Family Search for PF06806 (DUF1233)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF06806 hits 9 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
YPO2087 putative phage excisionase from Yersinia pestis CO92
Aligns to 4:73 / 86 (81.4%), covers 100.0% of PF06806, 125.4 bits
- Delineation and analysis of chromosomal regions specifying Yersinia pestis
Derbise, Infection and immunity 2010 - “...machinery, i.e., an integrase (YPO2084) and an excisionase (YPO2087) (see Table S5 in the supplemental material). However, the int gene is interrupted by the...”
- “...(in YPO2095 to YPO2135 in branch 0.PE4 and in YPO2087 to YPO2103 in the 1.ANT1 subbranch) (Fig. 3) suggests a single acquisition event and further argues for...”
- Molecular Darwinian evolution of virulence in Yersinia pestis
Zhou, Infection and immunity 2009 - Quorum sensing affects virulence-associated proteins F1, LcrV, KatY and pH6 etc. of Yersinia pestis as revealed by protein microarray-based antibody profiling
Chen, Microbes and infection 2006 - “...to form genomic islands that have increasing bacterial fitness. Three genomic islands (YPO0387 to YPO0397, YPO2087 to YPO2135, and YPO1087 to YPO1098) were tested in our present work, as they appear to be newly acquired [19] . The genomic island YPO2087 to YPO2135 is predicted to...”
- Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen
Chain, Journal of bacteriology 2006 - “...IS100 elements, the smaller deletion in Antiqua (from YPO2087 to YPO2106) is likely due to excision between two IS285 sequences (see the supplemental material)....”
- Protein microarray for profiling antibody responses to Yersinia pestis live vaccine
Li, Infection and immunity 2005 - “...fitness (15). Three genomic islands (YPO0387 to YPO0397, YPO2087 to YPO2135, and YPO1087 to YPO1098) were tested in our present work because they appear...”
t1928 excisionase from Salmonella enterica subsp. enterica serovar Typhi Ty2
STM1006 Gifsy-2 prophage; excisionase from Salmonella typhimurium LT2
STM14_1141 excisionase family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Aligns to 4:73 / 82 (85.4%), covers 100.0% of PF06806, 122.4 bits
- 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 - “...t1793 CC398 (1), t3171 CC398 (1). In 2019, spatypes t011 CC398 (10), t034 CC398 (57), t1928 CC398 (1), t4652 CC398 (1) were identified in isolates from multiplier pig herds. Pig herds (NO) : In 2014, spatype: t011 CC398 (1). In 2015, spatype: t034 CC398 (2), t177...”
- The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2019-2020
European, EFSA journal. European Food Safety Authority 2022 - “...(2). [11] Breeding pig herds (DK 2019): spatypes: t011 CC398 (10 isolates), t034 CC398 (57), t1928 CC398 (1), t4652 CC398 (1). These comprised multiplier herds. [12] Horse premises (DK 2019): spatypes: t011 CC398 (4 isolates), t034 CC398 (6), t1451 CC398 (1), t843 CC130 (1), t3256 CC130...”
- “...in an area with intensive animal husbandry in Germany (Kck etal., 2013 ) Spa type t1928 has been described in pigs in Germany in companion animals in Austria (Alt etal., 2011 ; Loncaric etal., 2019 ). Spa types t2383 and t2582, reported in pigs in 2019,...”
- The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019
European, EFSA journal. European Food Safety Authority 2021 - “...t3119 CC 398 (2).15: spa types: t011 CC 398 (10 isolates), t034 CC 398 (57), t1928 CC 398 (1), t4652 CC 398 (1).16: spa types: t011 CC 398 (6 isolates), t034 CC 398 (24), t1250 CC 398 (2), t1793 CC 398 (1), t3171 CC 398 (1).17:...”
- Staphylococcus aureus Isolated From Retail Meat and Meat Products in China: Incidence, Antibiotic Resistance and Genetic Diversity
Wu, Frontiers in microbiology 2018 - “...(2), t002 (2), t899 (1), t1456 (1), t011 (1), t1250 (1), t1255 (1), t9472 (1), t1928 (1) ST2392 (1) t1255 (1) ST4439 * (1) t12250 (1) ST4454 * t034 (2) ST4567 * (1) t034 (1) ST4074 * (1) t034 (1) ST4068 * (1) t034 (1) CC6...”
- High-throughput comparison of gene fitness among related bacteria
Canals, BMC genomics 2012 - “...STM0997 t1937 b0927 13 13 30 40 27 34 23 36 STM14_1141 xisW Excisionase STM1006 t1928 11 9 72 62 53 30 43 24 STM14_1152 dnaC Putative replication protein STM1015 t1917 16 16 27 36 34 31 41 32 STM14_1548 yeaM Putative regulatory protein STM1279 t1159...”
- High-throughput comparison of gene fitness among related bacteria
Canals, BMC genomics 2012 - “...lactamase STM0997 t1937 b0927 13 13 30 40 27 34 23 36 STM14_1141 xisW Excisionase STM1006 t1928 11 9 72 62 53 30 43 24 STM14_1152 dnaC Putative replication protein STM1015 t1917 16 16 27 36 34 31 41 32 STM14_1548 yeaM Putative regulatory protein STM1279...”
- Comparison of Salmonella enterica serovar Typhimurium LT2 and non-LT2 salmonella genomic sequences, and genotyping of salmonellae by using PCR
Kim, Applied and environmental microbiology 2006 - “...STM4317 220 65 STM4457 215 65 9 STM0339 232 65 10 STM1006 165 65 11 STM3752 165 65 2 3 4 5 6 Primer Sequence STM3098-f2 STM3098-r2 STM4444-f STM4444-r STM0349-f...”
- Host gene expression changes and DNA amplification during temperate phage induction
Frye, Journal of bacteriology 2005 - “...xis::Kan), JF106 (LT2 STM0893 Fels-1 int::Cm), JF107 (LT2 STM1006 * Corresponding author. Mailing address: Sidney Kimmel Cancer Center, 10835 Altman Row, San...”
- High-throughput comparison of gene fitness among related bacteria
Canals, BMC genomics 2012 - “...ycbL Putative metallo-beta- lactamase STM0997 t1937 b0927 13 13 30 40 27 34 23 36 STM14_1141 xisW Excisionase STM1006 t1928 11 9 72 62 53 30 43 24 STM14_1152 dnaC Putative replication protein STM1015 t1917 16 16 27 36 34 31 41 32 STM14_1548 yeaM Putative...”
STM0894 Fels-1 prophage; putative excisionase from Salmonella typhimurium LT2
Aligns to 5:74 / 80 (87.5%), covers 100.0% of PF06806, 121.8 bits
ECs1161 putative excisionase from Escherichia coli O157:H7 str. Sakai
Aligns to 19:88 / 94 (74.5%), covers 100.0% of PF06806, 105.5 bits
- Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex
Abu-Ali, BMC genomics 2009 - “...serotype O111:H8, had more Sp5 ( stx2 -phage) genes. Integrase and excisionase genes (ECs1160 and ECs1161), and the block of genes at the beginning of the phage, ECs11601187, were missing from most strains. The rest of Sp5 genes, which encode replication proteins O and P, NinE...”
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...fiber protein 100% 100% 0% S-loop#69/OI#45 ECs1160 (Z1424) 1 putative integrase 93% 0% 0% S-loop#69/OI#45 ECs1161 (Z1425) 1 putative excisionase 93% 0% 0% S-loop#69/OI#45 ECs1162 (Z1426) 1 hypothetical protein 93% 0% 0% S-loop#69/OI#45 ECs1163 (Z1428) 1 hypothetical protein 93% 0% 0% S-loop#69/OI#45 ECs1219 (Z1475) 2 putative...”
Z1425 putative excisionase for bacteriophage BP-933W from Escherichia coli O157:H7 EDL933
Aligns to 24:93 / 99 (70.7%), covers 100.0% of PF06806, 105.3 bits
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...protein 100% 100% 0% S-loop#69/OI#45 ECs1160 (Z1424) 1 putative integrase 93% 0% 0% S-loop#69/OI#45 ECs1161 (Z1425) 1 putative excisionase 93% 0% 0% S-loop#69/OI#45 ECs1162 (Z1426) 1 hypothetical protein 93% 0% 0% S-loop#69/OI#45 ECs1163 (Z1428) 1 hypothetical protein 93% 0% 0% S-loop#69/OI#45 ECs1219 (Z1475) 2 putative small...”
ECs3012 putative excisionase from Escherichia coli O157:H7 str. Sakai
Aligns to 5:74 / 84 (83.3%), covers 100.0% of PF06806, 101.4 bits
ESA_01609 excisionase family protein from Cronobacter sakazakii ATCC BAA-894
Aligns to 5:74 / 83 (84.3%), covers 98.6% of PF06806, 101.2 bits
XisR / b1346 Rac prophage; excisionase from Escherichia coli K-12 substr. MG1655 (see paper)
ECs1930 hypothetical protein from Escherichia coli O157:H7 str. Sakai
b1346 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 3:71 / 71 (97.2%), covers 91.4% of PF06806, 74.2 bits
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...Shigella OspG 100% 100% 0% Sp10 ECs1929 (Z2415) putative integrase; b1345 100% 0% 0% Sp10 ECs1930 (Z2414) 3 hypothetical protein; ydaQ 100% 0% 8% Sp10 ECs1931 (Z2413) 3 hypothetical protein; ydaC 100% 0% 8% Sp10 ECs1932 (Z2412) restriction alleviation and modification enhancement; lar 100% 0% 0%...”
- 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) - 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements
Maciag, Nucleic acids research 2011 - “...in recET-lar-ydaCQ operon b1347 1.74 as recT ydaQ Rac prophage, possible recombinase, in recET-lar-ydaCQ operon b1346 1.66 as recT Polyamine metabolism puuB -glutamylputrescine oxidase b1301 1.61 S ( 19 ) gabD Succinate semialdehyde dehydrogenase b2661 1.65 S , Nac ( 9 , 66 ) speB Agmatinase...”
- Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression
Soupene, Journal of bacteriology 2003 - “...primer set and of every other gene from b1330 to b1346 with the ORFmer primer sets of Sigma-Genosys yielded a single product of the expected size for each gene...”
- “...obtained only for b1330 and b1331 and for b1345 and b1346 from CGSC 6300. No products were detected for b1332 through b1344. The entire fnr region was amplified...”
- Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product
Plunkett, Journal of bacteriology 1999 - “...is found in the Rac prophage (25.3% identical to YdaQ, b1346), which is known to be excisable, but not in Qin, where an IS2 insertion near intQ is accompanied...”
Z2414 unknown protein encoded within prophage CP-933R from Escherichia coli O157:H7 EDL933
Aligns to 11:79 / 79 (87.3%), covers 91.4% of PF06806, 73.7 bits
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...OspG 100% 100% 0% Sp10 ECs1929 (Z2415) putative integrase; b1345 100% 0% 0% Sp10 ECs1930 (Z2414) 3 hypothetical protein; ydaQ 100% 0% 8% Sp10 ECs1931 (Z2413) 3 hypothetical protein; ydaC 100% 0% 8% Sp10 ECs1932 (Z2412) restriction alleviation and modification enhancement; lar 100% 0% 0% Sp10...”
Or search for genetic data about PF06806 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory