Family Search for PF06674 (DUF1176)

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

PF06674 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.

YpfG / b2466 DUF1176 domain-containing protein YpfG from Escherichia coli K-12 substr. MG1655 (see paper)
ypfG / RF|NP_416961 uncharacterized protein ypfG from Escherichia coli K12 (see paper)
b2466 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 25:347 / 347 (93.1%), covers 100.0% of PF06674, 368.5 bits

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ECs0880 ECs0927 ECs2042 b0802 b0847 b1438 b2530 b0124 b2466 b0449 ECs0512 ECs5566 ECs2316 ECs0252 b0459 b4458 b1610 b0255 ECs2817 b2015 Amino acid transport and...”
• IS1397 is active for transposition into the chromosome of Escherichia coli K-12 and inserts specifically into palindromic units of bacterial interspersed mosaic elements
  Clément, Journal of bacteriology 1999
  • “...at the same position within the Z2 PU, between b2466 and tktB, with the two possible IS1397 orientations. Transposition into a plasmid-borne target. pTZ99 and...”

Z3722 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs3328 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 25:347 / 347 (93.1%), covers 100.0% of PF06674, 361.3 bits

• Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
  Sharma, BMC microbiology 2017
  • “...0.01 rcnB Z3275 Putative nickel/cobalt efflux protein 1.61 0.02 ypeC Z3656 Unknown 23.74 1.9E-17 ypfG Z3722 Unknown 4.58 9.0E-09 Z3965 Unknown 2.33 1.5E-03 Z4126 Unknown 4.31 3.0E-04 Z4151 Unknown 3.84 7.4E-07 Z4267 Unknown +5.52 2.3E-03 Z4268 Unknown +4.92 4.3E-06 yggG Z4280 Unknown 1.71 0.02 Z4318 Unknown...”
• Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
  Landstorfer, BMC genomics 2014
  • “...(2) 2.2 (1) 1.4 (0) 1.4 (0) 3.1 (2) 1.4 (0) 2.5 (1) 6.0 (4) Z3722 contains functional domain feces 1 (21) 0.7 (21) 1.8 (12) 1.0 (9) 0.8 (35) 7.4 (0) 1.0 (14) 1.3 (33) 1.4 (5) 2.5 (70) 5.2 (129) 1 For each gene,...”
  • “...in cattle feces with a logFC higher than 5 (see Table 2 ). Z0387 and Z3722 are unknown genes which have never been reported to be active under any condition before. As in radish sprouts, several up-regulated genes are involved in biofilm formation, e.g. ycdT ....”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...and conversion ECs3081 b2190 ECs2359 ECs3396 ECs0128 ECs3328 ECs0503 ECs0880 ECs0927 ECs2042 b0802 b0847 b1438 b2530 b0124 b2466 b0449 ECs0512 ECs5566...”

STM2476 putative periplasmic protein from Salmonella typhimurium LT2
Aligns to 25:347 / 347 (93.1%), covers 100.0% of PF06674, 353.8 bits

• Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2
  Samuels, BMC genomics 2013
  • “...STM2430 cysK 4.8 - 11.7 2544207 2544190 TGGCATCACTGTTGCAGT STM2475 9.0 - 1.0 2585621 2585638 TGGCACATCAGGCAAAAG STM2476 ypfG 3.1 + 12.7 2586874 2586857 TGGCAGGTCACCTGCAAT STM2517 sinH 4.6 - 11.1 2650462 2650479 TGGTACGGATCTTGCCAT STM2563 yfhG 4.7 - 6.8 2705786 2705803 CGGCGTAATTTTTGCATC STM2939 ygcH 10 + 10.9 3080061 3080044...”

XCC1847 regulatory protein from Xanthomonas campestris pv. campestris str. ATCC 33913
Aligns to 26:338 / 342 (91.5%), covers 99.4% of PF06674, 337.2 bits

• Xanthomonas citri subsp. citri and Xanthomonas arboricola pv. pruni: Comparative analysis of two pathogens producing similar symptoms in different host plants
  Garita-Cambronero, PloS one 2019
  • “...presented an additional gene ( rpfl ) that is related to its regulation (analogue to XCC1847). c) Type secretion systems II and III Both species of Xanthomonas present genes associated with functional T2SS and T3SS and therefore the mechanisms to secrete a battery of degrading enzymes...”

BN49_4908 DUF1176 domain-containing protein from Klebsiella pneumoniae
Aligns to 26:337 / 695 (44.9%), covers 99.4% of PF06674, 311.3 bits

• Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent
  Storey, PLoS pathogens 2020
  • “...genes, locus tag BN49_1035, BN49_2747 and BN49_2887, and a cluster of five genes, locus tag BN49_4908 to BN49_4913, encoding four putative effectors and a PAAR protein ( Fig 1B ). 10.1371/journal.ppat.1007969.g001 Fig 1 Predicted T6SS gene loci K . pneumoniae CIP52.145. (A) Analysis of the three...”

Q2YRN7 DUF1176 domain-containing protein from Brucella abortus (strain 2308)
Aligns to 20:337 / 339 (93.8%), covers 99.1% of PF06674, 271.1 bits

• Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis
  Murugaiyan, Biomolecules 2020
  • “...Q2YK32 Catalase Q2YLX9 Lipoprotein putative Q2YN45 Probable cytosol aminopeptidase Q2YRJ0 ATP/GTP-binding site motif A (P-loop) Q2YRN7 Uncharacterized protein Q8YBU9 Putative uroporphyrin-iii c-methyltransferase Q2YKY2 Uncharacterized protein Q2YL40 Uncharacterized protein Q2YLM7 Uncharacterized protein Downregulated in B. abortus and Upregulated in B. melitensis Q2YME1 Threonylcarbamoyl-AMP synthase Q2YNW9 Dihydroxy-acid dehydratase...”

VV2_1149 Unknown from Vibrio vulnificus CMCP6
Aligns to 15:323 / 333 (92.8%), covers 99.4% of PF06674, 258.7 bits

• Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains
  Guerrero, PloS one 2019
  • “...VV2872 + + VVA1633 + + VV2_1138 + + VV2874 + + VVA1634 + + VV2_1149 + + VV2990 + + VVA1635 + + VV2_1186 + + VV3118 + + Sequences were assembled for the 2 chromosomes for the CICESE strains and CMCP6 and compared with...”
• SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes
  Gulig, BMC genomics 2010
  • “...resistance efflux pump - COG1566V VV2_1075 dehydrogenase - COG1028IQR VV2_1138 hypothetical protein VV2_1138 - COG3904S VV2_1149 hypothetical protein VV2_1149 - - VV2_1186 transcriptional regulator - COG0583K VV2_1203 hypothetical protein VV2_1203 - COG3930S VV2_1204 glutathione synthetase - COG0189HJ VV2_1273 transcriptional regulator - COG0583K VV2_1274 Ca2+/H+ antiporter -...”

A1S_2787 hypothetical protein from Acinetobacter baumannii ATCC 17978
Aligns to 1:276 / 279 (98.9%), covers 81.6% of PF06674, 242.3 bits

• An ribonuclease T2 family protein modulates Acinetobacter baumannii abiotic surface colonization
  Jacobs, PloS one 2014
  • “...usp putative universal stress protein family gi-126642696 2 3 A1S_2662 putative hydrolase gi-126642817 2.2 2 A1S_2787 hypothetical protein gi-126642835 2.2 10.9 A1S_2811 chemotactic signal transduction system component gi-126642836 3.7 13.4 A1S_2812 pilJ Type IV pili methyl-accepting chemotaxis protein gi-126642837 5.4 23.2 A1S_2813 twitching motility protein gi-126642838...”
  • “...of unknown function), A1S_1258 (transport protein), A1S_1319 (limited homology to RNA binding/nucleotide hydrolase), A1S_1476 (tautomerase/hydrolase), A1S_2787 (limited homology to Bartonella cell invasion associated protein) and A1S_3236 (homology to tRNA transferase/hydrolase) did not provide additional insight regarding how A1S_3026 modulates abiotic surface colonization. Thus, we surmise that...”

SYNPCC7002_A1480 hypothetical protein from Synechococcus sp. PCC 7002
Aligns to 21:201 / 393 (46.1%), covers 46.9% of PF06674, 37.9 bits

• Integrated transcriptomic and proteomic analysis of the global response of Synechococcus to high light stress
  Xiong, Molecular & cellular proteomics : MCP 2015
  • “...cpcG (L-RC 28.5), SYNPCC7002_ A0568, SYNPCC7002_A1479 or SYNPCC7002_A1480 were constructed by replacement of DNA sequence with a kanamycin cassette. The...”
  • “...encoding hypothetical proteins (SYNPCC7002_A0568, SYNPCC7002_A1479, SYNPCC7002_A1480, SYNPCC7002_F0063; hereafter A0568, A1479, A1480, and F0063) were also...”

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