Family Search for PF11230 (YjjI-like)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

PF11230 hits 10 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

VP1380 conserved hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 39:520 / 531 (90.8%), covers 100.0% of PF11230, 742.8 bits

• Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification
  Liu, BMC biotechnology 2021
  • “...0.83752 0.06318 DOWN VPA0969 Hypothetical protein 0.80972 0.00466 UP VPA0521 Hypothetical protein 0.79721 1.20070 DOWN VP1380 Hypothetical protein 0.78381 0.05645 UP VPA0114 Hypothetical protein 0.77526 1.45350 UP VP1288 Hypothetical protein 0.7717 0.94068 UP VP1980 Hypothetical protein 0.77034 0.34407 DOWN VPA1613 Hypothetical protein 0.7494 1.35230 DOWN VP1287...”

ETEC_4736 YjjI family glycine radical enzyme from Escherichia coli ETEC H10407
Aligns to 22:504 / 516 (93.6%), covers 100.0% of PF11230, 729.6 bits

• The molecular basis for control of ETEC enterotoxin expression in response to environment and host
  Haycocks, PLoS pathogens 2015
  • “...C GA TGAATG TCACA ETEC_4633 / ETEC_4634 gntP / uxuA 5129400 CG T ACCGTCGG TCACA (ETEC_4736) (yjjI) 5129944 TGTGA TGTATA TC GA A ETEC_4736 / ETEC_4737 yjjI / deoC a Chomosome coordinate of the ChIP-seq peak in H10407. Underlined text indicates that the ChIP-seq peak maps...”

YjjH / b4380 DUF3029 domain-containing protein YjjI from Escherichia coli K-12 substr. MG1655 (see 4 papers)
yjjI / RF|NP_418797 uncharacterized protein yjjI from Escherichia coli K12 (see paper)
b4380 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 22:504 / 516 (93.6%), covers 100.0% of PF11230, 729.1 bits

• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...5.8 b1942 fliJ Flagellar biosynthesis protein FliJ 27.2 5.8 b2971 yghG Lipoprotein YghG 3.4 5.8 b4380 yjjI DUF3029 domain-containing protein YjjI 128.5 5.7 b4034 malE Maltose ABC transporter periplasmic binding protein 402.0 5.7 b2997 hybO Hydrogenase 2 small subunit 245.6 5.7 b1241 adhE aldehyde-alcohol dehydrogenase 8441.5...”
• Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
  Myers, PLoS genetics 2013
  • “...Protein 1 TSS not in peak region + + None [17] , [18] 4,615,181 yjjI b4380 Conserved Protein 1 TSS not known + + None [18] , [19] 655,298 dcuC b0621 Dicarboxylate Transporter 1 TSS not in peak region + + None [137] 4,228,181 pepE b4021...”
• The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
  Oberto, PloS one 2009
  • “...1.51 0.31 1 2.21 1.6 0.11 1 4.19 0.57 0.53 FA putative activating enzyme yjjI b4380 yjjI 1 0.03 1.39 0.27 1 1.88 1.5 0.31 1 1.58 1.45 0.94 FA hypothetical protein 1 Regulation symbols: FA: FNR-activated and FR: FNR-repressed [63] ; FAec: FNR-activated (Ecocyc: http://ecocyc.org...”
• Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
  Pomposiello, Journal of bacteriology 2001
  • “...b3088 b3112 b3516 b3582 b3879 b3888 b4048 b4333 b4337 b4380 b4394 argR aspA b0218 b0271 b0938 b1029 b1567 b1903 b2102 b2355 b2629 b2768 carA criR dicB evgA...”

STM4566 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 22:504 / 516 (93.6%), covers 100.0% of PF11230, 720.5 bits

• Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters
  Timme, Genome biology and evolution 2013
  • “...2022982 yecG STM1927 + Putative universal stress protein 444415 Coding V_V GTA_GTT 109 4820845 yhhI STM4566 Putative cytoplasmic protein 457785 Intergenic 3515395 + Upstream of STM3348, serine endoprotease 461849 Coding T_T ACC_ACT 26 2438962 nuoB STM2327 NADH dehydrogenase I chain B 559334 Coding G_G GGG_GGT 294...”

SO2407 conserved hypothetical protein from Shewanella oneidensis MR-1
Aligns to 16:507 / 519 (94.8%), covers 100.0% of PF11230, 719.7 bits

• Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
  Gao, BMC genomics 2006
  • “...ATP synthase F1, suggested inhibition of aerobic respiration. The increased gel abundance of proteins included SO2407 (conserved hypothetical protein) and SO3505 (NagA). Again, the increased gel abundance of SO3505 agreed with the microarray data, in which the transcription of SO3505 gene displayed an increase at the...”
  • “...hypothetical protein 49308 (5917) 0 422 SO1117 putative cytosol aminopeptidase 21725 (1716) 10017 (771) 426 SO2407 conserved hypothetical protein 71070 (11798) 120011 (11641) 433 SO2767 asnB-1 asparagine synthetase B, glutamine-hydrolyzing 49614 (5917) 0 482 SO4749 atpA ATP synthase F1, alpha subunit 25802 (4670) 12153 (4837) 748...”

t4609 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
Aligns to 22:504 / 516 (93.6%), covers 100.0% of PF11230, 718.3 bits

• Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review
  Katale, Antimicrobial resistance and infection control 2020
  • “...SCC mec II (8.3% (2/24), SCC mec type 1 (16.7%, 4/24) t645, t4353, t064, t355, t4609, t10277 Uganda [ 76 ] September 2011 to April 2012 MRSA human PCR, Multiplex PCR, WGS SCC mec type I (56.4%), SCC mec type IV (17.9%) Rwanda [97] MRSA human...”

HI0521 conserved hypothetical protein from Haemophilus influenzae Rd KW20
P44744 Uncharacterized protein HI_0521 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Aligns to 17:505 / 514 (95.1%), covers 100.0% of PF11230, 705.0 bits

• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...HI0510 949577 P44740 tRNA (adenine(37)-N6)-methyltransferase 82. HP HI0520 949583 P44743 Radical SAM protein 83. HP HI0521 950665 P44744 glycine radical enzyme, YjjI family 84. HP HI0526 949589 P44012 Ribonuclease T2 85. HP HI0552 949603 P44013 Glucose-6-phosphate 1-dehydrogenase 86. HP HI0554 949606 P44014 Transposase IS200-like 87. HP...”
• Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
  Kolker, Nucleic acids research 2004
  • “...PSIBLAST searches revealed that the product of the HI0521 (yjjI) gene is distantly related to pyruvate-formate lyase (Table 2). Remarkably, this gene forms a...”
  • “...an additional degree of con(R)dence in annotating the HI0521 protein as glycyl radical enzyme, related to pyruvate-formate lyase'. In addition, OWEN searches...”
• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...P44740 tRNA (adenine(37)-N6)-methyltransferase 82. HP HI0520 949583 P44743 Radical SAM protein 83. HP HI0521 950665 P44744 glycine radical enzyme, YjjI family 84. HP HI0526 949589 P44012 Ribonuclease T2 85. HP HI0552 949603 P44013 Glucose-6-phosphate 1-dehydrogenase 86. HP HI0554 949606 P44014 Transposase IS200-like 87. HP HI0561 950224...”
• Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
  Kolker, Nucleic acids research 2004
  • “...yjhT yfgA ycfD yicC yjjW yjjI P44544 Q57065 P44683 P44726 P44743 P44744 379 303 404 287 262 514 1638 3090, 1593 3055 1426 2850 1561 1180 n/a NIF3 homolog, the...”

CGSHiEE_00395 hypothetical protein from Haemophilus influenzae PittEE
Aligns to 17:505 / 514 (95.1%), covers 100.0% of PF11230, 704.8 bits

• Biofilm-specific extracellular matrix proteins of nontypeable Haemophilus influenzae
  Wu, Pathogens and disease 2014
  • “...hr, 2 on 24 hr and 96 hr biofilm filters and one, a hypothetical protein (CGSHiEE_00395), identified only on the 96 hr biofilm filter (Table). The presence of bacterial cells in the residual material attached to the filters after biofilm removal made it impossible for us...”

YintA_01001142 hypothetical protein from Yersinia intermedia ATCC 29909
Aligns to 24:506 / 518 (93.2%), covers 100.0% of PF11230, 703.4 bits

• Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909)
  Babujee, PloS one 2013
  • “...11.4 12.1 AEH-0001127 YintA_01001141 yjjW predicted pyruvate formate lyase activating enzyme 2.1 9.5 10.5 AEH-0001128 YintA_01001142 yjjI glycyl radical enzyme 4.3 10.3 12.4 AEH-0002071 YintA_01002097 yidP predicted DNA-binding transcriptional regulator 1.7 10.2 11 AEH-0002879 YintA_01002903 cbiN synthesis of vitamin B12 adenosyl cobalamide precursor 2.3 11.5 12.7...”

NTHI0647 hypothetical protein from Haemophilus influenzae 86-028NP
Aligns to 17:505 / 514 (95.1%), covers 100.0% of PF11230, 702.4 bits

• Molecular Signatures of Non-typeable Haemophilus influenzae Lung Adaptation in Pediatric Chronic Lung Disease
  Aziz, Frontiers in microbiology 2019
  • “..., mao2 , nagAB , nanAEK , NTHI0229 , NTHI0232 , NTHI0235 , NTHI0646 , NTHI0647 , NTHI1183 , NTHI1243 , nrfCD , pckA , pilA , sdaA , siaT , and tnaB ), and the remaining 87 were DE in single NP-BAL pairs ( Figure...”
  • “...Dataset S1 ). However, only ten genes exhibited concordant downregulation ( mao2 , NTHI0646 , NTHI0647 , pckA , sdaA ) or upregulation ( asnA, hitA , hsdMS3 , hsdS3 , and tnaB ) in the BAL isolates. In all other DE genes, discordance in the...”
• Reprioritization of biofilm metabolism is associated with nutrient adaptation and long-term survival of Haemophilus influenzae
  Harrison, NPJ biofilms and microbiomes 2019
  • “...protein, membrane protein 2.7 0.0001 1.9 2.7E04 NTHI1806 GlgA Glycogen synthase 2.5 0.0002 2.0 2.1E04 NTHI0647 Hypothetical protein 2.4 0.00005 NS NS NTHI0660 Aspartate ammonia-lyase 2.3 0.00004 0.0 1.8E01 NTHI1808 GlgX Glycogen operon protein 2.2 0.00004 2.1 3.7E04 NTHI1816 Cdd Cytidine deaminase 2.2 0.0004 0.0 5.2E01...”

Or search for genetic data about PF11230 in the Fitness Browser