer membrane proteins in Bacteroides fragilis
  Nakayama-Imaohji, Journal of bacteriology 2009
  • “...AGTTC{N5}GAACT GTTAC{N7}GTAAC TACTTANTAGGTAANAGAA TCTGCAAAGNCTTTGCAGA ACTAAGTTCTATCGG BF2765 (mpi) BF0667 BF3038, BF4033, BF4283 BF2766 BF0667 BF0667 Capsular...”
  • “...as well as four Ssr-encoding genes (BF0513, BF2906, BF2765, and BF3012). Of the 37 site-specific recombinase-encoding genes, 19 Tsr- and 2 Ssr-encoding genes...”
• Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation
  Kuwahara, Proceedings of the National Academy of Sciences of the United States of America 2004
  • “...recognized by Mpi (33) (Table 5). The mpi gene (BF2765) is not colocalized with any PS loci. By reanalyzing the random shotgun clones used for genome...”
  • “...for a globally acting site-specific recombinase, Mpi (BF2765), and a tyrosine-type site-specific recombinase (BF2766) are indicated by red and pink arrows,...”

Francci3_3989 Recombinase from Frankia sp. CcI3
29% identity, 14% coverage

• Transcriptomes of Frankia sp. strain CcI3 in growth transitions
  Bickhart, BMC microbiology 2011
  • “...hypothetical protein Francci3_0038 899 sigma 38 Francci3_3505 1673 protein of unknown function Francci3_3347 892 Recombinase Francci3_3989 898 hypothetical protein Francci3_0227 1665 transposase, IS4 Francci3_0391 878 aldo/keto reductase Francci3_3416 890 hypothetical protein Francci3_1615 1634 major facilitator MFS_1 Francci3_2752 865 transposase, IS4 Francci3_1873 875 hypothetical protein Francci3_2943 1629...”

NWMN_0992 integrase from Staphylococcus aureus subsp. aureus str. Newman
YP_239679 ORF008 from Staphylococcus phage 53
34% identity, 15% coverage

• Staphylococcus aureus temperate bacteriophage: carriage and horizontal gene transfer is lineage associated
  McCarthy, Frontiers in cellular and infection microbiology 2012
  • “...scn, sea, seg, sek, sep 4 SAS0891 SAR0991 5 NWMN_1814 SAR1967 6 SACOL0318 SAR0317 7 NWMN_0992 SAR1102 sak 8 SAB1760 SAR1992 Staphylococcus aureus genomes Sequence data is currently available for the genomes of 74 Staphylococcus aureus isolates on the GenBank database 1 . In addition, genome...”
• Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution
  Fernandez, Nature communications 2024
  • “...Sa4int (SauS-IPLA35; NC_011612, YP_002332364), Sa5int (29; NC_007061, YP_240566), Sa6int (77; NC_005356, NP_958623), Sa7int (53; NC_007049, YP_239679), Sa8int (SauS-IPLA88; NC_011614, YP_002332477), Sa9int (vB_SauS_Mh1; OM439673, UKM36468.1) and Sa12int (MR11; NC_010147, YP_001604091.1) as well as SaPI integrases from SaPIpig1 (MW589252, QXJ78686.1), SaPIbov (AF217235, AAG29618.1), SaPIbov4 (HM211303, ADN95150.1), SaPIbov5 (HM228919,...”

MAB_p10 resolvase-like protein from Mycobacterium abscessus ATCC 19977
37% identity, 47% coverage

• Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus
  Ripoll, PloS one 2009
  • “...plasmid carries a mercury resistance operon flanked by two genes encoding site-specific recombinases (MAB_p04c and MAB_p10, orange); it also encodes a relaxase/helicase that may function in conjugation or mobilization (MAB_p15c, yellow). 10.1371/journal.pone.0005660.t001 Table 1 General features of the M. abscessus genome and comparison with other Mycobacterium...”

RSIPO_01131 resolvase protein from Ralstonia solanacearum IPO1609
32% identity, 42% coverage

• A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization
  Stevens, Antonie van Leeuwenhoek 2010
  • “...KZR-5 7 300 51.8 3.00E133 95 1219358 Non-coding 845bp 5 RSIPO_04991 (transposase protein) 265bp, 3 RSIPO_01131 (resolvase protein) KZR-5 8 246 49.2 8.00E123 99 1343620 Non-coding 305bp 5 RSIPO_04138, 4806bp 3 RSIPO_04140 KZR-5 9 301 55.2 2.00E134 97 1861380 Non-coding 259bp 5 RSIPO_04920 (ankyrin-repeat protein), 1981bp...”

PMM1515 Site-specific recombinase from Prochlorococcus marinus sp. MED4
33% identity, 34% coverage

• Frequency of mispackaging of Prochlorococcus DNA by cyanophage
  Laurenceau, The ISME journal 2021
  • “...GATCGCAAAATAGGTGCAACTATTCTG TTATCCAGAATGGAGTTTTCTTCCAATTG 4 1,362,140 100 PMM1420 Possible Fumarate reductase subunit GGCAAATGGCGATTAAATATTAAG CAACTATGCATAGGCAATGC 5 1,457,449 150 PMM1515 Site-specific recombinase GAGTTAGATAATTTAGATAATGAGTGTTTGGGAGAG GCAACCCTCATTACGTAACCTCATCAC 6 1,464,652 164 PMM1524 PhotosystemIPsaA protein CTACCAGGGCCATCACATGG ATCCCCTTAGGAACTGCTGAC Various loci were initially picked to look for specific gene mispackaging. Overall, our results showed a homogeneous mispackaging...”

WP_050226267 recombinase family protein from Streptococcus pneumoniae
31% identity, 19% coverage

• Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement
  Martín-Galiano, Frontiers in cellular and infection microbiology 2021
  • “...and WP_050221901), PPH080 (WP_000266839, WP_000266847, and WP_000266854)]; and 2) serine Ints [PPH100 (WP_024478469, WP_044812715, WP_050203932, WP_050226267, WP_050230313, and WP_050974546)]. These data strongly suggest that PPH integration into lytA Spn does not require a specific interaction between attB, attP , and the Int, and that some other...”

WP_130892475 recombinase family protein from Streptococcus pneumoniae
33% identity, 19% coverage

• Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement
  Martín-Galiano, Frontiers in cellular and infection microbiology 2021
  • “...The accession numbers for the other serine integrases studied are: PPH085, WP_050199652; PPH100, WP_024478469; PPH120, WP_130892475; and PPH125, WP_023396450. Table3 Sequence similarities among tyrosine and serine integrases of PPHs a . Integrases 2 3 4 5 6 7 8 9 10 11 12 13 14 15...”
  • “...Serine integrases 085 (1) WP_050199652 170 146 180 100 (2) WP_024478469 179 171 120 (3) WP_130892475 148 125 (4) WP_023396450 a Figures correspond to Log 10 E values calculated by pairwise alignments. NS, not significant. PPH Endolysins Endolysins encoded by virulent (lytic) phages infecting S. pneumoniae...”

SAOUHSC_02392 truncated resolvase from Staphylococcus aureus subsp. aureus NCTC 8325
36% identity, 41% coverage

• The extracytoplasmic function sigma factor σS protects against both intracellular and extracytoplasmic stresses in Staphylococcus aureus
  Miller, Journal of bacteriology 2012
  • “...SAOUHSC_02790, as well as a truncated resolvase, SAOUHSC_02392. Collectively, these observations suggest that RN4220 is perhaps more prone to DNA damage...”

SEQ_1765 phage integrase from Streptococcus equi subsp. equi 4047
31% identity, 19% coverage

• Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict
  Croucher, PLoS biology 2016
  • “...~46% identical with that of the prophage inserted into the orthologous gene in Streptococcus equi (SEQ_1765). ( D ) Comparison between Bacillus cereus isolates MHI 226 and VD214, the latter of which has a prophage inserted into the 5 half of the comFA competence gene. The...”

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Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.