Family Search for PF04235 (DUF418)

PF04235 hits 15 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

ECs3044 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 215:375 / 385 (41.8%), covers 99.4% of PF04235, 161.9 bits

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ECs5045 ECs1716 ECs3398 ECs4148 ECs0006 ECs0251 ECs1263 ECs2557 ECs3044 ECs3978 ECs4146 ECs4425 ECs4496 ECs5042 b3283 b3700 b2571 b1422 b2531 b3067 b3649 b3783...”

YeiB / b2152 DUF418 domain-containing protein YeiB from Escherichia coli K-12 substr. MG1655
P25747 Uncharacterized protein YeiB from Escherichia coli (strain K12)
b2152 conserved inner membrane protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 215:375 / 385 (41.8%), covers 99.4% of PF04235, 161.7 bits

• Enabling QTY Server for Designing Water-Soluble α-Helical Transmembrane Proteins
  Tao, mBio 2022
  • “...P15078 (CstA; 5 TM helices), P23482 (HyfB; 6 TM helices), P23930 (Lnt; 7 TM helices), P25747 (YeiB; 8 TM helices), P26459 (AppC; 9 TM helices), P31553 (CaiT; 10 TM helices), P32705 (ActP; 11 TM helices), P33607 (NuoL; 12 TM helices), P37019 (ClcA; 13 TM helices), P0AFE8...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...b1211 b2532 b3282 b0006 b0224 b1016 b1847 b2152 b3096 b3280 b3546 b3618 b4060 Signal transduction mechanisms Transcription Predicted methyltransferase Predicted...”

y2663 hypothetical protein from Yersinia pestis KIM
Aligns to 219:379 / 391 (41.2%), covers 98.8% of PF04235, 159.6 bits

• Yersinia pestis kills Caenorhabditis elegans by a biofilm-independent process that involves novel virulence factors
  Styer, EMBO reports 2005
  • “...oxidase subunit II Attenuated P 1/4 0.0001 23 5F1 y2663 Putative membrane protein Wild type P 1/4 1.000 23 6B4 y3913a Putative RNase R exoribonuclease ND ND...”

SC2208 putative inner membrane protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Aligns to 215:375 / 380 (42.4%), covers 99.4% of PF04235, 155.1 bits

• Use of pulsed field gel electrophoresis and transposon mutagenesis to estimate the minimal number of genes required for motility in Caulobacter crescentus
  Ely, Genetics 1989
  • “...( J ~ - 6 2 0 )SC2190 , ( f l ~ - 6 2 7 )SC2208 , (Ja-655), SC2249 ( f l ~ - 6 5 6 )SC3525 , (Ju659), SC3592 ( f l ~ - 6 1 2 )SC3598 , (Ju-661) 400 1040 D 165 A...”

STM14_2702 DUF418 domain-containing protein YeiB from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Aligns to 215:375 / 380 (42.4%), covers 99.4% of PF04235, 155.1 bits

• Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions
  Bourgeois, mBio 2022
  • “...NC_016856.1 __1834122 100 84 16 STM14_2089 trpB Genic CAGA*G 2.13 NC_016856.1 __2340851 98 81 17 STM14_2702 NA Genic GA*TC 2.79 NC_016856.1 __2746393 100 88 12 STM14_3133 NA Genic GATCA*G 1.80 NC_016856.1 __3270917 100 88 12 STM14_3733 metK Genic GA*TC 3.21 NC_016856.1 __3272719 100 88 12 STM14_3735...”

XF0651 transport protein from Xylella fastidiosa 9a5c
Aligns to 261:419 / 430 (37.0%), covers 98.8% of PF04235, 146.2 bits

• Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
  Meidanis, Microbiology and molecular biology reviews : MMBR 2002
  • “...and 4 TMSs Undefined Undefined Undefined Undefined Undefined XF0651 XF1192 XF0406 XF0772 XF0947 XF1025 XF1245 XF1454 XF0766 XF0383 XF0666 XF0757 XF2762 XF0140...”

BAS1477 membrane protein, putative from Bacillus anthracis str. Sterne
BA1593 membrane protein, putative from Bacillus anthracis str. Ames
Aligns to 217:376 / 387 (41.3%), covers 100.0% of PF04235, 143.0 bits

• Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
  Kudva, Infection and immunity 2005
  • “...BA5604 367 BAS5183 BA5578 380 BAS5217 BA5615 545 739 BAS1477 BAS1135 BA1593 BA1228 862 812d BAS5285 BAS0638 BA5681 BA0672 355 239 BAS0637 BAS1246 BAS4444 BA0670...”
• Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
  Kudva, Infection and immunity 2005
  • “...BA5578 380 BAS5217 BA5615 545 739 BAS1477 BAS1135 BA1593 BA1228 862 812d BAS5285 BAS0638 BA5681 BA0672 355 239 BAS0637 BAS1246 BAS4444 BA0670 BA1346 BA4789...”

BTHUR0008_RS07395 DUF418 domain-containing protein from Bacillus thuringiensis serovar berliner ATCC 10792
Aligns to 217:376 / 387 (41.3%), covers 100.0% of PF04235, 139.2 bits

• Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets
  Manga, Frontiers in microbiology 2016
  • “...threshold due to minor deviations from the set limits. For example, one of the genes BTHUR0008_RS07395 had a difference of 0.04 between the log 2-fold values from four and three replicates and thus fell below the fold-change cut-off with a difference of 0.02; yet another gene...”

SO_1396 conserved hypothetical protein from Shewanella oneidensis MR-1
Aligns to 233:386 / 399 (38.6%), covers 99.4% of PF04235, 127.0 bits

• Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences
  Cheng, Nucleic acids research 2022
  • “...at SO_0986 in S. oneidensis MR-1 This work MR-1/S4 Insertion of chloramphenicol resistance gene at SO_1396 in S. oneidensis MR-1 This work MR-1/S5 Insertion of chloramphenicol resistance gene at SO_1779 in S. oneidensis MR-1 This work MR-1/S6 Insertion of chloramphenicol resistance gene at SO_2727 in S....”
• Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis
  Sekar, Applied and environmental microbiology 2016
  • “...a mutation in an unknown membrane protein (SO_1396) resulting in a glutamine-to-histidine conversion at amino acid position 207. Homology modeling demonstrated...”
  • “...Primers used in this studya Gene/operon Q207H SO_1396 (knockout) SO_4230 (knockout) SO_0900 (cloning) SO_4673 (cloning) SO_4230 (cloning) SO_1396Q207H (cloning)...”

F1721_27895 DUF418 domain-containing protein from Saccharopolyspora hirsuta
Aligns to 180:339 / 361 (44.3%), covers 92.0% of PF04235, 111.4 bits

• Insight into Different Stages of Steroid Degradation in Thermophilic Saccharopolyspora hirsuta VKM Ac-666^T Strain
  Lobastova, International journal of molecular sciences 2022
  • “...15545 36.23 MBL fold metallo-hydrolase 4 F1721 _ 08445 26.54 FtsX-like permease family protein 5 F1721_27895 22.82 DUF418 domain-containing protein 6 F1721 _ 27890 17.11 Class I SAM-dependent methyltransferase 7 F1721 _ 22945 10.67 Polyprenyl synthetase family protein 8 F1721 _ 08470 9.71 Amidohydrolase 9 F1721...”

BACI_c51040 DUF418 domain-containing protein from Bacillus cereus biovar anthracis str. CI
Aligns to 189:340 / 347 (43.8%), covers 99.4% of PF04235, 108.9 bits

• The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids
  Klee, PloS one 2010
  • “...in PCR * BACI_c22180 (638 bp) BACI_c24230 (535 bp) BACI_c24450 (300 bp) BACI_c43090 (745 bp) BACI_c51040 (327 bp) BACI_c54520 (604 bp) BMA_pCI1400090 (448 bp) BACI_c22220 (677 bp) BACI_c24340 (619 bp) BACI_c24500 (438 bp) BACI_c43150 (748 bp) BACI_c51070 (354 bp) BACI_c54560 (756 bp) BACI_pCI1400190 (445 bp) BACI_c24550...”

BMB171_C4385 DUF418 domain-containing protein from Bacillus thuringiensis BMB171
Aligns to 164:334 / 340 (50.3%), covers 98.8% of PF04235, 105.8 bits

• The two-component signal transduction system YvcPQ regulates the bacterial resistance to bacitracin in Bacillus thuringiensis
  Zhang, Archives of microbiology 2016 (PubMed)
  • “...the promoter regions of genes yvcR (BMB171_C4100), BMB171_C4385, kapD (BMB171_C4525) and BMB171_ C4835 in Bacillus thuringiensis BMB171 which is a...”
  • “...the 200-bp promotor fragments of genes yvcR, BMB171_C4385, kapD (BMB171_C4525), BMB171_C4835 and yvcS1S2 (PyvcR, PC4385, PkapD, PC4835 and PyvcS1S2,...”

BC4744 hypothetical Membrane Spanning Protein from Bacillus cereus ATCC 14579
Aligns to 164:334 / 340 (50.3%), covers 98.8% of PF04235, 103.7 bits

• Response of Bacillus cereus ATCC 14579 to challenges with sublethal concentrations of enterocin AS-48
  Grande, BMC microbiology 2009
  • “...specific overexpression of the BC4207 membrane protein, we randomly selected two membrane proteins (BC4147 and BC4744) and introduced them into B. cereus ATCC14579 similar to the BC4207 protein. Expression of these proteins resulted in no significant growth difference in the presence of various amounts of AS-48...”
  • “...cDNA using the 2 -Ct method [ 34 ]. Overexpression of the BC4207, BC4147 and BC4744 proteins BC4207, BC4147 and BC4744 genes were amplified with oMJGB3 (5'-GATCGAAGCTTACGGTAAATAACTTATTACAG-3') and oMJGB4 (5'-GATCCAGGCATGCTCACGTCAACAATTAACTTT-3'), oBCE9 (5'-CATATAGGAGTAATGATATG-3') and oBCE10 (5'-AGAGAAGATACGGCATAG-3'), oBCE11 (5'-TACAAGGAGTTGCTTTATGG-3') and oBCE11 (5'-TTATATCGGCGCAACTAC-3'), respectively. PCR products were cloned into...”

MAB_4921c hypothetical protein from Mycobacterium abscessus ATCC 19977
Aligns to 226:382 / 387 (40.6%), covers 95.7% of PF04235, 91.2 bits

• Hierarchy and interconnected networks in the WhiB7 mediated transcriptional response to antibiotic stress in Mycobacterium abscessus
  Hurst-Hess, PLoS genetics 2023
  • “...1844715 11 MAB_1845c/MAB_1846 MAB_1846 Putative ABC transporter ATP-binding protein 4.57 1,2,3 25 5030041 1 MAB_4921c/MAB_4922 MAB_4921c probable integral membrane protein 4.04 1,2,3 26 2712704 1 MAB_2670c/MAB_2671 MAB_2670c hisD Histidinol dehydrogenase(AAB) 4.99 1,3 27 4932689 1 upstream of MAB_4820 MAB_4820 Hypothetical protein 4.84 1,3 28 3737457 2...”

cg2095 hypothetical protein from Corynebacterium glutamicum ATCC 13032
Aligns to 260:430 / 468 (36.5%), covers 99.4% of PF04235, 63.9 bits

• Target genes, consensus binding site, and role of phosphorylation for the response regulator MtrA of Corynebacterium glutamicum
  Brocker, Journal of bacteriology 2011
  • “...encoding a protein of unknown function, or cg2095 (NCgl1837), encoding a hypothetical membrane protein. By DNA-protein interaction studies, we provided evidence...”
  • “...cg1562 cg1612 cg1665 cg1671 cg1942 cg1943 cg2052 cg2054 cg2095 cg2096 cg2236 cg2500 cg2719 cg2720 cg2747 cg2777 cg3254 cg3395 Alternate designation VOL. 193,...”
• Acetohydroxyacid synthase, a novel target for improvement of L-lysine production by Corynebacterium glutamicum
  Blombach, Applied and environmental microbiology 2009
  • “...cg1085 cg1087 cg1090 cg1229 cg1279 cg1365 cg1367 cg1419 cg1998 cg2095 cg2438 cg2477 cg3256 0.49 0.45 3.30 2.95 2.38 2.09 2.15 2.68 2.21 2.71 0.45 0.44 0.47 0.47...”

Or search for genetic data about PF04235 in the Fitness Browser