Family Search for PF11392 (DUF2877)
Running HMMer for PF11392
PF11392 hits 6 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
STM0531 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 158:264 / 269 (39.8%), covers 99.1% of PF11392, 103.1 bits
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM0429, STM0431, STM0511, STM0519, STM0526, STM0530, STM0531, STM0550, STM0557, STM0558, STM0572, STM0574, STM0611, STM0652, STM0656, STM0659, STM0722,...”
YlbF / b0520 DUF2877 domain-containing protein YlbF from Escherichia coli K-12 substr. MG1655 (see paper)
ECK0513 DUF2877 domain-containing protein YlbF from Escherichia coli str. K-12 substr. MG1655
b0520 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 158:264 / 271 (39.5%), covers 99.1% of PF11392, 100.7 bits
- The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes
Smith, PLoS computational biology 2012 - “...allantoin are neighbors in E. coli K12's genome. The remaining three candidate genes (ECK0511 to ECK0513) were ranked at the family-level using CanOE-generated family-level scores; values are given in [ Table 3 ]. ECK0513/ ylbF and ECK0512/ ylbE belong to two distinct Pfam families harboring domains...”
- “...FR /rank Score RF /rank ECK0511 647/133 100,00% 0.9699/2nd 0.334/2nd ECK0512 639/130 100,00% 0.9701/3rd 0.252/3rd ECK0513 618/129 100,00% 0.9705/1st 0.344/1st None of the three candidate genes (ECK0511 to 0513) share any significant sequence similarities with known carbamoyltransferases. Thus, the candidate genes proposed by CanOE suggest that...”
- Oxamic transcarbamylase of Escherichia coli is encoded by the three genes allFGH (formerly fdrA, ylbE, and ylbF)
Kim, Applied and environmental microbiology 2024 - “...called candidate genes for orphan enzymes to find the missing enzyme. They predicted that ylbF (b0520) was the first candidate gene for OXTCase with an unknown function and that fdrA (b0518) was the second candidate as oxamate:CoA ligase, but there was no experimental evidence other than...”
- An Escherichia coli FdrA Variant Derived from Syntrophic Coculture with a Methanogen Increases Succinate Production Due to Changes in Allantoin Degradation
Kim, mSphere 2021 - “...encode an SCS or a succinate-related enzyme. Smith et al. selected fdrA (b0518) and ylbF (b0520) as candidate genes for oxamate:carbamoyltransferase (OXTCase) using a bioinformatics strategy, even though neither predicted protein had sequence similarity to known carbamoyltransferases ( Fig.4A ) ( 35 ). OXTCase is an...”
- Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
Wei, Infection and immunity 2003 - “...b1229 b2622 b0569 b0404 b2138 b3104 b0042 b0419 b0496 b0520 b0837 b1168 b1494 b1498 b1587 b1729 b2055 b2057 b2269 b2430 b2519 b2657 b2928 b3074 b3576 K-12...”
YahE / b0319 DUF2877 domain-containing protein YahE from Escherichia coli K-12 substr. MG1655 (see paper)
b0319 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 167:275 / 287 (38.0%), covers 99.1% of PF11392, 99.3 bits
- Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis
Zhao, Nucleic acids research 2010 - “...b# a Gene b Product Function Over c Del d Start e End promoter_sequence f b0319 yahE g conserved protein Unknown 2.6 5.4 215 198 ctacTGGAAGCGATTGTGCTTAatga b0045 yaaU putative transport protein (MFS family) Not classified 5.7 4.9 244 227 aaacAGGCGCTGGAGCTGCTGGtgaa b0534 sfmF putative fimbrial-like protein Not...”
- Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR
Zhong, BMC microbiology 2004 - “...insert between b0314 and b0315 and the IS1 -b insert associated with a deletion between b0319 and b0326 . Originally, TD2 and TD10 were constructed by P1 transduction of different lac operons into the lac of K12 derivative strain DD320 [ 18 ]. The IS insertion...”
- Definition of the Escherichia coli MC4100 genome by use of a DNA array
Peters, Journal of bacteriology 2003 - “...b0279, b0280, b0295, b0298, b030, b0303, b0309, b0317, b0319, b0320, b0321, b0322, b0326, b0327, b0329, b0332, b0334, b0335, b0347, b1137,a b1138, b1141, b1142,...”
UTI89_C0349 hypothetical protein YahE from Escherichia coli UTI89
Aligns to 167:275 / 287 (38.0%), covers 99.1% of PF11392, 98.9 bits
- High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
Mediati, BMC genomics 2018 - “...O 1123 6.9 197.3 UTI89_C0018 gef (hok) R 361,550364,162 UTI89_C0348 yahD R 2613 17.1 935.0 UTI89_C0349 yahE S UTI89_C0350 yahF C 640,717641,788 UTI89_C0629 ybeM R 1072 4.3 112.5 UTI89_C0630 tatE U UTI89_C0631 lipA H 690,222691,856 UTI89_C0684 glnS J 1635 79.2 8504.0 1,016,1701,016,793 UTI89_C1021 matP MD 624...”
t2330 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
Aligns to 158:264 / 269 (39.8%), covers 99.1% of PF11392, 98.5 bits
- 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 - “...meat (1) 1 t2011 2022 Pigs (5) 5 Broiler meat (2), Turkey meat (7) 9 t2330 2022 0 Broiler meat (1) 1 t2346 2022 0 Turkey meat (1) 1 2021 Calves (1) 1 0 t2370 2021 Calves (1) 1 0 t2576 2022 0 Turkey meat (1)...”
- “...following classifications were made: spa types t011, t034, t571, t588, t1255, t1451, t1580, t1793, t2011, t2330, t2346, t2546, t5452, t6228, t6575 and t10485 were classified as CC398 (EFSA, 2009a ; Kinross etal., 2017 ; Kck etal., 2013 ; Pauly etal., 2019 ). spa type t899 were...”
- 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 - “...(1), t4475 (1). In 2017, spatypes: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). In 2019, spatypes were not reported; however, 159/160 isolates were confirmed to belong to CC398 using the sau1hsdS1 CC398 PCR reaction (Stegger et al., 2011). The remaining...”
- 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 - “...(1), t4475 (1). In 2017, spatypes: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). In 2019, spatypes were not reported; however, 159/160 isolates were confirmed to belong to CC398 using the sau1hsdS1 CC398 PCR reaction (Stegger etal., 2011). The remaining isolate...”
- 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 - “...(1), t4475 (1).In 2017, spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1).In 2019, spa types were not reported; however, 159/160 isolates were confirmed to belong to CC 398 using the sau1hsdS1 CC 398 PCR reaction (Stegger etal., 2011 )....”
- The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018
European, EFSA journal. European Food Safety Authority 2020 - “...(1), t17627 (1). 13. spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). 14. spa types: t011 CC 398 (6 isolates), t034 CC 398 (24), t1250 CC 398 (2), t1793 CC 398 (1), t3171 CC 398 (1). 15. spa types:...”
- “...t4475 (1). In 2017, spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). 2: In 2011, spa types: t011 (97 isolates), t034 (8), t108 (3), t1197 (7), t1451 (3), t2346 (3), unspecified (68). In 2015, spa types not reported. In...”
- The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017
European, EFSA journal. European Food Safety Authority 2019 - “...with CC398). The other spa types detected in Switzerland in fattening pigs were t899, t1451, t2330 and t2876 (all associated with CC398). Table 53 Meticillinresistant Staphylococcus aureus in foodproducing animals (excluding clinical investigations), 2017 Country Production type/monitoring description (where specified)) Sample unit Number Units tested Positive...”
- “...(1), t17627 (1). g spa types: t034 (63 isolates), t011 (61), t899 (2), t1451 (3), t2330 (1), t2876 (1). h spa types not reported. John Wiley & Sons, Ltd Clinical investigations for MRSA in foodproducing animals Typically, clinical investigations differ from monitoring studies in foodproducing animals;...”
- Abstracts of the 19th ECCMID (European Congress of Clinical Microbiology and Infectious Diseases). Helsinki, Finland. May 16-19, 2009
, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2009 - “...+ (t108) b 6 + (t011, t108, t1456) + (t108) c 7 + (t011, t108, t2330) + (t108) + (t567) + (t567) 8 + (t108) + (t108) 9 + (t011) + (t011) + (t011) d 10 + (t011) + (t011) 11 + (t108) + (t108) 12...”
c4768 Hypothetical protein from Escherichia coli CFT073
APECO1_2633 hypothetical protein from Escherichia coli APEC O1
Aligns to 168:279 / 286 (39.2%), covers 99.1% of PF11392, 95.7 bits
Or search for genetic data about PF11392 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory