Family Search for PF04074 (DUF386)
PF04074.12 hits 25 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
SO4189, SO_4189 conserved hypothetical protein (NCBI ptt file) from Shewanella oneidensis MR-1
Aligns to 1:152 / 153 (99.3%), covers 100.0% of PF04074, 159.7 bits
BT_0770 conserved hypothetical protein (NCBI ptt file) from Bacteroides thetaiotaomicron VPI-5482
Aligns to 1:147 / 148 (99.3%), covers 100.0% of PF04074, 159.6 bits
YjgK / b4252 DUF386 domain-containing toxin-antitoxin biofilm protein TabA from Escherichia coli K-12 substr. MG1655 (see 3 papers)
TABA_ECOLI / P0AF96 Toxin-antitoxin biofilm protein TabA from Escherichia coli (strain K12) (see paper)
b4252 orf, hypothetical protein (VIMSS) from Escherichia coli str. K-12 substr. MG1655
S4500 hypothetical protein (NCBI ptt file) from Shigella flexneri 2a str. 2457T
Aligns to 1:148 / 150 (98.7%), covers 99.3% of PF04074, 153.1 bits
- function: Influences biofilm formation. Represses fimbria genes in 8 hours biofilms. May act in response to the combined activity of several toxin-antitoxin (TA) systems.
disruption phenotype: Deletion increases biofilm formation after 8 hours and decreases biofilm formation after 24 hours. - Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae
Kim, Journal of bacteriology 2009 - “...h. From the whole genome, only one gene, yjgK (b4252), was induced (3.0-fold) by deleting the five TA systems; there were no repressed genes (other than those...”
- Detecting horizontally transferred and essential genes based on dinucleotide relative abundance
Baran, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...ending 4474 kb from sequence start, which overlaps (by >300 bp each) two genes, yjgK (b4252) and yjgL (b4253), which encode hypothetical proteins. Classified as a conserved protein in EcoCyc, yjgK has homologs in S . enterica ( E < 10 65 ) and proteobacteria outside...”
- Non-Resorbable Nanocomposite Membranes for Guided Bone Regeneration Based On Polysulfone-Quartz Fiber Grafted with Nano-TiO2
Nechifor, Nanomaterials (Basel, Switzerland) 2019 - “...Germany). The morphology studies were done through SEM analysis equipped with EDX facilities (FESEM Hitachi S4500- Hitachi High-Technologies Europe GmbH, Krefeld, Germany). The thermal properties of the obtained composite membranes were analyzed using a Netzsch Thermal Analyzer (NETZSCH-Gertebau GmbH, Selb, Germany). Measurements for the samples placed...”
- “...cm) were mounted on aluminum specimen support and introduced into the electron microscope systemFESEM Hitachi S4500 (Hitachi High-Technologies Europe GmbH, Krefeld, Germany). For high resolutions, the samples were covered with gold, but for combined SEMEDX analysis, this procedure was avoided. The electronic microscopy offers the possibility...”
- High-speed imaging of glutamate release with genetically encoded sensors
Dürst, Nature protocols 2019 - “...acid (Merck cat. no. G1251) L-Aspartic acid (Merck cat. no. A8949) L-Serine (Merck cat. no. S4500) Testing in cell lines HEK293T cells (Merck cat. no. 85120602) CAUTION : The cell lines used in your research should be regularly checked to ensure they are authentic and are...”
- Antimicrobial Activity of New Materials Based on Lavender and Basil Essential Oils and Hydroxyapatite
Predoi, Nanomaterials (Basel, Switzerland) 2018 - “...of the newly developed materials was investigated by scanning electron microscopy (SEM), using a HITACHI S4500 microscope (Tokyo, Japan) equipped with an energy dispersive X-ray attachment (EDAX) (Tokyo, Japan). Dynamic Light Scattering (DLS) measurements were conducted using a SZ-100 Nanoparticle Analyzer (HORIBA, Ltd., Kyoto, Japan) at...”
- Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection
Patrick, Cell systems 2018 - “...Methionine Sigma M9625 Para-aminobenzoic acid Sigma A0254 Phenylalanine Sigma P2126 Proline Sigma P0380 Serine Sigma S4500 Threonine Sigma T8625 Tryptophan Sigma T0254 Tyrosine Sigma T3754 Uracil Sigma U0750 Valine Sigma V0500 Critical Commercial Assays Biotin CAPture Kit GE Healthcare product# 28920233 DirectZol RNA miniprep kit Zymo...”
- Afa/Dr diffusely adhering Escherichia coli strain C1845 induces neutrophil extracellular traps that kill bacteria and damage human enterocyte-like cells
Marin-Esteban, Infection and immunity 2012 - “...by field emission-gun scanning electron microscopy (FEGSEM; Hitachi S4500, Tokyo, Japan) with a microscope operated at 5 kV at the MIMA2 microscopy platform...”
B2G73_RS15490 YhcH/YjgK/YiaL family protein from Citrobacter werkmanii
Aligns to 1:148 / 150 (98.7%), covers 99.3% of PF04074, 150.7 bits
STY4806 conserved hypothetical protein (NCBI ptt file) from Salmonella enterica subsp. enterica serovar Typhi str. CT18
Aligns to 1:148 / 150 (98.7%), covers 99.3% of PF04074, 149.6 bits
SEET0819_06210 YhcH/YjgK/YiaL family protein from Salmonella enterica subsp. enterica serovar Tennessee str.
Aligns to 1:148 / 150 (98.7%), covers 99.3% of PF04074, 148.3 bits
P44583 Uncharacterized protein HI_0227 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI0227 conserved hypothetical protein (NCBI ptt file) from Haemophilus influenzae Rd KW20
Aligns to 1:151 / 155 (97.4%), covers 100.0% of PF04074, 147.5 bits
- Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
Kolker, Nucleic acids research 2004 - “...on structure and genome context HI0227 HI0315 HI0442 HI0719 P44583 P44634 P44711 P44839 155 246 121 130 2731 0217 0718 0251 1jop 1kon, 1lfp 1j8b 1j7h nanRATEK...”
- A new model for non-typeable Haemophilus influenzae middle ear infection in the Junbo mutant mouse
Hood, Disease models & mechanisms 2016 - “...made by insertion of a kanamycin resistance cassette onto a position in the NTHi genome (HI0227) that had no characterized phenotype. These strains enabled antibiotic selection of NTHi during culture and counter-selection against any indigenous bacteria; this increased the number of ME providing quantitative data during...”
- Identification of biofilm proteins in non-typeable Haemophilus Influenzae
Gallaher, BMC microbiology 2006 - “...1573163 All 80 6 J RimM protein, required for 16S rRNA processing RimM N N HI0227 1573192 1 4 2731 S Uncharacterized BCR - y y HI0246 1573213 1 3 4 0 x No related COG - y y HI0719 1573721 all 251 J Putative translation...”
- Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism
Teplyakov, Journal of bacteriology 2005 - “...Inc., Radnor, Pa. Cloning, expression, and purification. The YhcH (HI0227) gene was cloned by PCR, using genomic H. influenzae DNA as a template, into the...”
- “...to that of YhcH from H. influenzae (HI0227). Sequences are labeled with the gene tags in the GenBank database (http://www.ncbi.nlm.nih.gov/GenBank)....”
- Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
Kolker, Nucleic acids research 2004 - “...below), found to be appropriate. In one case (HI0227, a member of COG2731, annotated as beta subunit of beta-galactosidase'), the CDD/COG annotation could not...”
- “...genes Functional predictions based on structure and genome context HI0227 HI0315 HI0442 HI0719 P44583 P44634 P44711 P44839 155 246 121 130 2731 0217 0718 0251...”
- Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli
Plumbridge, Journal of bacteriology 1999 - “...any proteins in GenBank except an ORF in H. influenzae (HI0227), two ORFs (YigK and YiaL) in E. coli, and an ORF (ORF-1) in Streptococcus pneumoniae. The HI0227...”
STY4129 conserved hypothetical protein (NCBI ptt file) from Salmonella enterica subsp. enterica serovar Typhi str. CT18
Aligns to 1:150 / 154 (97.4%), covers 100.0% of PF04074, 145.2 bits
S3474 hypothetical protein (NCBI ptt file) from Shigella flexneri 2a str. 2457T
Aligns to 1:149 / 154 (96.8%), covers 100.0% of PF04074, 140.9 bits
YiaL / b3576 DUF386 domain-containing protein YiaL from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b3576 hypothetical protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
Aligns to 1:150 / 155 (96.8%), covers 100.0% of PF04074, 140.7 bits
PBPRA2282 conserved hypothetical protein (NCBI) from Photobacterium profundum SS9
Aligns to 1:159 / 163 (97.5%), covers 100.0% of PF04074, 140.4 bits
c3975 Hypothetical protein yhcH (NCBI ptt file) from Escherichia coli CFT073
Aligns to 1:149 / 154 (96.8%), covers 100.0% of PF04074, 139.5 bits
YhcH / b3221 DUF386 domain-containing protein YhcH from Escherichia coli K-12 substr. MG1655 (see 5 papers)
YHCH_ECOLI / P45424 Uncharacterized protein YhcH from Escherichia coli (strain K12) (see paper)
yhcH / RF|NP_417688 uncharacterized protein yhcH from Escherichia coli K12 (see paper)
b3221 hypothetical protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
Aligns to 1:149 / 154 (96.8%), covers 100.0% of PF04074, 139.5 bits
- Genome-wide localization of mobile elements: experimental, statistical and biological considerations
Martinez-Vaz, BMC genomics 2005 - “...yejO, b2191, yi52_8, ccmH 10. glcC, b2981, yi52_9, b2983, pitB 11. yhcD, yhcE, yi52_10, b3219, b3221, sspB, b3238 12. yhiS, yi52_11 , yhiF, tnaA We confirmed the presence of an IS5 element in the flhDC / yecG intergenic region by PCR. A 2720 bp PCR product...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...1.02 b3218 yi52_10 1 IS5 transposase 0.61* 0.50* 1.04 b3221 b3222 yhcH nanK 1 1 ORF, hypothetical protein ManNAc kinase 0.27* 0.22* 0.47 0.29 0.86 0.78*...”
SpnNT_01747 YhcH/YjgK/YiaL family protein from Streptococcus pneumoniae
spr1535 Hypothetical protein (NCBI ptt file) from Streptococcus pneumoniae R6
SPD_1503 hypothetical protein (NCBI) from Streptococcus pneumoniae D39
Aligns to 1:148 / 150 (98.7%), covers 100.0% of PF04074, 137.9 bits
- Foreign peptide triggers boost in pneumococcal metabolism and growth
Nasher, BMC microbiology 2018 - “...phosphotransferase enzyme IIB component 6.6 0.04 SpnNT_01738 yesO_1 Putative ABC transporter for carbohydrate 6.3 0.001 SpnNT_01747 tabA Toxin-antitoxin biofilm protein TabA 6.2 0.001 SpnNT_01751 nanA_3 Sialidase 5.3 0.001 SpnNT_01537 CsbD-like protein, general stress response protein 4.6 0.001 SpnNT_01944 tRNA-Leu 4.5 0.005 SpnNT_00467 grpE HSP-70 cofactor, heat...”
- The pneumococcal response to oxidative stress includes a role for Rgg
Bortoni, Microbiology (Reading, England) 2009 - “...SPR1280 Hypothetical protein 6 0.0000002 SPR1313 Hypothetical protein 3 0.0001 SPR1348 Hypothetical protein 4 0.006 SPR1535 Conserved hypothetical protein 5 0.0007 SPR1537 Hypothetical protein 2 0.001 SPR1572 Hypothetical protein 3 0.0000003 SPR1623 Hypothetical protein 3 0.003 SP2004 Hypothetical protein 4 0.007 SPR1830 Hypothetical protein 3 0.0001...”
- Pneumococcal neuraminidases A and B both have essential roles during infection of the respiratory tract and sepsis
Manco, Infection and immunity 2006 - “...comparable. In addition, we measured the transcriptional expression of SPR1535 (the gene downstream of nanA) in both the wild type and in the nanA isogenic...”
- “...no significant difference in the transcriptional level of SPR1535 in the nanA mutant strain compared to the parent wild-type strain (data not shown). Therefore,...”
- Deletion of the Zinc Transporter Lipoprotein AdcAII Causes Hyperencapsulation of Streptococcus pneumoniae Associated with Distinct Alleles of the Type I Restriction-Modification System
Durmort, mBio 2020 - “...3.29 1.25 SPD_1498 Oxidoreductase 2.21 2.23 1.34 SPD_1501 Sugar ABC transporter permease 3.73 3.58 1.42 SPD_1503 Hypothetical protein 3.25 4.03 1.09 SPD_1513 Hypothetical protein 1.77 2.68 1.40 SPD_1568 GTP cyclohydrolase 1.80 1.55 1.53 SPD_1584 ABC transporter permease 2.30 2.16 2.08 SPD_1650 fatC Iron uptake ABC transporter...”
- Sialic acid-mediated gene expression in Streptococcus pneumoniae and role of NanR as a transcriptional activator of the nan gene cluster
Afzal, Applied and environmental microbiology 2015 - “...assays. Chromosomal transcriptional lacZ fusions to the nanA, spd_1503, and nanE promoters were constructed in the integration plasmid pPP2 (30) via double...”
- “...spd_1488), the nanA gene (spd_1504), and nan operon II (spd_1503 to spd_1498) (Fig. 1A). nanA encodes a sialidase that has been shown to cleave sialic 3124...”
SP_1680 hypothetical protein (RefSeq) from Streptococcus pneumoniae TIGR4
Aligns to 1:148 / 150 (98.7%), covers 99.3% of PF04074, 127.7 bits
SPD_1492 hypothetical protein (NCBI) from Streptococcus pneumoniae D39
Aligns to 1:148 / 150 (98.7%), covers 99.3% of PF04074, 126.5 bits
- N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae
Afzal, Frontiers in cellular and infection microbiology 2016 - “...protein 11.4 spd_1489 N-acetylneuraminate lyase, NanA2 3.7 spd_1490 Hypothetical protein 3.5 spd_1491 Hypothetical protein 7.4 spd_1492 Hypothetical protein 3.9 spd_1493 Sugar ABC transporter, permease protein, NanW 4.8 spd_1494 Sugar ABC transporter, permease protein, NanV 2.5 spd_1495 Sugar ABC transporter, sugar-binding protein, NanU 6.4 spd_1496 PTS system,...”
- N-acetylglucosamine-Mediated Expression of nagA and nagB in Streptococcus pneumoniae
Afzal, Frontiers in cellular and infection microbiology 2016 - “...component 2.3 spd_1246 glucosamine-6-phosphate isomerase, NagB 2.3 spd_0264 PTS system, mannose-specific IIAB components, ManL 2.1 spd_1492 Hypothetical protein 2.0 spd_1491 Hypothetical protein 2.0 spd_1100 Glucose-6-phosphate 1-dehydrogenase, Zwf 2.2 spd_0448 Glutamine synthetase, GlnA 3.3 spd_1099 Amino acid ABC transporter, ATP-binding protein 3.3 spd_0447 Transcriptional regulator, GlnR 3.7...”
- Sialic acid-mediated gene expression in Streptococcus pneumoniae and role of NanR as a transcriptional activator of the nan gene cluster
Afzal, Applied and environmental microbiology 2015 - “...to spd_1495), three hypothetical proteins (spd_1490 to spd_1492), an N-acetylneuraminate lyase (spd_1489), and a ROK family protein (NanK) (spd_1488). The...”
- “...spd_1267 spd_1330 spd_1488 spd_1489 spd_1490 spd_1491 spd_1492 spd_1493 spd_1494 spd_1495 spd_1496 spd_1497 spd_1504 spd_1505 spd_1800 spd_2012 spd_2013...”
ESA_03609 hypothetical protein (RefSeq) from Enterobacter sakazakii ATCC BAA-894
ESA_03609 YhcH/YjgK/YiaL family protein from Cronobacter sakazakii ATCC BAA-894
Aligns to 1:148 / 154 (96.1%), covers 99.3% of PF04074, 121.3 bits
- Sialic acid utilization by Cronobacter sakazakii
Joseph, Microbial informatics and experimentation 2013 - “...universalis 581 C. muytjensii 530 C. dublinensis 582 C. dublinensis 1210 C. condimenti 1330 yhcH ESA_03609 Putative sugar isomerase + + + + + - - - - - - - - - nanK ESA_03610 N-acetylmannosamine kinase + + + + + - - - -...”
- Comparative analysis of genome sequences covering the seven cronobacter species
Joseph, PloS one 2012 - “...to commensal bacteria in the intestinal tract and to pathogens [62] . In C. sakazakii ESA_03609 encodes a putative sugar isomerase (YhcH). Genes ESA_03610-13 encode the nanKTAR genes involved in the N-acetylneuraminate and N-acetylmannosamine degradation pathway. The nanK gene (ESA_03610) encodes N-acetylmannosamine kinase; nanT (ESA_03611) encodes...”
RUMGNA_02700 hypothetical protein (RefSeq) from Ruminococcus gnavus ATCC 29149
RUMGNA_02700 YhcH/YjgK/YiaL family protein from [Ruminococcus] gnavus ATCC 29149
Aligns to 1:148 / 149 (99.3%), covers 100.0% of PF04074, 113.9 bits
- Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut
Bell, Nature microbiology 2019 - “...Supplementary Table 1 ). In contrast, RUMGNA_02701 with homology to sialic acid esterase proteins and RUMGNA_02700 with homology to the YhcH protein family did not cluster with proteins from the same set of bacteria ( Supplementary Figure 1 and Supplementary Table 1 ). The candidate genes...”
- “...Diagram depicting the genomic organisation of the nan operon RUMGNA_02701 (putative sialic acid esterase; tan) RUMGNA_02700 (putative YhcH family protein; dark blue), RUMGNA_02699 (predicted transcriptional regulator; purple), RUMGNA_02698 02696 (putative sialic acid ABC transporter of the SAT2 family; green), RUMGNA_02695 (putative oxidoreductase, pink), RUMGNA_02694 (RgNanH (Intramolecular...”
- Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent
Crost, PloS one 2013 - “...The first gene of the cluster encodes a protein of unknown function. The second gene (RUMGNA_02700) encodes a putative sugar isomerase involved in sialic acid catabolism. The following one (RUMGNA_02699) encodes a protein with homology with transcriptional regulators of the AraC family. The following 3 genes...”
gbs0036 Unknown (NCBI ptt file) from Streptococcus agalactiae NEM316
SAG0037 conserved hypothetical protein (NCBI ptt file) from Streptococcus agalactiae 2603V/R
Aligns to 1:145 / 147 (98.6%), covers 99.3% of PF04074, 113.5 bits
BN865_07130 YhcH/YjgK/YiaL family protein from Campylobacter coli 76339
Aligns to 1:161 / 162 (99.4%), covers 98.6% of PF04074, 98.6 bits
- Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3
Skarp-de, BMC genomics 2014 - “...BN865_07110 NAD-dependent epimerase/dehydratase C1a C1b; C1c; C2 BN865_07120 Putative cyclase superfamily C1a C1b; C1c; C2 BN865_07130 Conserved hypothetical protein 22 C1a C1b; C1c; C2 BN865_07140 Hydrolase, haloacid dehalogenase-like family C1a C1b; C1c; C2 BN865_07150 CMP-N-acetylneuraminate-beta-galactosamide- alpha-2,3-sialyltransferase (EC 2.4.99.-) C1a C1b; C1c; C2 BN865_07160 FIG 00470714: hypothetical...”
c0758 Hypthetical protein (NCBI ptt file) from Escherichia coli CFT073
Aligns to 1:150 / 156 (96.2%), covers 100.0% of PF04074, 95.9 bits
VP2404 evolved beta-D-galactosidase, beta subunit; cryptic gene (NCBI ptt file) from Vibrio parahaemolyticus RIMD 2210633
Aligns to 1:141 / 150 (94.0%), covers 99.3% of PF04074, 91.6 bits
EbgC / b3077 DUF386 domain-containing evolved β-D-galactosidase subunit β from Escherichia coli K-12 substr. MG1655 (see paper)
EBGC_ECOLI / P0AC73 Evolved beta-galactosidase subunit beta from Escherichia coli (strain K12) (see paper)
b3077 cryptic beta-D-galactosidase, beta subunit (NCBI) from Escherichia coli str. K-12 substr. MG1655
Aligns to 1:140 / 149 (94.0%), covers 99.3% of PF04074, 86.5 bits
HP1029 hypothetical protein (NCBI ptt file) from Helicobacter pylori 26695
Aligns to 2:170 / 178 (94.9%), covers 79.7% of PF04074, 73.7 bits
- The crystal structure of Helicobacter pylori HP1029 highlights the functional diversity of the sialic acid-related DUF386 family
Vallese, The FEBS journal 2015 (PubMed)- “...HP1029 highlights the functional diversity of the sialic acid-related DUF386 family Francesca Vallese1, Riccardo Percudani2, Wolfgang Fischer3 and Giuseppe Zanotti1 1 Department of Biomedical Sciences,...”
- “...We present here the crystal structure of protein HP1029 from Helicobacter pylori. The protein is a homodimer, in which each monomer comprises a molecular...”
- The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori
Douillard, BMC microbiology 2010 - “...1.271 0.214 HP0908 flagellar hook ( flgE ) 1.175 0.119 HP1028 hypothetical protein 0.852 0.286 HP1029 hypothetical protein 0.799 0.019 HP1030 fliY protein ( fliY ) 0.860** 0.308 HP1031 flagellar motor switch protein ( fliM ) 0.835 0.054 HP1032 alternative transcription initiation factor, sigma28 ( fliA...”
- Effect of FliK mutation on the transcriptional activity of the {sigma}54 sigma factor RpoN in Helicobacter pylori
Douillard, Microbiology (Reading, England) 2009 - “...0.909 0.40 HP0908 Flagellar hook ( flgE ) 0.802 0.06 HP1028 Hypothetical protein 1.271 0.17 HP1029 Hypothetical protein 1.035 0.57 HP1030 FliY protein ( fliY ) 1.094 0.54 HP1031 Flagellar motor switch protein ( fliM ) 1.018 0.82 HP1032 Alternative transcription initiation factor, sigma 28 (...”
- The Gaggle: an open-source software system for integrating bioinformatics software and data sources
Shannon, BMC bioinformatics 2006 - “...pathogenesis protein [ 33 ]. Another set of interesting unknown function proteins were HP1028 and HP1029 connected via gene cluster (operon) edges to FliY and FliM key flagellar switch proteins. Also present in this operon is an alternate sigma factor ( 28 ) gene fliA which...”
- Acid-adaptive genes of Helicobacter pylori
Wen, Infection and immunity 2003 - “...HP0270 HP0369 HP0582 HP0603 HP0838 HP0863 HP0864 HP1029 HP1106 HP1124 HP1217 HP1334 HP1377 HP1502 HP1546 Downloaded from http://iai.asm.org/ on February 11,...”
jhp0395 putative (NCBI ptt file) from Helicobacter pylori J99
Aligns to 14:170 / 178 (88.2%), covers 78.4% of PF04074, 72.0 bits
Or search for genetic data about PF04074 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory