Family Search for PF06288 (DUF1040)

April 2024: GapMind for amino acid biosynthesis has been updated to include newly-discovered enzymes and comparative genomics predictions (see details)

PF06288 hits 5 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

KPHS_00170 YihD family protein from Klebsiella pneumoniae subsp. pneumoniae HS11286
Aligns to 1:86 / 89 (96.6%), covers 100.0% of PF06288, 156.0 bits

• Unsupervised Machine Learning Organization of the Functional Dark Proteome of Gram-Negative "Superbugs": Six Protein Clusters Amenable for Distinct Scientific Applications
  Sicilia, ACS omega 2022
  • “...solubility spec_distr PDB25 DUF essentiality 1 HMMPREF0010_02899 0 0.749 0.949 84.85 DUF493 rich medium 1 KPHS_00170 0.00129 0.693 1.000 100.00 DUF1040 1 KPHS_38450 0.00150 0.697 0.996 85.86 DUF1131 1 KPHS_48910 0.00019 0.467 0.993 94.44 lung infection 1 PA1076 0.00232 0.619 0.998 100.00 DUF5064 1 PA1233 0.00536...”
  • “...of these cluster members, four proteins were deemed antibacterial target candidates showing 12 druggable pockets: KPHS_00170 (DUF1040), PA1076 (DUF5064), PA3229 (DUF2790), and PA4535 (DUF1780). Structures for most of these proteins have been solved by structural genomics projects 76 and are invaluable for further analysis. In addition,...”

YihD / b3858 DUF1040 domain-containing protein YihD from Escherichia coli K-12 substr. MG1655 (see 3 papers)
yihD / RF|NP_418295 protein yihD from Escherichia coli K12 (see 2 papers)
b3858 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
NP_418295 DUF1040 domain-containing protein YihD from Escherichia coli str. K-12 substr. MG1655
P0ADP9 Protein YihD from Escherichia coli (strain K12)
Aligns to 1:86 / 89 (96.6%), covers 100.0% of PF06288, 154.0 bits

• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...galactitol-specific EIIA component 6.09E05 1719 1.4 b2106 rsnA Nickel/cobalt efflux system RcnA 5.47E07 323 1.5 b3858 yihD Protein YihD 1.29E06 42 2.6 b3938 metJ Met repressor 3.84E04 191 1.4 b4142 groS 10kDa chaperonin 1.40E04 197 1.9 b4207 fklB FKBP-type peptidyl-prolyl cistrans isomerase 2.03E05 539 1.5 b4314...”
• Small genes/gene-products in Escherichia coli K-12.
  Wasinger, FEMS microbiology letters 1998 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Identification of Functional Interactome of Colistin Resistance Protein MCR-1 in Escherichia coli
  Li, Frontiers in microbiology 2020
  • “...P0C054 Small heat shock protein IbpA 15,764 ibpA 16 P0AEH5 Protein ElaB 11,299 elaB 17 P0ADP9 Protein YihD 10,323 yihD 18 P0AG55 50S ribosomal protein L6 18,949 rplF 19 P0AF36 Cell division protein ZapB 9,629 zapB 20 P37903 Universal stress protein F 16,064 uspF 21 P0A6Y1...”

t3625 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
STM3995 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 1:86 / 89 (96.6%), covers 100.0% of PF06288, 153.9 bits

• Scientific Achievements in the Study of the Occurrence and Antimicrobial Susceptibility Profile of Major Foodborne Pathogenic Bacteria in Foods and Food Processing Environments in Romania: Review of the Last Decade
  Imre, BioMed research international 2020
  • “...nine profiles, including t304 (3 isolates), t524 (2), t011, t091, t398, t449 (4), t1606 (2), t3625, and t803, respectively. The first five enumerated types have been frequently reported as being implicated in human infections. Other studies have demonstrated the presence of S. aureus in drinking milk...”
  • “...other products (0/16) S. aureus (16)t449 (4), t304 (3), t1606 (2), t524 (2), t011, t091, t3625, t803, unknown (1) N. A. N. A. Ciolacu et al., [ 22 ] S. aureus MSSA/MRSA (9), MRSA (5), MSSA (1) 28. Black-market sold food (16/200, 8) S. aureus MSSA...”
• Tracking Foodborne Pathogenic Bacteria in Raw and Ready-to-Eat Food Illegally Sold at the Eastern EU Border
  Ciolacu, Foodborne pathogens and disease 2016 (PubMed)
  • “...unhygienic conditions during processing. S. aureus t011 and t3625, both included in the livestock-associated CC398, were isolated from pork lard and poultry...”
  • “...07-23-21-17-34-1223-02-12-23 E5 E8 07.02.2013 06.11.2012 t3625 t803 (ST15) 08-16-34-25 07-23-02-12-23 E23 14.09.2012 Unknown 08-21-17-36-34-3434-33-34 Raw milk...”
• Contribution of Asparagine Catabolism to Salmonella Virulence
  McLaughlin, Infection and immunity 2017
  • “...strains with a plasmid carrying STM3993, STM3994, STM3995, STM3996, STM3997, or STM3998. Only the plasmid carrying STM3997 (pSTM3997) complemented the phenotype...”
  • “...STM3998 F n.s. 120 STM3997 E n.s. 100 STM3996 WT D STM3995 UI STM3993 STM3997 FIG 1 STM3997 is required for S. Typhimurium to cause inhibition of T cells. (A)...”
• Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
  Harvey, Infection and immunity 2011
  • “...sigma N modulation factor Function unknown STM2390 STM3995 STM2697 STM4088 yfcZ yihD Putative cytoplasmic protein Putative cytoplasmic protein Phage tail-like...”

YPTB0015 hypothetical protein from Yersinia pseudotuberculosis IP 32953
YPO0013a conserved hypothetical protein from Yersinia pestis CO92
Aligns to 1:86 / 89 (96.6%), covers 100.0% of PF06288, 151.1 bits

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.016) YPTB3953 (yieG) YPO4107 Xanthine/uracil permeases family protein 0.638 (0.046) 1.583 (0.042) S: function unknown YPTB0015 (mobA) YPO0013A molybdopterin-guanine dinucleotide biosynthesis protein A 0.703 (0.032) YPTB0020 YPO0020 conserved hypothetical protein 0.493 (< 0.001) YPTB0040 YPO0043 conserved hypothetical protein 0.705 (0.029) 0.656 (0.011) YPTB0089 YPO0093 conserved hypothetical...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(yieG) YPO4107 Xanthine/uracil permeases family protein 0.638 (0.046) 1.583 (0.042) S: function unknown YPTB0015 (mobA) YPO0013A molybdopterin-guanine dinucleotide biosynthesis protein A 0.703 (0.032) YPTB0020 YPO0020 conserved hypothetical protein 0.493 (< 0.001) YPTB0040 YPO0043 conserved hypothetical protein 0.705 (0.029) 0.656 (0.011) YPTB0089 YPO0093 conserved hypothetical protein 1.682...”

HI0845 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 1:86 / 88 (97.7%), covers 100.0% of PF06288, 148.1 bits

• The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon
  Whitby, BMC genomics 2009
  • “...-1.26 HI0811 -2.20 -1.07 ns 1.06 ns 1.45 HI0833 ns -1.25 -1.64 -1.25 ns 1.64 HI0845 ns 1.20 -1.51 -1.65 ns 1.03 HI0889 1.83 5.82 1.68 4.90 -1.09 2.99 HI0890m 2.50 4.60 3.48 7.49 ns 3.20 HI1010 ns 5.52 1.91 12.00 1.86 1.32 HI1047 ns -1.4...”

Or search for genetic data about PF06288 in the Fitness Browser