Family Search for PF07166 (DUF1398)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF07166 hits 14 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
STMMW_18451 DUF1398 domain-containing protein from Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
STM1856 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 8:126 / 131 (90.8%), covers 100.0% of PF07166, 160.4 bits
- The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Canals, PLoS pathogens 2019 - “...putative amino acid transporter; hnr , encoding a regulator; pth , encoding a peptidyl-tRNA hydrolase; STMMW_18451 , with unknown function; and ddhB ( rfbG ), an O-antigen gene involved in the biosynthesis of CDP-abequose. Intriguingly, hns was only required in S . Typhimurium D23580 and 14028...”
- Identification of novel factors involved in modulating motility of Salmonella enterica serotype typhimurium
Bogomolnaya, PloS one 2014 - “..., STM3783, STM4216,STM4219, sRNA candidate C1023 STM0056, STM0362, STM1131, pagC, STM1254, STM1258, STM1543, srfC, STM1632, STM1856, STM1926, STM1958, STM2303, STM2508, ygaU, STM3125, lpfE , STM3944, STM4030.S, STM4197, STM4204, STM4529, STM4574, STM4599, invR *Based on COGs (Clusters of Orthologous Groups of protein). **Mutants with previously known motility...”
- High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach
Allard, BMC genomics 2012 - “...L/R 155 a1 putative cytoplasmic protein STM1671 SEEM020_05759 A/C V 122 a1 putative regulatory protein STM1856 SEEM020_06993 G/T E/Stop 316 putative cytoplasmic protein fliC STM1959 SEEM020_07518 T/A N/K 723 a1 phase 1 flagellin uhpA STM3790 SEEM020_08264 A/G l 60 a1 1) sensor histidine kinase UhpB, 2)transcriptional...”
- C-ring requirement in flagellar type III secretion is bypassed by FlhDC upregulation
Erhardt, Molecular microbiology 2010 - “...2 transcription in the cases of ecnR7 (insertion in yjek , upstream of ecnR ), STM1856, ddg/yfdZ1 and STM2011 ( Figure 5A ). We therefore asked the question whether the Tc-Ap S phenotype of the ecnR7 T-POP (insertion in yjek , upstream of ecnR ) was...”
- “...in S. enterica . We additionally identified several putative regulators of Class 2 transcription like STM1856 and STM2401/STM2402. A summary of the regulatory network influencing Class 1 gene expression is given in Figure 8A . Taken together we conclude that the upregulation of flhDC expression by...”
- Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system
Tomljenovic-Berube, PLoS genetics 2010 - “...0.86 SL1341-SL1346 6 42.72 SL1341 STM1407: ssaH SPI-2 gene 3-IGR-overlap 0.84 SL1785-SL1785 1 11.81 SL1785 STM1856 IGR 0.81 SL0037-SL0038 2 4.00 SL0037 STM0036 5-IGR-overlap 0.78 SL1170-SL1171 2 2.84 SL1171 STM1233: ycfC 5-IGR-overlap 0.74 SL1337-SL1339 3 8.51 SL1337 STM1403: sscB SPI-2 gene 3-IGR-overlap 0.72 SL1878-SL1878 1 7.65...”
t1022 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
Aligns to 8:126 / 131 (90.8%), covers 100.0% of PF07166, 160.4 bits
YcgX / b1161 DUF1398 domain-containing protein YcgX from Escherichia coli K-12 substr. MG1655
b1161 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 8:126 / 134 (88.8%), covers 99.2% of PF07166, 159.3 bits
YbcV / b0558 DLP12 prophage; DUF1398 domain-containing protein YbcV from Escherichia coli K-12 substr. MG1655 (see paper)
b0558 putative an envelop protein from Escherichia coli str. K-12 substr. MG1655
ECK0550 DUF1398 domain-containing protein YbcV from Escherichia coli str. K-12 substr. MG1655
SR35_02760 DUF1398 domain-containing protein from Escherichia coli
Aligns to 8:126 / 136 (87.5%), covers 99.2% of PF07166, 157.1 bits
- CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis
Jalili, PloS one 2015 - “...(b3340), rpsG (b3341), rpsI (b3230), rplC (b3320), rplM (b3231), rplQ (b3294), rpoC (b3988) and ybcV (b0558). Except rplA (b3984) and htpG (b0473), all of these genes were marked as essential ones previously. The result of this analysis emphasized that the centrality is an anticipative topological measurement...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...b1172 b4131 b0770 b1880 b3784 b4015 b3226 b1759 b4016 b0558 b1503 b1734 b2155 b2361 b2650 b0505 b0655 b0726 b2779 b3732 b0727 b0763 0.01 0.02 0.03 0.03 0.03...”
- Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases
De, PLoS genetics 2014 - “...:: Kan (in Dlp12 prophage) was constructed by P1 transduction from the Keio collection strain ECK0550 [85] . The Ur ble phage was constructed from Ur isolated from the E. coli K12 ancestral strain. The phleomycine/bleomycine resistance gene ble , cloned under the Bacillus subtilis promoter...”
- Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA+)
Jeong, Frontiers in microbiology 2017 - “...gpt-proA exist only in K-12 MG1655 quuD (SR35_02745) SR35_02750 IS 5 ( nmpC-borD ) ybcV (SR35_02760) Within DLP12 prophage region ttcA (SR35_06950) ( intR-ynaE ) uspF (SR35_06955) Rac prophage exists only in K-12 MG1655; First eight amino acids of TtcA protein are not identical between RR1...”
YdfO / b1549 Qin prophage; DUF1398 domain-containing protein YdfO from Escherichia coli K-12 substr. MG1655
P76156 Uncharacterized protein YdfO from Escherichia coli (strain K12)
b1549 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 8:126 / 136 (87.5%), covers 99.2% of PF07166, 156.6 bits
c1440 Hypothetical protein ydfO from Escherichia coli CFT073
Aligns to 13:131 / 141 (84.4%), covers 100.0% of PF07166, 156.4 bits
NP_597781 putative envelope protein from Enterobacteria phage lambda
NP_597781 head protein from Escherichia phage Lambda
Aligns to 49:167 / 177 (67.2%), covers 99.2% of PF07166, 156.2 bits
- Improving gene annotation of complete viral genomes
Mills, Nucleic acids research 2003 - “...RefSeq version of the phage annotation (NC_001416). Two genes, coding for a putative envelope protein (NP_597781) and Bor protein precursor (NP_597780), are similar to genes in prophage CP933X, being a part of the E.coli O157 genome (NC_002655). A gene for superinfection exclusion protein B (NP_597779) must...”
EC1303_c12530 DUF1398 family protein from Escherichia coli 1303
Aligns to 8:126 / 136 (87.5%), covers 99.2% of PF07166, 148.4 bits
- No evidence for a bovine mastitis Escherichia coli pathotype
Leimbach, BMC genomics 2017 - “...contained in MAEC 1303 prophage 1, encoding for an exonuclease (EC1303_c12230) and an envelope protein (EC1303_c12530), are also associated with phylogroups A/B1/E. In summary, the putative mastitis-eliciting function of any of the genes within the significantly MAEC-associated OGs is unclear. A truly meaningful correlation between OGs...”
MW0324 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MW2
Aligns to 9:126 / 129 (91.5%), covers 92.4% of PF07166, 88.8 bits
- Bioinformatics and Functional Assessment of Toxin-Antitoxin Systems in Staphylococcus aureus
Habib, Toxins 2018 - “...MW2380, and MW1230 were shorter in length and showed homology towards YefM-YoeB sub-family, while the MW0324 and MW1394 were longer in length and displayed less conservation, possibly making a new sub-family. ( B ) The GNATs toxins showed a functional site of 28 residues (4168 aa)...”
- “...MW1888, MW1919, MW1928 Staphylokinase VSa-beta 31,977 3 MW1725, MW1733, MW1779 Proteases VSa-alpha 34,481 3 MW0302, MW0324, MW0405 -- VSa-3 14,380 2 MW0749, MW0771 Enterotoxins, exotoxin VSa-4 2710 0 --...”
SATW20_04160 DUF1398 family protein from Staphylococcus aureus subsp. aureus TW20
SAUSA300_0349 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
USA300HOU_0369 possible bacteriophage envelope protein from Staphylococcus aureus subsp. aureus USA300_TCH1516
Aligns to 9:126 / 129 (91.5%), covers 92.4% of PF07166, 87.6 bits
LMOf2365_0649 hypothetical protein from Listeria monocytogenes str. 4b F2365
Aligns to 8:126 / 130 (91.5%), covers 96.6% of PF07166, 86.4 bits
SA0336 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAV0348 hypothetical protein from Staphylococcus aureus subsp. aureus Mu50
Aligns to 9:126 / 129 (91.5%), covers 92.4% of PF07166, 85.7 bits
- An Alternative Terminal Step of the General Secretory Pathway in Staphylococcus aureus
Craney, mBio 2015 - “..., SA0338; ayrB , SA0339; ayrC , SA0340) and the region immediately upstream that includes SA0336. Below is the sequence of the putative promoter region upstream of ayrR ending with its GTG translational start site. A 22-nt palindromic repeat (arrows) is located 43 to 65bp upstream...”
- “...translational start site. (C) RT-PCR analysis of the ayrRABC operon and divergent genes (SA0334 to SA0336). Fold change in gene expression in ARC0001 with respect to N315. gyrB was used as an external control, and gene expression was normalized using gmk . See TableS1 in the...”
- Serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus
Cameron, The Journal of infectious diseases 2012 - “...Hypothetical protein Hypothetical protein 1.96 1.58 SA0336 Hypothetical protein 1.56 Unknown function Abbreviations: ABC, adenosine triphosphate binding...”
- Role of the twin-arginine translocation pathway in Staphylococcus
Biswas, Journal of bacteriology 2009 - “...as immediately upstream of tatA there is a gene (SA0336 and SC2209, respectively) which encodes a protein with similarity to a phage envelope protein present in...”
- Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression
Grandgirard, BMC genomics 2015 - “...phage protein 6.0 5.9 10.6 17.9 SAV0240 / SATW20_02420 / flavohemoprotein 10.6 18.4 26.0 13.7 SAV0348 / SATW20_04160 / hypothetical protein 2.1 2.1 3.5 2.3 SAV0465 / SATW20_05330 / putative exported protein 7.0 3.8 7.7 13.7 SAV0663 / SATW20_07380 / conserved hypothetical protein 4.8 5.4 9.0...”
SAR0345 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
Aligns to 9:126 / 129 (91.5%), covers 92.4% of PF07166, 85.1 bits
MT2067 hypothetical protein from Mycobacterium tuberculosis CDC1551
Rv2012 hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 35:151 / 164 (71.3%), covers 86.6% of PF07166, 37.0 bits
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...MT2066 Rv2011c Putative MarR family transcriptional regulator, unknown function Lee et al., 2016 2.63 3.92E-10 MT2067 Rv2012 Conserved hypothetical protein 2.38 1.25E-05 MT2468 * Rv2397c cysA ABC import systems functioning as a sulfate importer Soni et al., 2020 1.01 4.03E-05 MT2469 * Rv2398c cysW Sulfur metabolism...”
- The Mycobacterium tuberculosis sRNA F6 Modifies Expression of Essential Chaperonins, GroEL2 and GroES
Houghton, Microbiology spectrum 2021 - “...observed nine differentially expressed genes, of which five ( dnaK , groEL2 , rv0990c , rv2012 , and rv3224 ) are associated with heat shock in M. tuberculosis (Fig. S3) ( 22 ). FIG6 Volcano plot of sfdS versus H37Rv upon starvation in PBS. The plot...”
- Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate
Willemse, Frontiers in microbiology 2021 - “...Rv2011c Putative MarR family transcriptional regulator, unknown function Lee et al., 2016 2.63 3.92E-10 MT2067 Rv2012 Conserved hypothetical protein 2.38 1.25E-05 MT2468 * Rv2397c cysA ABC import systems functioning as a sulfate importer Soni et al., 2020 1.01 4.03E-05 MT2469 * Rv2398c cysW Sulfur metabolism Zeng...”
- Bioinformatic and empirical analysis of novel hypoxia-inducible targets of the human antituberculosis T cell response
Gideon, Journal of immunology (Baltimore, Md. : 1950) 2012 - “...0.00 0.30 0.00 0.00 51 Rv2011c 0.00 4.43 1.74 2.00 2.50 1.44 3.55 2.33 52 Rv2012 0.00 2.14 0.70 0.00 3.80 2.90 3.17 2.20 53 Rv2021c 0.00 3.24 1.70 5.00 2.46 2.50 2.68 4.00 54 Rv2022c 1.50 1.70 0.70 3.00 1.30 1.30 1.81 1.30 55 Rv2025c...”
- “...fdxA 80 98 74 252 98 51 Rv2011c Rv2011c 66 60 56 182 75 52 Rv2012 Rv2012 36 67 52 155 55 53 Rv2021c Rv2021c 87 29 54 170 64 54 Rv2022c Rv2022c 61 66 76 203 81 55 Rv2025c Rv2025c 68 10 42 120 32...”
- Transcriptional profiling of mycobacterium tuberculosis during infection: lessons learned
Ward, Frontiers in microbiology 2010 - “...al., 2006a ; Fontn et al., 2008 ). Two of these genes ( rv1057 , rv2012 ) are completely uncharacterized, and one is a putative methyltransferase ( rv1405c ) of unknown biological function that was identified as necessary for infection within a mouse model (Sassetti and...”
Or search for genetic data about PF07166 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory