Family Search for PF06004 (DUF903)

PF06004 hits 23 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

3fifF / P65294 Crystal structure of the ygdr protein from e.Coli. Northeast structural genomics target er382a.
Aligns to 3:51 / 56 (87.5%), covers 100.0% of PF06004, 85.9 bits

• Ligand: peptide (3fifF)

Ent638_3274 protein of unknown function DUF903 (RefSeq) from Enterobacter sp. 638
Aligns to 23:71 / 72 (68.1%), covers 100.0% of PF06004, 85.7 bits

• Entericidin is required for a probiotic treatment (Enterobacter sp. strain C6-6) to protect trout from cold-water disease challenge
  Schubiger, Applied and environmental microbiology 2015
  • “...This analysis identified three hypothetical proteins (Ent638_0594, Ent638_3274, and Ent638_3824), an lpp repeatcontaining protein, and an entericidin B membrane...”

KPN_03160 hypothetical protein (RefSeq) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Aligns to 25:73 / 76 (64.5%), covers 95.9% of PF06004, 85.5 bits

• Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578
  Huang, BMC research notes 2014
  • “...0.0085 6.10 KPN_01977 Lysozyme inhibitor 9.57 12.45 0.0007 7.34 KPN_02742 Hypothetical 8.95 11.38 0.0057 5.40 KPN_03160 Hypothetical 11.17 13.82 0.0028 6.30 KPN_04221 Periplasmic repressor CpxP 10.08 12.49 0.0044 5.32 KPN_04433 Putative stress-response protein 9.46 11.81 0.0083 5.09 KPN_04512 a N-glycosyl-transferase PgaC 6.40 9.74 0.0003 10.13 KPN_04513...”

Z4126 hypothetical protein (NCBI) from Escherichia coli O157:H7 EDL933
Aligns to 25:73 / 76 (64.5%), covers 100.0% of PF06004, 85.5 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
  • “...0.02 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 +1.30 0.04 ygjT Z4441 Unknown 2.25 5.0E-03 yhaM...”
• Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies
  Pieper, PloS one 2011
  • “...19150 L (IM or OM) unkn 7180 37 LSAC 21 T 2 putative lipoprotein YgdI Z4126 (ygdI) 8342 L (IM or OM) unkn 5912 1112 LSAC 21 S 3 putative Bor protein of bacteriophage BP-933W Z1474 (borW) 10477 L (hydr LS) unkn 5666 0 ITGC 17...”

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
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, 84.8 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...”
• 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
• 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...”
• 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...”

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, 84.7 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...”
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...transport and metabolism Cell membrane 305 P64429 YPFJ General function prediction only Cell membrane 306 P65292 YGDI Function unknown Cell membrane 307 P67244 YQHA Function unknown Cell membrane 308 P0ACE0 MBHM Energy production and conversion Cell membrane 309 P0AFB1 NLPI Function unknown Cell membrane 310 P69741...”
• 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, 84.7 bits

• Cathelicidin Peptides Restrict Bacterial Growth via Membrane Perturbation and Induction of Reactive Oxygen Species.
  Rowe-Magnus, mBio 2019
  • “...protein yacH UTI89_C1870 1.34 5.84E05 Peptidoglycan d -transpeptidase ynhG UTI89_C0026 1.32 4.08E09 Hypothetical protein yaaY UTI89_C3182 1.31 4.40E09 Hypothetical protein ygdI UTI89_C0880 1.31 5.86E07 ATP-dependent endonuclease ybjD UTI89_C3181 1.30 1.36E04 Hypothetical protein ygdI UTI89_C2702 1.30 1.83E03 Two-component system acid-sensing sensor kinase evgS UTI89_C2303 1.29 1.31E03 Hypothetical...”
• High yield production process for Shigella outer membrane particles
  Berlanda, PloS one 2012
  • “...22 1 RpoE-regulated lipoprotein [S. flexneri 2a str. 301] SF2485 gi|24113773 23 1 hypothetical protein SSON_2966 [S. sonnei Ss046] SSON_2966 gi|74313380 24 1 lipoprotein [S. flexneri 2a str. 2457T] nlpB gi|30063856 25 2 entry exclusion protein 2 [S. sonnei Ss046] exc gi|145294038 26 2 LPS-assembly lipoprotein...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs2306 ECs2348 ECs2515 ECs2690 ECs2859 ECs2914 ECs3151 ECs3669 ECs3860 ECs4321 ECs4493 ECs4666 ECs4884 ECs5011 ECs5098 ECs5188 ECs5350 lpxC yceK hslJ mdtJ...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...cysJ -4.11 1 ECs3055 yeiL 2.38 2 ECs3655 ygdH 2.14 2 ECs3073 yejG 2.91 2 ECs3669 - 2.28 2 ECs3077 rplY -3.64 1 ECs3742 ygeV 3.64 2 ECs3078 yejK -2.55 1 ECs3750 ygfJ 4.14 2 ECs3102 ada 2.24 2 ECs3761 - 2.76 2 ECs3114 gyrA -3.38...”

B5XUP5 Putative lipoprotein from Klebsiella pneumoniae (strain 342)
Aligns to 23:71 / 72 (68.1%), covers 98.0% of PF06004, 84.4 bits

• Exposure of Aspergillus fumigatus to Klebsiella pneumoniae Culture Filtrate Inhibits Growth and Stimulates Gliotoxin Production
  Curtis, Journal of fungi (Basel, Switzerland) 2023
  • “...periplasmic glutathione-binding protein B5XYQ7 2 2.92 Inhibitor of vertebrate lysozyme B5Y004 2 15.54 Putative lipoprotein B5XUP5 1 36.1 Structurally bound Outer membrane protein A B5XY48 6 19.1 Chaperone protein DnaK B5Y242 2 2.7 jof-09-00222-t002_Table 2 Table 2 The Top 20 proteins most increased in abundance in...”

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, 83.1 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...”

STM1585 putative outer membrane lipoprotein (NCBI ptt file) from Salmonella typhimurium LT2
Aligns to 23:71 / 73 (67.1%), covers 98.0% of PF06004, 82.3 bits

• Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
  Han, Heliyon 2020
  • “...STM4263 inner membrane protein 1.1 0.008 STM1650 STM1650 putative reverse transcriptase 1.4 0.004 1.3 0.006 STM1585 STM1585 outer membrane lipoprotein 1.4 0.003 STM2240 STM2240 Protein of unknown function (DUF968) 1.1 0.006 STM1869A STM1869A glycoside hydrolase, family 19, chitinase 1.1 0.007 STM1870 STM1870 RecE-like protein 1.2 0.006...”

A6T9R7 YgdI/YgdR family lipoprotein from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
Aligns to 18:66 / 68 (72.1%), covers 100.0% of PF06004, 81.5 bits

• Identification of Outer Membrane and Exoproteins of Carbapenem-Resistant Multilocus Sequence Type 258 Klebsiella pneumoniae
  Brinkworth, PloS one 2015
  • “...protein 99.6 24 W8V0V3 YncD 701 3qIb Enantio-pyochelin receptor 100 19 2grx FhuA 100 24 A6T9R7 Hyp. 68 2k57 Sm-like ribonucleoprotein 99.9 25 2rb6 Sm-like ribonucleoprotein 99.9 45 W8UZI7 Slp 215 4f54 Vpi-5482 67 13 2vbc NS3 hydrolase/protease 46.1 18 W8V038 YdiY 252 2k0I OmpA 97.4...”

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, 79.9 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...”

PSPTO2350, PSPTO_2350 lipoprotein, putative (NCBI ptt file) from Pseudomonas syringae pv. tomato str. DC3000
Aligns to 25:73 / 74 (66.2%), covers 98.0% of PF06004, 79.8 bits

• Proteomic Profiling Reveals Distinct Bacterial Extracellular Vesicle Subpopulations with Possibly Unique Functionality
  McMillan, Applied and environmental microbiology 2023 (secret)
• 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...”

G3XCW5 YgdI/YgdR family lipoprotein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA3031 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 24:72 / 73 (67.1%), covers 100.0% of PF06004, 77.4 bits

• Pseudomonas aeruginosa and Staphylococcus aureus Display Differential Proteomic Responses to the Silver(I) Compound, SBC3
  Piatek, Antibiotics (Basel, Switzerland) 2023
  • “...interchange protein DsbG Q9I106 Disulfide bond formation +142.1 PA4578 Uncharacterised Q9HVK6 Unknown +43.7 PA3031 Uncharacterised G3XCW5 Unknown +27.1 PA2479 Probable two-component response regulator Q9I103 DNA binding +22.5 PA3205 Uncharacterised Q9HZ35 Unfolded protein binding +12.2 amrZ Transcription factor AmrZ G3XCY4 Transcription; transcription regulation +12.2 PA2523 Probable two-component...”
• Pseudomonas aeruginosa and Staphylococcus aureus Display Differential Proteomic Responses to the Silver(I) Compound, SBC3
  Piatek, Antibiotics (Basel, Switzerland) 2023
  • “...dsbG Thiol:disulfide interchange protein DsbG Q9I106 Disulfide bond formation +142.1 PA4578 Uncharacterised Q9HVK6 Unknown +43.7 PA3031 Uncharacterised G3XCW5 Unknown +27.1 PA2479 Probable two-component response regulator Q9I103 DNA binding +22.5 PA3205 Uncharacterised Q9HZ35 Unfolded protein binding +12.2 amrZ Transcription factor AmrZ G3XCY4 Transcription; transcription regulation +12.2 PA2523...”
• Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa
  Fraser-Pitt, Frontiers in cellular and infection microbiology 2021
  • “...NP_252418.1 hypothetical protein PA3729 Uncharacterised NP_253999.1 aldehyde dehydrogenase PA5312 pauC Polyamine catabolism NP_251721.1 hypothetical protein PA3031 Uncharacterised NP_253256.1 GTPase ObgE PA4566 obgE Response to stimulus NP_254244.1 ATP synthase F0F1 subunit delta PA5557 atpH ATP synthesis coupled proton transport NP_249578.1 acetyl-CoA synthetase PA0887 acsA Acetate utilisation NP_254101.1...”
• 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...”

BP2782 lipoprotein (NCBI) from Bordetella pertussis Tohama I
Aligns to 24:71 / 73 (65.8%), covers 100.0% of PF06004, 70.1 bits

• Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution
  Dienstbier, Emerging infectious diseases 2021
  • “...found that protein levels of hydroxymethylglutaryl-CoA lyase (BP3695), ArsR family transcriptional factor BP2946, small lipoprotein BP2782, and nicotinate-nucleotide diphosphorylase NadC were increased, but levels of several central metabolism enzymes (BP0624BP0629), tryptophan synthesis genes, and polysaccharide capsule proteins were decreased in recent isolates compared with historic strains...”
  • “...3.3 Capsular biosynthesis protein toh_01584 wza BP1628 6.8 2.2 Capsular polysaccharide export protein toh_02732 Group_1068 BP2782 3.9 3.0 Lipoprotein toh_02896 Group_128 BP2946 3.6 2.3 ArsR family transcriptional regulator toh_03214 trpD BP3262 2.1 1.4 Anthranilate phosphoribosyltransferase toh_03215 trpG BP3263 2.4 1.5 Anthranilate synthase component II toh_03216 trpE...”
• Immuno-proteomics analysis between OMV of vaccine and dominant wild type strains of Bordetella pertussis in Iran
  Badamchi, Iranian journal of microbiology 2020
  • “...protein 22.641 6 203 cytoplasm 15 BP3465 4.167 Uncharacterized protein 18.809 6.2 168 cytoplasm 16 BP2782 32.88 Lipoprotein 8.056 4.7 73 Outer membrane 17 adhI 9.239 S-(hydroxymethyl)glutathione dehydrogenase 39.4 6.2 368 periplasm 18 minD 60.89 Site-determining protein 29.6 5.2 271 cytoplasm 19 BP0103 59.2 Probable class...”
• 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:...”

H5409_13535 YgdI/YgdR family lipoprotein from Pseudomonas aeruginosa
PA2453 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 24:72 / 73 (67.1%), covers 98.0% of PF06004, 69.5 bits

• Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms
  Hao, BMC microbiology 2021
  • “...H5409_06535 VapC family toxin, conjugative transfer protein TrbJ, TrbL GI 4 2,864,029 2,901,720 37,691 H5409_13445- H5409_13535 Proteins involved in iron acquisition and virulence, IS4 family transposase, IS3 family transposase GI 5 4,885,149 4,896,402 11,253 H5409_22590- H5409_22650 tyrosine-type recombinase/integrase, adenylyltransferase GI 6 5,386,356 5,411,738 25,382 H5409_24840- H5409_24980...”
• Unraveling Pseudomonas aeruginosa and Candida albicans Communication in Coinfection Scenarios: Insights Through Network Analysis
  Grainha, Frontiers in cellular and infection microbiology 2020
  • “...24, 48 YNBNP MALDI-TOF MS/MS PAO1 SC5314 ( Purschke et al., 2012 ) Upregulation 3 PA2453 Downregulation Cell Biofilm 24, 48 YNBNP MALDI-TOF MS/MS PAO1 SC5314 ( Purschke et al., 2012 ) Upregulation 1.5, 4.5, 6 PA3313 Downregulation Cell Biofilm 24 YNBNP MALDI-TOF MS/MS PAO1 SC5314...”
• Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
  Crabbé, Applied and environmental microbiology 2011
  • “...PA2009 PA2021 PA2024 PA2225 PA2247 PA2248 PA2300 PA2321 PA2453 PA2570 PA2573 PA2612 PA2619 PA2620 PA2634 PA2639 PA2662 PA2743 PA2747 PA2753 PA2788 PA2851 PA2966...”
  • “...maiA hmgA PA2021 PA2024 PA2225 bkdA1 bkdA2 chiC PA2321 PA2453 palL PA2573 serS infA clpA PA2634 nuoD PA2662 infC PA2747 PA2753 PA2788 efp acpP rpmF PA2971...”

Ent638_0594 protein of unknown function DUF903 (RefSeq) from Enterobacter sp. 638
Aligns to 25:74 / 77 (64.9%), covers 95.9% of PF06004, 62.6 bits

• Entericidin is required for a probiotic treatment (Enterobacter sp. strain C6-6) to protect trout from cold-water disease challenge
  Schubiger, Applied and environmental microbiology 2015
  • “...This analysis identified three hypothetical proteins (Ent638_0594, Ent638_3274, and Ent638_3824), an lpp repeatcontaining protein, and an entericidin B...”

PSPTO_2366 lipoprotein, putative (NCBI ptt file) from Pseudomonas syringae pv. tomato str. DC3000
Aligns to 24:72 / 74 (66.2%), covers 98.0% of PF06004, 62.6 bits

• Proteomic Profiling Reveals Distinct Bacterial Extracellular Vesicle Subpopulations with Possibly Unique Functionality
  McMillan, Applied and environmental microbiology 2023 (secret)

PA5526 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 21:69 / 70 (70.0%), covers 95.9% of PF06004, 61.1 bits

• Genomic and transcriptomic characterization of Pseudomonas aeruginosa small colony variants derived from a chronic infection model.
  Irvine, Microbial genomics 2019
  • “...PA4387 NHmuc_04950 18 3.310 6 Molecular chaperone DnaK PA4761 NHmuc_05744 17 5.810 5 Putative lipoprotein PA5526 dapB 17 2.810 6 Dihydrodipicolinate reductase PA4759 hslV 17 4.110 7 ATP-dependent protease subunit PA5053 NHmuc_01173 16 4.710 6 Hypothetical protein PA2756 NHmuc_01024 16 6.110 7 Putative transporter PA4365 NHmuc_04180...”
• Pseudomonas aeruginosa rugose small-colony variants have adaptations that likely promote persistence in the cystic fibrosis lung
  Starkey, Journal of bacteriology 2009
  • “...PA2560 PA3340 PA3819 PA3901 PA4312 PA4624 PA4625 PA5212 PA5526 Gene PAO1wspF mutant Biolog profiles. (see Fig. S6 in the supplemental material). Clinical and...”
• Microarray analysis reveals induction of lipoprotein genes in mucoid Pseudomonas aeruginosa: implications for inflammation in cystic fibrosis
  Firoved, Infection and immunity 2004
  • “...Gene name Descriptionc Fold activation P value PA1323 PA3691 PA5526 PA3819 PA3692d PA4876 PA0737 PA1592 PA0062 lptE lptG slyB lptF osmE lptD lptA lptC Unknown...”
  • “...with AlgU promoter consensus sequence PA0737 PA1323 PA5526 PA1592 PA3262 PA3819 PA4876 Lpt-encoding genes with no discernible AlgU promoter consensus sequence...”

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 95.9% of PF06004, 60.7 bits

• Comparative profiling of Pseudomonas aeruginosa strains reveals differential expression of novel unique and conserved small RNAs
  Ferrara, PloS one 2012
  • “...bkdR 5070 SPA0078 I 2421/2422 33370/33380 + 2040 SPA0079 I 2763/2764 28350/28360 + 50 70 SPA0081 I 3069/3070 moxR /24440 + 90 SPA0084 I 3535/3536 + 18620/18630 7050 SPA0085 c I rsmZ rpoS / fdxA + 120 ; RsmZ SPA0086 I 3919/1920 13170/13190 + 70 430...”
• Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium
  Hu, Genetics 2006
  • “...TM3124_2 TM3211_1 TM3211_2d TM3230_1 TM3230_2 TM3230_3d TM3275_1d TM3275_2 G to A (ns, STM0080) C to A T to C C to T (s, dsbG) G to A G to T G to A A to...”
• RNA sequencing reveals differences between the global transcriptomes of Salmonella enterica serovar enteritidis strains with high and low pathogenicities
  Shah, Applied and environmental microbiology 2014
  • “...particular interest are genes encoding putative lipoproteins (SEN0081, yfbK, and ygdI). Bacterial lipoproteins perform various roles, including nutrient uptake,...”

KPN_00042 hypothetical protein (RefSeq) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Aligns to 25:74 / 77 (64.9%), covers 93.9% of PF06004, 58.5 bits

• Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578
  Huang, BMC research notes 2014
  • “...Gene product Expression level (wild-type) Expression level ( cps) p -value Fold change Up-regulated genes KPN_00042 Hypothetical 9.00 13.38 0.0021 20.82 KPN_00321 Hypothetical 6.63 9.20 0.0007 5.92 KPN_01030 Hypothetical 8.15 10.65 0.0170 5.66 KPN_01107 Hypothetical 9.41 13.32 0.0021 15.03 KPN_01226 Periplasmic protein 10.59 13.27 0.0052 6.38...”

STM1673 putative outer membrane lipoprotein (NCBI ptt file) from Salmonella typhimurium LT2
Aligns to 29:77 / 84 (58.3%), covers 98.0% of PF06004, 57.7 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...”

PMI1737 lipoprotein (RefSeq) from Proteus mirabilis HI4320
Aligns to 25:74 / 77 (64.9%), covers 93.9% of PF06004, 47.4 bits

• Transcriptome of swarming Proteus mirabilis
  Pearson, Infection and immunity 2010
  • “...PMI1472 PMI1616 PMI0360 PMI1730 PMI2268 PMI0047 PMI2036 PMI1737 PMI3401 PMI2890 PMI1509 PMI3701 PMI0952 PMI3204 PMI3115 PMI3449 Fold change Gene Annotation 9.09...”

Or search for genetic data about PF06004 in the Fitness Browser