Family Search for PF02639 (DUF188)

PF02639 hits 21 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

Spro_3465 protein of unknown function DUF188 from Serratia proteamaculans 568
Aligns to 18:147 / 152 (85.5%), covers 98.5% of PF02639, 175.3 bits

• The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus
  Vicente, BMC genomics 2016 (no snippet)

YPO3033 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 17:146 / 152 (85.5%), covers 98.5% of PF02639, 172.8 bits

• Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague
  Eichelberger, mSphere 2020
  • “...3.77 (1.25) 3.59 (3.00) YPO1299 fruK 1-Phosphofructokinase 1.89 (1.59) 2.00 (1.65) 3.99 (1.68) 4.09 (3.41) YPO3033 Hypothetical protein 6.29 (6.96) 6.16 (6.57) 6.22 (5.42) 6.56 (5.94) YPO0901 Hypothetical protein 2.72 (3.32) 2.61 (2.98) 3.07 (2.24) 3.41 (2.74) YPO2075 rnd Ribonuclease D 2.61 (2.87) 2.63 (2.67) 3.13...”

STM0387 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 17:146 / 151 (86.1%), covers 97.7% of PF02639, 166.6 bits

• Identification of novel factors involved in modulating motility of Salmonella enterica serotype typhimurium
  Bogomolnaya, PloS one 2014
  • “...bcfF 1.320.26 ** 2.550.64 STM0032 1.490.24 1.42 0.75 STM0098 1.650.37 1.460.29 STM0266 1.13 0.35 1.590.45 STM0387 yaiI 1.420.23 1.15 0.25 STM0549 fimZ 1.320.20 1.89 1.13 STM0557 gtrC 1.380.24 2.130.52 STM0573 1.14 0.17 1.640.32 STM0839 1.200.20 1.570.67 STM0847 ybiK 1.530.49 1.360.29 STM1087 pipA 1.300.22 1.500.35 STM1231 phoP...”

YaiI / b0387 DUF188 domain-containing protein YaiI from Escherichia coli K-12 substr. MG1655 (see paper)
yaiI / ECOCYC|G6230-MONOMER UPF0178 protein yaiI from Escherichia coli K12 (see paper)
b0387 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 17:146 / 152 (85.5%), covers 97.7% of PF02639, 165.2 bits

• Comprehensive classification of the PIN domain-like superfamily
  Matelska, Nucleic acids research 2017
  • “...range of taxonomic phyla, comprising YqxD from B. subtilis (BSU25230) and YaiI from Escherichia coli (b0387). Multiple sequence alignment of the family shows at least five conserved positions of acidic residues following the predicted core S1, S3 and S4 strands. The predicted secondary structure profile resembles...”
• Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons
  Macvanin, Journal of bacteriology 2007
  • “...b3824 b0654 b2258 b4539 b1317 b2277 b0638 b3564 b1746 b0387 b2896 b3960 b4221 b3603 b2725 Expression in the indicated medium (percentile)c LB M9 28 19 25 42...”
• A cross-genomic approach for systematic mapping of phenotypic traits to genes
  Jim, Genome research 2004
  • “...b1924 b0316 b1659 b1339 b0504 b3105 b1925 b1946 b0494 b0387 b2213 b2681 b3686 b3687 b3081 b0898 b4119 b1542 b2172 b4323 b1521 b3356 b3924 b1256 b1813 b2069...”

VP2328 conserved hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 17:146 / 147 (88.4%), covers 99.2% of PF02639, 157.5 bits

• 47th Annual Meeting March 1-5, 2003 Henry B. Gonzalez Convention Center, San Antonio, Texas : Wednesday Posters, Part 2
  , Biophysical journal 2003

ABBFA_000867 hypothetical protein from Acinetobacter baumannii AB307-0294
Aligns to 15:144 / 150 (86.7%), covers 97.7% of PF02639, 155.7 bits

• Polymyxin Resistance in Acinetobacter baumannii: Genetic Mutations and Transcriptomic Changes in Response to Clinically Relevant Dosage Regimens
  Cheah, Scientific reports 2016
  • “...1.66 7.02E-07 ABBFA_000601 HMPREF0010_02763 52.0% MFS transporter, metabolite:H+ symporter (MHS) family protein 0.59 0.69 5.28E-05 ABBFA_000867 HMPREF0010_02122 52.0% Hypothetical protein 0.43 0.71 3.25E-05 ABBFA_000206 HMPREF0010_02442 51.7% Methyltransferase domain protein 0.83 1.45 6.02E-06 ABBFA_003085 HMPREF0010_01789 51.7% Coniferyl aldehyde dehydrogenase (CALDH) 1.23 1.60 3.22E-06 ABBFA_000998 HMPREF0010_02245 51.3% Phthalate...”

HMPREF0010_02122 YaiI/YqxD family protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Aligns to 26:155 / 161 (80.7%), covers 97.7% of PF02639, 155.4 bits

• Polymyxin Resistance in Acinetobacter baumannii: Genetic Mutations and Transcriptomic Changes in Response to Clinically Relevant Dosage Regimens
  Cheah, Scientific reports 2016
  • “...7.02E-07 ABBFA_000601 HMPREF0010_02763 52.0% MFS transporter, metabolite:H+ symporter (MHS) family protein 0.59 0.69 5.28E-05 ABBFA_000867 HMPREF0010_02122 52.0% Hypothetical protein 0.43 0.71 3.25E-05 ABBFA_000206 HMPREF0010_02442 51.7% Methyltransferase domain protein 0.83 1.45 6.02E-06 ABBFA_003085 HMPREF0010_01789 51.7% Coniferyl aldehyde dehydrogenase (CALDH) 1.23 1.60 3.22E-06 ABBFA_000998 HMPREF0010_02245 51.3% Phthalate dioxygenase...”

Bphyt_5655 protein of unknown function DUF188 from Burkholderia phytofirmans PsJN
Aligns to 17:146 / 165 (78.8%), covers 98.5% of PF02639, 155.1 bits

• The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus
  Vicente, BMC genomics 2016 (no snippet)

CC1215 conserved hypothetical protein from Caulobacter crescentus CB15
Aligns to 17:146 / 153 (85.0%), covers 98.5% of PF02639, 154.9 bits

• Release of nonstop ribosomes is essential
  Feaga, mBio 2014
  • “...39 2,930 1.87 lepA 90 5,478 1.78 Efp 3 139 1.54 pth 0 24 1.39 CC1215 85,851 1,011 1.93 smpB 1,644 38 1.62 a Number of insertions normalized with respect to total number of insertions in ssrA background. b Ratio as calculated after adding 1 to...”
  • “...of transcription are represented with colored arrows. Genes with a high ratio include smpB and CC1215 ( Table1 ). Deletion of smpB in wild-type cells causes slow growth, but deletion of smpB in ssrA cells does not cause any additional growth defect, resulting in a relatively...”

CAETHG_RS07860 YaiI/YqxD family protein from Clostridium autoethanogenum DSM 10061
Aligns to 15:143 / 147 (87.8%), covers 99.2% of PF02639, 144.7 bits

• Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation
  de, Frontiers in bioengineering and biotechnology 2022
  • “...was used as the annotation genome, including only coding (CDS) and non-coding (ncRNA) sequences. Additionally, CAETHG_RS07860 was removed from the annotation and replaced with the carbon monoxide dehydrogenase genes with initial IDs of CAETHG_1620 and 1621 ( Brown et al., 2014 ) which were given the...”
• Absolute Proteome Quantification in the Gas-Fermenting Acetogen Clostridium autoethanogenum
  Valgepea, mSystems 2022
  • “...NC_022592.1 ( 69 ) was used as the annotation genome for C. autoethanogenum , with CAETHG_RS07860 being removed and replaced with the carbon monoxide dehydrogenase genes named CAETHG_RS07861 and CAETHG_RS07862 with initial identifications of CAETHG_1620 and CAETHG_1621, respectively. Functional categories were assigned to protein sequences with...”
• H₂ drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
  Valgepea, Biotechnology for biofuels 2018
  • “...annotation of sequence NC_022592.1 [ 59 ] was used as the annotation genome here, with CAETHG_RS07860 removed and replaced with the carbon monoxide dehydrogenase genes named CAETHG_RS07861 and CAETHG_RS07862 with initial IDs of CAETHG_1620 and 1621 [ 59 ], respectively. The workflow editor was used to...”

Q9KD45 UPF0178 protein BH1374 from Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
Aligns to 24:153 / 157 (82.8%), covers 98.5% of PF02639, 144.5 bits

• Protein signatures as potential surrogate biomarkers for stratification and prediction of treatment response in chronic myeloid leukemia patients.
  Alaiya, International journal of oncology 2016
  • “...Rv1290c P07083 1 0.000415 11.8324 CML-PBP-No-MMR CML-PBP-TKI-N Hypothetical 9.8 kDa protein in Gp55-nrdG intergenic region Q9KD45 2 1.21E-10 3.97407 CML-PBP-MMR CML-PBP-TKI-Y Hypothetical protein BH1374 P47679 2 0.000507 4.0852 CML-PBP-TKI-Y CML-PBP-TKI-N Hypothetical protein MG441 P42962 a 2 0.000554 9.91114 CML-PBP-TKI-Y CML-PBP-TKI-N Hypothetical protein ycsE P54462 2 2.28E-13...”

BSU25230 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
Aligns to 28:158 / 164 (79.9%), covers 99.2% of PF02639, 143.6 bits

• Comprehensive classification of the PIN domain-like superfamily
  Matelska, Nucleic acids research 2017
  • “...uncharacterized bacterial proteins from a wide range of taxonomic phyla, comprising YqxD from B. subtilis (BSU25230) and YaiI from Escherichia coli (b0387). Multiple sequence alignment of the family shows at least five conserved positions of acidic residues following the predicted core S1, S3 and S4 strands....”

EF_0842 YaiI/YqxD family protein from Enterococcus faecalis EnGen0310 = MMH594
Q837J5 UPF0178 protein EF_0842 from Enterococcus faecalis (strain ATCC 700802 / V583)
Aligns to 15:146 / 148 (89.2%), covers 98.5% of PF02639, 142.9 bits

• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...reductase Absent N/A 3 14.8 Q836Y3 3-demethylubiquinone-9 3-methyltransferase Absent N/A 2 12.1 Q837B9 UPF0178 protein EF_0842 Absent N/A 5 45.3 Q837J5 DUF1189 domain-containing protein Absent N/A 2 8.2 Q838I5 Putative N-acetylmannosamine-6-phosphate 2-epimerase Absent N/A 3 18.1 Q839T3 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase Absent N/A 4 15.2 Q839U9 PTS system,...”
• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...Q836Y3 3-demethylubiquinone-9 3-methyltransferase Absent N/A 2 12.1 Q837B9 UPF0178 protein EF_0842 Absent N/A 5 45.3 Q837J5 DUF1189 domain-containing protein Absent N/A 2 8.2 Q838I5 Putative N-acetylmannosamine-6-phosphate 2-epimerase Absent N/A 3 18.1 Q839T3 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase Absent N/A 4 15.2 Q839U9 PTS system, IIB component* Absent N/A 8...”

SERP0336 hypothetical protein from Staphylococcus epidermidis RP62A
Aligns to 17:148 / 149 (88.6%), covers 98.5% of PF02639, 141.2 bits

• Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
  Sivaranjani, Frontiers in microbiology 2019
  • “...1.27 2.15 10 -08 SERP2326 Acetoin dehydrogenase, E1 component, alpha subunit 1.63 3.39 10 -08 SERP0336 Conserved hypothetical protein 2.02 3.46 10 -08 SERP1988 sumT Uroporphyrinogen-III methylaseSirB, putative 1.85 1.02 10 -07 SERP0216 Hexulose phosphate synthase, putative 1.31 1.05 10 -07 SERP1782 Alkaline shock protein 23...”
• Gram-positive three-component antimicrobial peptide-sensing system
  Li, Proceedings of the National Academy of Sciences of the United States of America 2007
  • “...Further up-regulated genes 3.23* 3.93* SE0106 SERP0020 SERP0336 SERP0387 Arginine deiminase (EC 3.5.3.6) ABC transporter permease protein EMG2 protein...”

SA0636 hypothetical protein from Staphylococcus aureus subsp. aureus N315
Aligns to 16:147 / 152 (86.8%), covers 98.5% of PF02639, 139.5 bits

• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...acyl-carrier sa_c312s155_a_at 20.3 2.5 2.5 fabH SA0987 3-oxoacyl-(acyl-carrier-protein) synthase III sa_c7805s6807_a_at 2.2 2.5 2.5 mvk SA0636 mevalonate kinase sa_c1256s1031_a_at 7.9 2.5 2.5 plsX SA1243 putative glycerol-3-phosphate acyltransferase sa_c7092s6204_a_at 5.8 2.5 2.5 SA0426 acetyl-CoA acetyltransferase sa_c8003s6987_a_at 4.5 2.5 ND SA0708 DAK2 domain protein sa_c8019s7004_a_at 5.2 2.5 2.5...”
• Transcription Profiling of the mgrA Regulon in Staphylococcus aureus
  Luong, Journal of bacteriology 2006
  • “...CYL907 contains a Tn917 insertion (at the hypothetical gene SA0636 of N315) that is not present in strain Newman and CYL1050. To ensure that this insertion does...”

SACOL0741 hypothetical protein from Staphylococcus aureus subsp. aureus COL
NWMN_0650 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
Aligns to 16:147 / 152 (86.8%), covers 98.5% of PF02639, 139.3 bits

• Global analysis of the Staphylococcus aureus response to mupirocin
  Reiss, Antimicrobial agents and chemotherapy 2012
  • “...SACOL0678, SACOL0679, SACOL0680, SACOL0681, SACOL0682, SACOL0684, SACOL0685, SACOL0741, SACOL0742, SACOL2136, SACOL2174, and sarA) (Table 3; see Table S2 in the...”
• Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions
  McClary, Frontiers in microbiology 2018
  • “...Fold change FDR (%) hemY Protoporphyrinogen oxidase 5.97 3.1 NWMN_1978 Conserved hypothetical protein 5.64 13.0 NWMN_0650 Conserved hypothetical protein 4.50 5.5 NWMN_1466 Conserved hypothetical protein 4.16 7.9 vraB Acetyl-CoA C-acetyltransferase VraB 3.57 9.3 NWMN_1608 Conserved hypothetical protein 3.54 5.0 NWMN_2520 Conserved hypothetical protein 3.35 5.3 narG...”

SAR0734 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
Aligns to 16:147 / 152 (86.8%), covers 98.5% of PF02639, 139.1 bits

• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...protein 2.01 4.80E-04 SAR0721 multicopper oxidase protein 2.29 4.39E-03 SAR0733 conserved hypothetical protein 3.04 1.99E-03 SAR0734 conserved hypothetical protein 2.23 1.59E-03 SAR0821 conserved hypothetical protein 3.19 6.54E-03 SAR0825 conserved hypothetical protein 5.06 1.86E-03 SAR0840 putative membrane protein 5.25 2.63E-03 SAR0849 hypothetical protein 2.81 6.05E-03 SAR0850 hypothetical...”

D5ANM3 UPF0178 protein RCAP_rcc00612 from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)
Aligns to 15:145 / 148 (88.5%), covers 100.0% of PF02639, 138.1 bits

• Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins
  Selamoglu, Metallomics : integrated biometal science 2020
  • “...29 Rcc00088 D5AKL1 Uncharacterized metal-sensing transcriptional regulator CsoR ( csoR ) C nr - Rcc00612 D5ANM3 Periplasmic protein CusF ( cusF ) P nr - Rcc00613 D5ANM4 Transcriptional regulator, TetR family CusR ( cusR ) C nr - Rcc00614 D5ANM5 RND efflux system, CusC ( cusC...”

LMRG_00908 hypothetical protein from Listeria monocytogenes 10403S
Aligns to 16:145 / 146 (89.0%), covers 98.5% of PF02639, 127.4 bits

• Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σ^B
  Liu, Frontiers in microbiology 2017
  • “...No Host factor-I protein 8 LMRG_00884 LMRG_00885 B , A No 9 LMRG_00906 LMRG_00910, LMRG_00909, LMRG_00908, LMRG_00907 A , H , B No RpoD ( A ) 10 LMRG_01076, LMRG_01077 LMRG_01078, LMRG_01079, LMRG_01080 A , B LMRG_01078, LMRG_01079, LMRG_01080 11 LMRG_01140 A , B No Alpha-acetotactate...”
  • “...TU, is co-transcribed from an upstream B -dependent promoter, a H -dependent promoter upstream of LMRG_00908 and a A -dependent promoter upstream of LMRG_00911. Strong expression from the A -dependent promoter as well as the absence of H may explain why no significant differential expression of...”
• An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes
  Liu, BMC genomics 2016
  • “...control strain BCHL::P rha , which does not contain sigH . These 5 genes represented LMRG_00908, LMRG_00935 ( comEA ), LMRG_00937 ( comEC ), LMRG_01629 ( lytG ), and LMRG_01643 ( coiA ) (see Additional file 1 : Table S1). A total of four H -dependent...”
  • “...], these 5 H -dependent genes were found to represent 2 multigene operons, including (i) LMRG_00908, LMRG_00907 ( dnaG ) and LMRG_00906 ( rpoD ); and (ii) LMRG_00935 ( comEA ), LMRG_00936 ( comEB ) and LMRG_00937 ( comEC )) and 2 monocistronic genes, coiA and...”

Q71ZL4 UPF0178 protein LMOf2365_1475 from Listeria monocytogenes serotype 4b (strain F2365)
LMOf2365_1475 hypothetical protein from Listeria monocytogenes str. 4b F2365
Aligns to 16:145 / 146 (89.0%), covers 98.5% of PF02639, 126.8 bits

• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...0.613 Non-allergen 162 Q71XW0 0.917 Non-allergen 163 Q720B7 0.621 Non-allergen 164 Q721A0 0.643 Non-allergen 165 Q71ZL4 0.912 Non-allergen `166 Q721A5 0.545 Non-allergen 167 Q71YW0 0.48 Non-allergen 168 Q2N761 1.386 Non-allergen 169 L9WZX9 0.694 Non-allergen 170 A0A0X1KHF9 0.575 Non-allergen 171 Q1KT30 0.508 Non-allergen 172 Q1KT48 0.458 Non-allergen...”
  • “...VILLKLFHV 49.4 1.5441 Antigen Q724P3 DRB1_1301 IRCKYTKTR 22.7 2.0203 Antigen DRB1_1301 RCKYTKTRR 43 1.5601 Antigen Q71ZL4 DRB1_1301 LMLDIRYRH 33.2 1.656 Antigen DRB1_1301 SLMLDIRYR 35.4 1.4323 Antigen Q2N761 DRB1_0101 LLSLSPELF 1010 1.2376 Antigen DRB1_0101 WLLSLSPEL 1136 2.0048 Antigen DRB1_0101 NVAIRTLRL 1262 1.4269 Antigen DRB1_0701 WLLSLSPEL 59.8 2.0048...”
• Genetic analysis of the Staphylococcus epidermidis macromolecular synthesis operon: Serp1129 is an ATP binding protein and sigA transcription is regulated by both sigma(A)- and sigma(B)-dependent promoters
  Bryant, BMC microbiology 2010
  • “...does not have a yqxD orthologue as found in B. subtilis and L. monocytogenes ( Lmof2365_1475 ). yqxD and Lmof2365_1475 share 48% amino acid identity [ 17 ]. Just upstream of dnaG in S. epidermidis were two ORFs, serp1129 and serp1130 . An ortholog of serp1129...”

BAPKO_0028 hypothetical protein from Borrelia afzelii PKo
Aligns to 19:142 / 143 (86.7%), covers 95.4% of PF02639, 78.0 bits

• Proteomic as an Exploratory Approach to Develop Vaccines Against Tick-Borne Diseases Using Lyme Borreliosis as a Test Case
  Talagrand-Reboul, Vaccines 2020
  • “...gi|365823340 1 1 hypothetical protein BB_J48 gi|364556751 1 hypothetical protein BAPKO_4515 gi|117621815 1 hypothetical protein BAPKO_0028 gi|111114851 1 hypothetical protein BAPKO_0593 gi|111115391 1 hypothetical protein BAPKO_2500 gi|117621647 1 50S ribosomal protein L7/L12 gi|123046997 1 30S ribosomal protein S16 gi|123145645 1 1 Neutrophil activating protein gi|111115523 2...”

Or search for genetic data about PF02639 in the Fitness Browser