Family Search for PF04239 (DUF421)

PF04239 hits 16 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

NP_388595 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
O31533 UPF0702 transmembrane protein YetF from Bacillus subtilis (strain 168)
BSU07140 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
Aligns to 81:215 / 231 (58.4%), covers 98.5% of PF04239, 156.8 bits

• Identification and characterization of new proteins crucial for bacterial spore resistance and germination
  Yu, Frontiers in microbiology 2023
  • “...homologs of B. subtilis YetF was conducted using its amino acid sequence (GenBank accession number NP_388595) as a query on the SubtiWiki server. 2 The search included completed genomes of a variety of Bacilli and Clostridia species, both spore forming and asporogenous species, though not all...”
• Membrane Proteomes and Ion Transporters in Bacillus anthracis and Bacillus subtilis Dormant and Germinating Spores
  Chen, Journal of bacteriology 2019
  • “...P35160 O32047 P16336 P40868 P40869 P31845 Q02115 P42199 O31533 O34348 O34348 O34348 O31656 O07634 O31816 O31816 P38490 P54178 P54481 C0SP90 O05241 O32128 P39668...”
• rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2
  Liu, BMC biotechnology 2022
  • “...Up BSU00640 30.035 135.911 2.17 1.36E-05 1.06E-03 Up BSU00650 107.821 484.02 2.17 1.50E-05 1.14E-03 Up BSU07140 30.763 135.31 2.13 3.92E-05 2.80E-03 Up BSU32850 3.438 15.261 2.12 1.31E-03 4.18E-02 Up BSU30270 9.623 41.992 2.11 6.52E-05 4.32E-03 Up BSU00830 81.386 319.295 1.97 6.36E-05 4.30E-03 Up BSU28060 23.9 93.458...”
• Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant
  Gibbons, PloS one 2011
  • “...Identity) Mutation AA change Position in protein/total length 246382 BG236 (01550) PS yetF hypothetical protein BSU07140 (73.9) C:T * 217/231 259001 BG250 (12250) SYN yfnL hypothetical protein BSU07230 (91.5) C:T 419580 BG405 (02000) 1 bp INS katA vegetative catalase BSU08820 (94.4) +T 197/483 546358 BG536 (02620)...”

Q812J9 Hypothetical Membrane Associated Protein from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
Aligns to 84:217 / 289 (46.4%), covers 100.0% of PF04239, 150.3 bits

• Identification and characterization of new proteins crucial for bacterial spore resistance and germination
  Yu, Frontiers in microbiology 2023
  • “...to B. subtilis YetF (UniProt ID Q813Q8), as well as a 2Duf homolog (UniProt ID Q812J9), were also present in the B. cereus spore IM proteome (iBAQ ranks 559 and 626, respectively out of 1,254), but not in vegetative cells or the vegetative cell membrane fraction...”

Q813Q8 Hypothetical Membrane Associated Protein from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
Aligns to 81:216 / 228 (59.6%), covers 99.3% of PF04239, 145.6 bits

• Identification and characterization of new proteins crucial for bacterial spore resistance and germination
  Yu, Frontiers in microbiology 2023
  • “...germination. The B. cereus homolog with the best match to B. subtilis YetF (UniProt ID Q813Q8), as well as a 2Duf homolog (UniProt ID Q812J9), were also present in the B. cereus spore IM proteome (iBAQ ranks 559 and 626, respectively out of 1,254), but not...”

CPR_1348 hypothetical protein from Clostridium perfringens SM101
Aligns to 78:212 / 232 (58.2%), covers 98.5% of PF04239, 143.0 bits

• Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics
  Xiao, PloS one 2015
  • “...hmp ) Uncharacterized (S COGs) CPR_1859 ( ytxC ), CPR_0147 (CD1511), CPR_1448 (CD3032), CPR_2589 (CD3613) CPR_1348 ( ydfR/ydfS ), CPR_2517( yerB ), CPR_1333 ( yhbH ), CPR_1731 ( ymxH ), CPR_1929 ( yunB ), CPR_1626 ( yuzA ), CPR2663 ( yyaC ), CPR2565 ( yyaD/ykvI ),...”

BAS4309 conserved hypothetical protein from Bacillus anthracis str. Sterne
Aligns to 80:204 / 215 (58.1%), covers 99.3% of PF04239, 137.5 bits

• Membrane Proteomes and Ion Transporters in Bacillus anthracis and Bacillus subtilis Dormant and Germinating Spores
  Chen, Journal of bacteriology 2019
  • “...have highly similar proteins in B. anthracis (BAS4465, BAS4309, and BAS5195, respectively) but were detected only in B. subtilis. Membrane protein changes...”

CD1789 hypothetical protein from Clostridium difficile 630
Q187A0 Membrane protein from Clostridioides difficile (strain 630)
Aligns to 78:206 / 219 (58.9%), covers 99.3% of PF04239, 137.4 bits

• Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile
  Soutourina, Frontiers in microbiology 2020
  • “...TSS, the expression of CD2266 , CD2599 and CD2856 was only controlled by SigF. Unexpectedly, CD1789 , CD2245.1 and sigG were controlled by SigG but not by SigF despite the fact that a consensus recognized by SigF is proposed upstream of these genes ( Supplementary Tables...”
• Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile
  Saujet, PLoS genetics 2013
  • “...protein 0.31 0.38 CD3551.1 Putative membrane protein 0.11 0.18 G CD2051 Putative membrane protein 0.52 CD1789 Putative membrane protein, DUF421 family 0.61 G + CD1789-CD1788 CD1788 Conserved hypothetical protein 0.43 CD2465 Putative amino acid/polyamine transporter 0.36 0.52 G + stress CD1567 cotG putative manganese catalase 0.25...”
  • “...has been recently identified [48] . Nine genes encoding probable membrane proteins (CD0792, CD0793, CD1677, CD1789, CD2051, CD2465, CD2635, CD2636, CD3551.1) were downregulated in the sigG mutant and these proteins may be involved in germination. 55% of our G -controlled genes encode proteins associated to the...”
• Identification and characterization of new proteins crucial for bacterial spore resistance and germination.
  Yu, Frontiers in microbiology 2023
  • “...2021 ). In addition, the one C. difficile spores 219 aa YetF homolog (UniProt ID Q187A0) was also identified in these spores IM proteome, with an approximate abundance at the median out of 1,021 proteins identified; this protein was also absent from the vegetative cell membrane...”

SM12261_0438 DUF421 domain-containing protein from Streptococcus mitis NCTC 12261
Aligns to 82:201 / 211 (56.9%), covers 99.3% of PF04239, 131.8 bits

• High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes
  Salvadori, BMC genomics 2018
  • “...uptake comFA SM12261_0765 TTTTT 9- TACGAATA 25- ATG SMSK321_1614 TTTT 0- TACGAATA 7- ATG cilC SM12261_0438 TTTTT 0- TACGAATA 7- ATG SMSK321_1050 TTTTT 0- TACGAATA 7- ATG comEA SM12261_1388 TTTTTT 8- TACGAATA 19- ATG SMSK321_0421 TTTTTT 8- TACGAATA 19- ATG Fratricide cbpD SM12261_0760 TTTTTTT 1- T...”

LACR_2411 Predicted membrane protein from Lactococcus lactis subsp. cremoris SK11
Aligns to 81:200 / 211 (56.9%), covers 98.5% of PF04239, 128.3 bits

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...protein positive 3.3 LACR_0629 major facilitator superfamily permease positive 0.3 LACR_0164 hypothetical protein positive 3.8 LACR_2411 hypothetical protein negative 0.9 LACR_1362 transcriptional regulator positive 1.1 LACR_0982 ring-cleavage extradiol dioxygenase positive 3.6 LACR_0742 transcriptional regulator positive 2.0 LACR_0537 cysteine synthase positive 0.4 LACR_0743 flavodoxin positive 1.2 LACR_D16...”

Ddes_1374 protein of unknown function DUF421 from Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774
Aligns to 89:208 / 248 (48.4%), covers 97.0% of PF04239, 108.3 bits

• Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria
  Martínez-del, mBio 2015
  • “...of the cut cluster and the genes immediately upstream ( Ddes_1354 ) and downstream ( Ddes_1374 ) during growth on lactate and choline ( Fig.2A ). Transcript levels of all 19 cut genes increased dramatically during growth on choline relative to growth on lactate (49- to...”
  • “...that expression is induced in response to substrate. While the gene downstream of cutS ( Ddes_1374 ) was expressed at the same level in both media, we detected a 32-fold induction of the gene upstream of cutA , the predicted transporter Ddes_1354 , in the presence...”

EC958_1062 DUF421 domain-containing protein from Escherichia coli O25b:H4-ST131
c1044 Hypothetical protein ycaP from Escherichia coli CFT073
Aligns to 96:186 / 230 (39.6%), covers 53.3% of PF04239, 62.3 bits

• Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131
  Ben, mBio 2016
  • “...small permease protein (DctQ-like) 1001668 T T C C C C C C C Syn EC958_1062 115 ycaP Hypothetical protein 1167464 C C T T T T T T T CR EC958_1238 268 ymdC Putative synthase 1317794 G G A A A A A A A...”
• Fortieth Annual Meeting February 17-21, 1996 Baltimore Convention Center Baltimore, Maryland : Tuesday Symposia and Posters, Part V
  , Biophysical journal 1996
• A C-terminal domain of GAP is sufficient to stimulate ras p21 GTPase activity
  Marshall, The EMBO journal 1989 (secret)

YcaP / b0906 DUF421 domain-containing protein YcaP from Escherichia coli K-12 substr. MG1655
b0906 conserved inner membrane protein from Escherichia coli str. K-12 substr. MG1655
P75839 UPF0702 transmembrane protein YcaP from Escherichia coli (strain K12)
Aligns to 96:186 / 230 (39.6%), covers 53.3% of PF04239, 62.3 bits

• Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
  Mariño-Ramírez, Journal of bacteriology 2004
  • “...yphG yqeB yqjI yrbD yrbK ysgA ytfH ytfL b0866 b0897 b0906 b1011 b1067 b1253 b1284 b1299 b1359 b1547 b1606 b1669 b1800 b1853 b1834 b1970 b2007 b2101 b2157 b2160...”
• Functional Prediction of Biological Profile During Eutrophication in Marine Environment
  Sbaoui, Bioinformatics and biology insights 2022
  • “...P77359 Putative chaperone with DnaJ-like domain YbgG P54746 Putative sugar hydrolase with alpha-mannosidase domain YcaP P75839 DUF421 domain-containing protein YcdG P75892 Putative uracil transport protein (NCS2 family) YcfJ P0AB35 Putative membrane protein YcgR P76010 Flagellar brake protein YdeP P77561 Putative formate dehydrogenase, related to acid resistance...”

ECs0989 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 96:187 / 230 (40.0%), covers 51.9% of PF04239, 62.1 bits

• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...lrp -3.19 1 ECs0201 abc -3.32 1 ECs0979 dmsA -3.37 4 ECs0216 O157 2.02 2 ECs0989 ycaP 2.56 2 ECs0248 fadE 4.57 2 ECs0990 serC -3.29 1 ECs0253 dinJ 2.46 2 ECs0991 aroA -4.24 1 ECs0269 proB -2.11 1 ECs1007 mukB -2.12 1 ECs0383 yahO 4.53...”

KP1_2896 hypothetical protein from Klebsiella pneumoniae NTUH-K2044
Aligns to 77:148 / 148 (48.6%), covers 51.9% of PF04239, 57.0 bits

• YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43
  Huang, PloS one 2013
  • “...ParB family protein HP 3.3 KP1_2152 formylglycine generating sulfatase 2.6 KP1_3378 Membrane anchored protein 2 KP1_2896 Table2 and 3 . Significantly upregulated and downregulated genes by YjcC overexpression. The selected genes show more than 2 log 2 fold change (in absolute value) in the abundance of...”

MSMEG_1844 hypothetical protein from Mycobacterium smegmatis str. MC2 155
Aligns to 95:170 / 174 (43.7%), covers 50.4% of PF04239, 51.1 bits

• The SigF regulon in Mycobacterium smegmatis reveals roles in adaptation to stationary phase, heat, and oxidative stress
  Hümpel, Journal of bacteriology 2010
  • “...MSMEG_1435 MSMEG_1440 MSMEG_1698 MSMEG_1742 MSMEG_1784 MSMEG_1844 MSMEG_1919 MSMEG_2200d MSMEG_2335 MSMEG_2425 MSMEG_2466 MSMEG_2780 MSMEG_2804 MSMEG_2837...”

MSMEG_4414 hypothetical protein from Mycobacterium smegmatis str. MC2 155
Aligns to 93:174 / 179 (45.8%), covers 51.9% of PF04239, 43.7 bits

• Genome-Wide Transcriptome Profiling of Mycobacterium smegmatis MC² 155 Cultivated in Minimal Media Supplemented with Cholesterol, Androstenedione or Glycerol
  Li, International journal of molecular sciences 2016
  • “...MSMEG_1150 MSMEG_1364 MSMEG_1375 MSMEG_1435 MSMEG_1448 MSMEG_2705 MSMEG_2713 MSMEG_6115 MSMEG_6125 MSMEG_2854 MSMEG_2865 MSMEG_2854 MSMEG_2861 MSMEG_3997 MSMEG_4005 MSMEG_4414 MSMEG_4427 MSMEG_4419 MSMEG_4427 MSMEG_4835 MSMEG_4843 MSMEG_4461 MSMEG_4468 MSMEG_5953 MSMEG_5966 MSMEG_4864 MSMEG_4873...”

BPSS2213 putative membrane protein from Burkholderia pseudomallei K96243
Aligns to 96:167 / 167 (43.1%), covers 51.1% of PF04239, 38.8 bits

• BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei
  Capelli, Antibodies (Basel, Switzerland) 2018
  • “...candidate proteins based on the initial set of eight B. pseudomallei proteomes. Remarkably, only four (BPSS2213, BPSS1498, BPSL1626, and BPSS1267) of the 104 proteins were fully conserved in the strains analyzed. The sequence variability of these four proteins with 349 B. pseudomallei strains is indicated in...”
  • “...methods adopted and applied to the dimer structure of BPSL1626; Figure S1: Variability profile of BPSS2213, BPSS1498, BPSS1267 and BPSL1626 generated from multiple protein sequence alignments using 349 B. pseudomallei strains; Figure S2: Raw epitope prediction data made with structure- and sequence-based predictors. Click here for...”

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