Family Search for PF06004 (DUF903)
PF06004.12 hits 20 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
Z4126 hypothetical protein (NCBI) from Escherichia coli O157:H7 EDL933
Aligns to 25:73 / 76 (64.5%), covers 100.0% of PF06004, 88.0 bits
YgdI / b2809 DUF903 domain-containing lipoprotein YgdI from Escherichia coli K-12 substr. MG1655 (see 3 papers)
b2809 orf, hypothetical protein (VIMSS) from Escherichia coli str. K-12 substr. MG1655
P65292 Uncharacterized lipoprotein YgdI from Escherichia coli (strain K12)
Aligns to 24:72 / 75 (65.3%), covers 100.0% of PF06004, 87.2 bits
- Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
Cortés-Tolalpa, Microbial cell factories 2014 - “...Conserved protein Other metabolic process 18.9020 ydiS b1699 Putative flavoprotein Other metabolic process 20.0646 ygdI b2809 Putative lipoprotein Out of OGs 15.8477 slp b3506 Starvation lipoprotein Out of OGs 16.3895 ybaY b0453 Predicted OM lipoprotein Out of OGs 31.4852 yhjR b3535 Conserved protein Out of OGs...”
- Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
Lee, Applied and environmental microbiology 2009 - “...b2080 b2112 b2135 b2165 b2660 b2654 b2655 b2658 b2672 b2809 b2856 b2857 b3099 b3170 b3184 b3260 b3512 b4068 b4126 b4127 Change in expression (fold) SdiA vs no...”
- Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
González, Journal of bacteriology 2006 - “...dsdX ygdI b3254 yiaG tra5_3 yhjS rbsC b2365 b2809 b3254 b3555 b0372 b3536 b3750 Hypothetical protein Transcriptional regulator of cryptic csgA gene for curli...”
- Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655
Brokx, Journal of bacteriology 2004 - “...b2214 b2346 b2432 b2477 b2512 b2593 b2595 b2605 b2701 b2742 b2809 b2813 b2833 b2865 b2963 b3150 b3163 b3267 b3369 b3661 b4149 b4189 b4288 1,177.4 P 2,142.5 P 75...”
- Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli
Cooper, Proceedings of the National Academy of Sciences of the United States of America 2003 - “...cdsA ybaC yaeT yafU ybcU b0762 b1044 b1490 b2445 b2462 b2772 b2809 syd yaeJ ydfC ydfE yjgF yjiD yjjY ykfB yohH nrdA yliJ b1168 ynbD yqhC yhcJ yidJ yjcP hsdR...”
- A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli
Cheung, Genome research 2003 - “...for Supercoiling-Dependent Gene Regulation Gene Product acnA b1664 b1724 b2809 bax btuE dps gcd grxB nlpD osmE otsA otsB poxB proV Aconitate hydrase 1 Possible...”
- Semiconductor Nanomaterials-Based Fluorescence Spectroscopic and Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometric Approaches to Proteome Analysis
Kailasa, Materials (Basel, Switzerland) 2013 - “...proteins ecnB (P56549), lpp (P69776), and osmE (P23933); hypothetical membrane proteins yifL (P39166) and ygdI (P65292); acetylacyl carrier protein ( ydhI ; acetyl-ACP , P0A6A8) and lipoproteins ( ecnB , lpp , osmE , yifL , ygdI ) and water-insoluble ATPase proteolipid (at m / z...”
UTI89_C3182 hypothetical protein (NCBI) from Escherichia coli UTI89
SSON_2966 hypothetical protein (NCBI) from Shigella sonnei Ss046
ECs3669 hypothetical protein (NCBI ptt file) from Escherichia coli O157:H7 str. Sakai
Aligns to 25:73 / 76 (64.5%), covers 100.0% of PF06004, 87.2 bits
KPN_03160 hypothetical protein (RefSeq) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Aligns to 25:73 / 76 (64.5%), covers 95.9% of PF06004, 86.8 bits
STM14_3597 YgdI/YgdR family lipoprotein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM2983 putative lipoprotein (NCBI ptt file) from Salmonella typhimurium LT2
Aligns to 24:72 / 75 (65.3%), covers 98.0% of PF06004, 85.4 bits
- Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation
Lago, Scientific reports 2017 - “.... coli YodC, DUF2158 IPR019226 61 Yes yodC 11, 13, 14 -, -, - Proteobacteria STM14_3597 Sm-like protein IPR010920, pdb 2RA2, SP, Lipo, DUF903 IPR010305 75 Yes ygdI 1214 Bacteria STM14_4398 Putative transcriptional regulator, DNA-binding domain IPR010982 96 Yes yiaG 7, 1114 Bacteria STM14_4446 79% identity...”
- 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 - “...2.3 0.02 Not in COGs STM0471 STM1059 STM1092 STM1601 STM2983 ylaC ycbW ugtL orfX Putative Putative Putative Putative Putative 2.06 2.71 2.32 2.1 2.09 0.003 0.03...”
- The Rcs phosphorelay system is specific to enteric pathogens/commensals and activates ydeI, a gene important for persistent Salmonella infection of mice
Erickson, Molecular microbiology 2006 - “...STM1174 STM3445 STM3433 STM4064 STM4561b STM4239b STM4222 STM2983 STM4336b STM4240 STM3269 STM1285b STM1491 STM3443 STM1515 STM1492 STM3363 STM2311 STM2795...”
Ent638_3274 protein of unknown function DUF903 (RefSeq) from Enterobacter sp. 638
Aligns to 23:71 / 72 (68.1%), covers 100.0% of PF06004, 85.0 bits
YgdR / b2833 DUF903 domain-containing lipoprotein YgdR from Escherichia coli K-12 substr. MG1655 (see 2 papers)
S3041 hypothetical protein (NCBI ptt file) from Shigella flexneri 2a str. 2457T
P65294 Uncharacterized lipoprotein YgdR from Escherichia coli (strain K12)
b2833 hypothetical protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
c3428 Hypothetical lipoprotein ygdR precursor (NCBI ptt file) from Escherichia coli CFT073
Z4151 orf, hypothetical protein (NCBI ptt file) from Escherichia coli O157:H7 EDL933
Aligns to 23:71 / 72 (68.1%), covers 100.0% of PF06004, 84.1 bits
- Acidic pH sensing in the bacterial cytoplasm is required for Salmonella virulence
Choi, Molecular microbiology 2016 - “...et al. , 1972 ). All S. bongori strains were derived from the wild-type strain S3041 (SARC11) ( Boyd et al. , 1996 ). Bacteria were grown at 37C in Luria-Bertani (LB) broth or N-minimal media (pH 7.7) ( Snavely et al. , 1991 ) supplemented...”
- “...the strain JC369 was replaced with the PCR products amplified from the S. bongori strain S3041 using primers 14890/14891. To generate S. enterica with variant phoQ allele (D233E, H409N, Q460H), the tetRA fragment was amplified using primers 14835/14836 and used to electroporate the S. enterica strain...”
- Analysis of the type 1 pilin gene cluster fim in Salmonella: its distinct evolutionary histories in the 5' and 3' regions
Boyd, Journal of bacteriology 1999 - “...2 1 1 1 1 1 1 1 1 1 1 1 1 1 2 S3041 S3044 2 2 2 2 2 2 2 2 2 2 2 2 1, positive hybridization signal; 2, indicates no hybridization signal. bp and the fimY-fimW...”
- Identification of a putative Salmonella enterica serotype typhimurium host range factor with homology to IpaH and YopM by signature-tagged mutagenesis
Tsolis, Infection and immunity 1999 (secret) - Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica
Boyd, Journal of bacteriology 1997 - “...S3049 S3043 S3046 S3041 S3047 S3042 S3044 S3040 48:z39:-60:z41:-66:z35:-61:z35:-44:r:-1,13,22:i:-48:z35:-44:z39:-66:z41:-1,40:z35:-48:a:-48:z41:-66:z65 Human...”
- “...could not be PCR amplified from subspecies V isolates S3041 and S3044. In order to determine whether invH is absent from this subspecies, 13 strains from this...”
- Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria
Nelson, Proceedings of the National Academy of Sciences of the United States of America 1994 - “...S2976 S So297I 53013 S2983 . ~~~~~VII II S83047 S3041 S3044 V FIG. 2. Neighbor-joining tree for gnd sequences of strains of S. enterica, based on synonymous...”
- A community resource of experimental data for NMR / X-ray crystal structure pairs
Everett, Protein science : a publication of the Protein Society 2016 (secret) - Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655
Brokx, Journal of bacteriology 2004 - “...b2432 b2477 b2512 b2593 b2595 b2605 b2701 b2742 b2809 b2813 b2833 b2865 b2963 b3150 b3163 b3267 b3369 b3661 b4149 b4189 b4288 1,177.4 P 2,142.5 P 75 P 45.55 P...”
- mRNA expression profiles for Escherichia coli ingested by normal and phagocyte oxidase-deficient human neutrophils
Staudinger, The Journal of clinical investigation 2002 - “...1. With the exception of trxC, the fold change metabolism, b2833, napD and napA, trpE, and yadI. estimates by PCR agreed well with estimates of One gene codes...”
- “...b0605 b2597 3.8 3.8 0.0004 0.004 b1172 trxC yfiG soxS katG b2833 b1172 b2582 b4062 b3942 b2833 3.7 3.3 2.8 2.6 2.6 0.02 0.001 0.02 0.001 0.02 osmB b1283 2.4...”
- The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota
Milani, Microbiology and molecular biology reviews : MMBR 2017 (secret) - 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 - “...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 +1.30 0.04 ygjT Z4441 Unknown 2.25 5.0E-03 yhaM Z4462 Unknown +2.34 0.03...”
- Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
Pieper, PloS one 2011 - “...19440 L (IM or OM) PP 3878 91 LAAC 19 A 2 uncharacterized lipoprotein YgdR Z4151 (ygdR) 7877 L (IM or OM) unkn 3742 376 VSGC 19 S 2 putative OM lipoprotein YiaD Z4977 yiaD 22196 L (IM or OM) OM 3322 45* VSGC 21 T...”
SF2823 orf, conserved hypothetical protein (NCBI ptt file) from Shigella flexneri 2a str. 301
Aligns to 25:73 / 76 (64.5%), covers 100.0% of PF06004, 82.0 bits
- Virulence and Stress Responses of Shigella flexneri Regulated by PhoP/PhoQ
Lin, Frontiers in microbiology 2017 - “...0.43 0.0016 ND Chromosome Putative carnitine operon oxidoreductase SF3143 0.45 0.0002 ND Chromosome Hypothetical protein SF2823 0.47 0.0092 ND Chromosome Hypothetical protein yqjE 0.48 0.0065 0.58 0.21 Chromosome Hypothetical protein yqjD 0.49 0.0031 ND Chromosome Hypothetical protein SF0551 0.50 0.0197 ND Chromosome Putative homeobox protein ipgB1...”
STM1585 putative outer membrane lipoprotein (NCBI ptt file) from Salmonella typhimurium LT2
Aligns to 23:71 / 73 (67.1%), covers 98.0% of PF06004, 81.5 bits
A6T9R7 Uncharacterized protein from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
Aligns to 18:66 / 68 (72.1%), covers 100.0% of PF06004, 81.0 bits
PSPTO2350 lipoprotein, putative (NCBI ptt file) from Pseudomonas syringae pv. tomato str. DC3000
Aligns to 25:73 / 74 (66.2%), covers 98.0% of PF06004, 78.5 bits
- A coarse-grained approach to protein design: learning from design to understand folding
Coluzza, PloS one 2011 - “...L7/L12 of E. coli (PDB ID 1CTF), a putative lipoprotein from Pseudomonas syringae (Gene Locus PSPTO2350, PDB code 2K57), and the UBA domain of Tap/NXF1 (PDB ID 1OAI). 10.1371/journal.pone.0020853.g003 Figure 3 Plot of the design free energy surface for protein L7/L12 (PDB ID 1CTF) as a...”
- “...C-terminal domain of the ribosomal protein, (c) a putative lipoprotein from Pseudomonas syringae (Gene Locus PSPTO2350, PDB code 2K57), and (d) the UBA domain of Tap/NXF1 (PDB ID 1OAI). The free energy is shown for two temperatures, the first ( ) slightly below the folding temperature...”
PA3031 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 24:72 / 73 (67.1%), covers 100.0% of PF06004, 75.8 bits
- Analysis of Pseudomonas aeruginosa cell envelope proteome by capture of surface-exposed proteins on activated magnetic nanoparticles
Vecchietti, PloS one 2012 - “...U,3 + PA4639 f Putative uncharacterized protein 4 U,3 PA0505 Putative uncharacterized protein 4 U,3 PA3031 f Putative uncharacterized protein 4 U,3 rpsH PA4249 30S rP S8 2 C,1 + algP algR3 PA5253 Transcriptional regulatory protein AlgP 1 C,3 - U,3 + tsf PA3655 Elongation factor...”
- “...their function at the envelope level remains unclear. Finally, 4 proteins (FimV, PA4639, PA0505, and PA3031), detected as NP-CbP, had an unknown localization according to PSORTb 3.0 [5] . Our results would strongly suggest that they have at least surface localization and this could overcome the...”
- Comparisons of Two Proteomic Analyses of Non-Mucoid and Mucoid Pseudomonas aeruginosa Clinical Isolates from a Cystic Fibrosis Patient
Rao, Frontiers in microbiology 2011 - “...o-acetyltransferase AlgF 1 6.31 17.41 11.86 221 PA0315 Hypothetical protein 2 8.40 4.85 6.63 317 PA3031 Hypothetical protein 1 5.52 7.29 6.41 110 PA3385 Alginate and motility regulator AmrZ 5 9.90 0.0001 6.08 0.0066 7.99 32 PA3540 GDP-mannose 6-dehydrogenase AlgD 9 4.26 0.0003 7.27 0.0001 5.76...”
- Lipotoxin F of Pseudomonas aeruginosa is an AlgU-dependent and alginate-independent outer membrane protein involved in resistance to oxidative stress and adhesion to A549 human lung epithelia
Damron, Microbiology (Reading, England) 2009 - “...0.6 0.6 0.5 PA1852 PA2622 (CspD) PA2966 (AcpP) PA3031 PA3745 (RpsP) 0.2 0.6 0.6 0.5 0.6 Hypothetical protein (unknown) Peptidyl-prolyl cis-trans isomerase...”
Ent638_0594 protein of unknown function DUF903 (RefSeq) from Enterobacter sp. 638
Aligns to 25:74 / 77 (64.9%), covers 98.0% of PF06004, 68.9 bits
BP2782 lipoprotein (NCBI) from Bordetella pertussis Tohama I
Aligns to 24:71 / 73 (65.8%), covers 100.0% of PF06004, 68.7 bits
- Immuno-proteomics analysis between OMV of vaccine and dominant wild type strains of Bordetella pertussis in Iran
Badamchi, Iranian journal of microbiology 2020 (no snippet) - Transcriptional profiling of human macrophages during infection with Bordetella pertussis
Petráčková, RNA biology 2020 - “...factor RpoE BP2468 ND 2.90 vrg6 virulence repressed gene BP2871 2.72 0.90 BP2871 cysteine dioxygenase BP2782 ND 2.41 BP2782 lipoprotein BP3213 1.49 1.46 gloB glyoxalase II BP3748 2.33 1.71 BP3748 sigma factor RpoH Values which did not pass the statistical significance but showed similar trend are...”
- Distinct virulence ranges for infection of mice by Bordetella pertussis revealed by engineering of the sensor-kinase BvgS
Lesne, PloS one 2018 - “...i . e . fimB ), the intermediate phase marker bipA , and the vrg bp2782 . We tested the effect of modulation on gene expression in BP-BvgS 65 . 10.1371/journal.pone.0204861.g005 Fig 5 Quantitative RT-PCR analysis of selected genes in the recombinant strains. The values represent...”
- “...levels similar to or higher than BPSM. The expression levels of the selected vrg , bp2782 , were significantly lower in several of them, but not in BP-BvgS 65 -rev79 harboring the R 572 L mutation, than in BPSM. Discussion We genetically engineered a chimera, BvgS...”
- The vaccine potential of Bordetella pertussis biofilm-derived membrane proteins
de, Emerging microbes & infections 2014 - “...11.15 1.33 1.32 4.96 2.16 1.12 1.61 1.47 1.95 C BP2039 Amidase 3.62 9.89 C BP2782 Lipoprotein 10.64 15.84 1.18 0.80 0.93 Un BP2873 tctC Tripartite tricarboxylate transporter family receptor 2.52 3.80 3.12 1.79 0.37 0.33 0.27 0.32 0.11 P BP2896 Hydrolase 4.19 6.81 C Abbreviations:...”
PA2453 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 24:72 / 73 (67.1%), covers 98.0% of PF06004, 67.4 bits
SPA0081 putative lipoprotein (NCBI) from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
STM0080 putative outer membrane lipoprotein (NCBI ptt file) from Salmonella typhimurium LT2
SEN0081 putative lipoprotein (RefSeq) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Aligns to 24:73 / 76 (65.8%), covers 98.0% of PF06004, 67.2 bits
PMI1737 lipoprotein (RefSeq) from Proteus mirabilis HI4320
Aligns to 25:74 / 77 (64.9%), covers 98.0% of PF06004, 66.2 bits
KPN_00042 hypothetical protein (RefSeq) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Aligns to 25:74 / 77 (64.9%), covers 98.0% of PF06004, 65.1 bits
PA5526 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 21:69 / 70 (70.0%), covers 95.9% of PF06004, 58.6 bits
STM1673 putative outer membrane lipoprotein (NCBI ptt file) from Salmonella typhimurium LT2
Aligns to 29:77 / 84 (58.3%), covers 98.0% of PF06004, 56.5 bits
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM1035, STM1045, STM1521, STM1534, STM1549, STM1579, STM1673, STM1869, STM1869A, STM2030, STM2033, STM2055, STM2094, STM2177, STM2438, STM2591, STM2601,...”
- Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium
Hu, Genetics 2006 - “...1766735-1766881 8 bp (dp) IG (STM1672, STM1673) 3062413-3062595 (Ec) 791460 456364 720484-720485 481632-481650 907035 6 (Ec) 1096771-1096774 1766792-1766799...”
- Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar typhimurium reveals phage-type- specific markers and potential for microarray typing
Hu, Journal of clinical microbiology 2002 - “...re- spectively, in an intergenic region between STM1672 and STM1673 at serovar Typhimurium LT2 genome sequence bases 1766792 to 1766799 (26). For both pairs of...”
Or search for genetic data about PF06004 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory