Family Search for PF02639 (DUF188)
Running HMMer for PF02639
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
YPO3033 conserved hypothetical protein from Yersinia pestis CO92
Aligns to 17:146 / 152 (85.5%), covers 98.5% of PF02639, 172.8 bits
STM0387 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 17:146 / 151 (86.1%), covers 97.7% of PF02639, 166.6 bits
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
VP2328 conserved hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 17:146 / 147 (88.4%), covers 99.2% of PF02639, 157.5 bits
ABBFA_000867 hypothetical protein from Acinetobacter baumannii AB307-0294
Aligns to 15:144 / 150 (86.7%), covers 97.7% of PF02639, 155.7 bits
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
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
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
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 V583
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
SA0636 hypothetical protein from Staphylococcus aureus subsp. aureus N315
Aligns to 16:147 / 152 (86.8%), covers 98.5% of PF02639, 139.5 bits
NWMN_0650 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SACOL0741 hypothetical protein from Staphylococcus aureus subsp. aureus COL
Aligns to 16:147 / 152 (86.8%), covers 98.5% of PF02639, 139.3 bits
- 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...”
- 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...”
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
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
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 σB
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...”
LMOf2365_1475 hypothetical protein from Listeria monocytogenes str. 4b F2365
Q71ZL4 UPF0178 protein LMOf2365_1475 from Listeria monocytogenes serotype 4b (strain F2365)
Aligns to 16:145 / 146 (89.0%), covers 98.5% of PF02639, 126.8 bits
BAPKO_0028 hypothetical protein from Borrelia afzelii PKo
Aligns to 19:142 / 143 (86.7%), covers 95.4% of PF02639, 78.0 bits
Or search for genetic data about PF02639 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory