Family Search for PF09972 (DUF2207)

PF09972 hits 14 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

SMc00852 HYPOTHETICAL TRANSMEMBRANE SIGNAL PEPTIDE PROTEIN from Sinorhizobium meliloti 1021
Aligns to 26:215 / 644 (29.5%), covers 98.3% of PF09972, 133.5 bits

• Development of a functional genomics platform for Sinorhizobium meliloti: construction of an ORFeome
  Schroeder, Applied and environmental microbiology 2005
  • “...been cloned, and these (SMb21298, SMb21548, SMb20514, SMc00852, SMc01316, SMc01710, SMc02086, SMc02273, SMc03761, SMc04028, SMc04382, TGc2812, and TGc1901) are...”

Q8REH6 Hypothetical membrane-spanning protein from Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)
Aligns to 24:209 / 606 (30.7%), covers 100.0% of PF09972, 112.2 bits

• Immunogenic peptides putatively from intratumor microbes: Opportunities for colorectal cancer treatment
  Guan, iScience 2024
  • “...located in the membrane. Notably, SFSASFSIS and VSKTNSRASSAI might be generated from the same protein Q8REH6, a hypothetical membrane-spanning protein. Similarly to Immunogenic bacterial peptides proved in this study, these 5 peptides were located within or near a 3D structure or domain of their source proteins,...”

Bbr_0375 DUF2207 domain-containing protein from Bifidobacterium breve UCC2003
Aligns to 39:274 / 751 (31.4%), covers 97.7% of PF09972, 104.3 bits

• Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003
  Ruiz, PloS one 2013
  • “...fam prot) G 1719332 ccccggagg Bbr_1383 Conserv. Hypothetical protein with DUF domain H 502520 gccgacgtc Bbr_0375 Conserv. Hypothetical membrane spanning protein I 633832 cccgatgac Bbr_0482 Conserv. Hypothetical protein J 1771618 gatgaggtt - 223 nt upstream Bbr_1420 K 634533 gttcacgcg Bbr_0482 Conserv. Hypothetical protein UCC1 1167747 gataagaag...”

Spy49_0238 hypothetical protein from Streptococcus pyogenes NZ131
Aligns to 27:207 / 604 (30.0%), covers 100.0% of PF09972, 95.3 bits

• Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays
  Patenge, BMC genomics 2012
  • “...4 sRNASpy490229 238850 238899 49 + prgA rpsL b 5 sRNASpy490238 248530 248579 49 + Spy49_0238 bacA a 6 sRNASpy490241 251595 251644 49 + rgpG Spy49_0242 a 7 sRNASpy490305 318826 318910 84 + Spy49_0305 Spy49_0306 23S-methyl b 8 sRNASpy490306 319622 319776 154 + Spy49_0306 Spy49_0307 FMN...”

SPD_0414 hypothetical protein from Streptococcus pneumoniae D39
Aligns to 26:206 / 629 (28.8%), covers 100.0% of PF09972, 94.8 bits

• [ComE-deficient mutant affects in vivo-induced genes expression in Streptococcus pneumoniae]
  Liu, Wei sheng wu xue bao = Acta microbiologica Sinica 2010 (PubMed) (secret)

YPO2731 putative membrane protein from Yersinia pestis CO92
Aligns to 51:247 / 679 (29.0%), covers 99.4% of PF09972, 93.9 bits

• Molecular Darwinian evolution of virulence in Yersinia pestis
  Zhou, Infection and immunity 2009
• Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus
  Zhou, Journal of bacteriology 2004
  • “...pMT026 pMT056 YP1700 YP1715 YPO2258 YP2054 YPO2729 YPO2731 YPO3049 YP2435 YP2433 YP2671 YPO1986-1987 (RD1) YPO2096-2135 (RD2) YPO2469 (RD3) YPO2487-2489 (RD4)...”
  • “...YPCD1.39c, YPMT1.23c, YPMT1.25c, YPMT1.43c, YPO1956, YPO1973, YPO2729, YPO2731, and YPO3049 according to the CO92 genome annotation [Table 3]), each with a...”

SP_0454 hypothetical protein from Streptococcus pneumoniae TIGR4
Aligns to 27:207 / 630 (28.7%), covers 100.0% of PF09972, 93.1 bits

• A bacterial pan-genome makes gene essentiality strain-dependent and evolvable
  Rosconi, Nature microbiology 2022
  • “...peptidoglycan synthesis, and the second mutation is located in a non-characterized membrane protein coding gene (SP_0454 H581N), which forms a complex with BacA 71 (right panel). Source data Many of the putative bypass mutations and synthetic lethal interactions obtained from Tn-seq in SP_1205-PG06 associate with two...”
• Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control
  Hör, The EMBO journal 2020
  • “...example, the membraneassociated, virulencerelated protein UppP (a.k.a. BacA) (Chalker etal , 2000 ) comigrated with SP_0454, a protein of unknown function with several transmembrane domains that are encoded in the same operon. While we cannot assess whether these putative membrane proteins remain properly folded, this illustrates...”

TRNA_RS23240 DUF2207 domain-containing protein from Bacillus licheniformis DSM 13 = ATCC 14580
BLi00351 hypothetical protein from Bacillus licheniformis DSM 13
Aligns to 27:203 / 631 (28.1%), covers 100.0% of PF09972, 89.5 bits

• Exploitation of ammonia-inducible promoters for enzyme overexpression in Bacillus licheniformis
  Shen, Journal of industrial microbiology & biotechnology 2021
  • “...sacA ), TRNA_RS23130 ( pdpX ), TRNA_RS42535 ( ald ), TRNA_RS31535 ( plp ), and TRNA_RS23240 ( dfp ) were selected out of the 859 upregulated genes and each showed higher transcription levels (FPKM values) in the presence of ammonia and glucose than that of the...”
  • “...Operon TRNA_RS23130 37.49 2,115.45 5.82 ald TRNA_RS23130 Gene TRNA_RS42535 246.39 4,651.72 4.3 pdbX TRNA_RS31535 Gene TRNA_RS23240 137.77 4,263.28 4.91 plp TRNA_RS23240 Gene TRNA_RS31535, TRNA_RS31540 172.8 2,005.56 3.54 dfp Promoter Structure and Sequence Analysis of the Putative Ammonia-Inducible Genes in B. licheniformis CBBD302 It is well recognized...”
• Cell envelope stress response in Bacillus licheniformis: integrating comparative genomics, transcriptional profiling, and regulon mining to decipher a complex regulatory network
  Wecke, Journal of bacteriology 2006
  • “...-- Putative ECF target genes abh Bli00351 Bli00968-yhcHI Bli01943-Bli1945 Bli02007 Bli02027 Bli02331 Bli02477-ypuD Bli02851 Bli04079-dltABCD Bli04206 lytR pbpE...”

YP_002236173 hypothetical protein from Klebsiella pneumoniae 342
Aligns to 50:246 / 681 (28.9%), covers 98.8% of PF09972, 87.7 bits

• Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?
  Pini, Genes 2011
  • “...YP_001178228 YP_002237662 YP_002008874 YP_002238064 2791 Phosphoesterase 2853 Electron transfer flavoprotein, beta subunit YP_001796225 2898 Unknown YP_002236173 2908 Electron transfer flavoprotein, alpha subunit YP_001796224 2912 Methyltransferase YP_935409 YP_001176000 YP_002237443 YP_001177854 YP_002239590 2927 Aminoacid aldolase or racemase YP_002007445 2981 Mg 2+ and Co 2+ transporters YP_002006900 YP_001176870 YP_002238775...”

Balac_0325 hypothetical protein from Bifidobacterium animalis subsp. lactis Bl-04
Aligns to 39:273 / 738 (31.8%), covers 97.7% of PF09972, 84.2 bits

• Genome-wide identification of small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and their regulation role in the adaption to gastrointestinal environment
  Zhu, PloS one 2015
  • “...Signal recognition particle protein cysteinyl-tRNA synthetase IGR-130 406, 166 406, 479 + 313 Hypothetical protein Balac_0325 ribonucleoside-diphosphate reductase subunit beta IGR-136 426, 611 426, 713 + 102 Response regulator of two-component system Phosphate-binding transport protein of ABC transporter system IGR-2 5, 224 5, 584 + 360...”

ECs1840 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Z2542 No description from Escherichia coli O157:H7 EDL933
Aligns to 34:225 / 527 (36.4%), covers 72.7% of PF09972, 82.3 bits

• Construction and Analysis of Gene Co-Expression Networks in Escherichia coli
  Liu, Cells 2018
  • “...Ornithine carbamoyltransferase subunit I Green rpsN 30S ribosomal protein S14 Greenyellow c0944 Hypothetical protein Grey60 ECs1840 Hypothetical protein Ivory fecR Anti-sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA-bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator Lightcyan1 ECs3950 RNA polymerase sigma factor...”
• Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs
  Laserson, Nucleic acids research 2005
  • “...K12 1 324 039 yciQ 6.10 57.8 + 2.24 18 E.coli O157:H7 1 826 735 ECs1840 19 E.coli O157:H7 EDL933 2 260 441 Z2542 20 E.coli CFT073 1 569 619 yciQ 21 E.coli O157:H7 1 373 724 ECs1300 22 5-ATTCACTGGG CGACATGTTT GATGAAT E.coli O157:H7 EDL933 1...”
• Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs
  Laserson, Nucleic acids research 2005
  • “...interestingly, the 39 nt sequences 1720 are identical copies found in hypothetical genes (yciQ, ECs1849, Z2542) of four different E.coli species. It is unlikely that candidate sequences 7/8 and 17/18/19/20 occur by chance. Table 3 shows that several other mostly shorter sequences (23, 1315, 2124, 2527,...”
  • “...2.24 18 E.coli O157:H7 1 826 735 ECs1840 19 E.coli O157:H7 EDL933 2 260 441 Z2542 20 E.coli CFT073 1 569 619 yciQ 21 E.coli O157:H7 1 373 724 ECs1300 22 5-ATTCACTGGG CGACATGTTT GATGAAT E.coli O157:H7 EDL933 1 457 496 Z1560 5.55 61.4 1.41 23 E.coli...”

YciP / b1268 DUF2207 domain-containing protein YciQ from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b1268 predicted inner membrane protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 34:228 / 631 (30.9%), covers 72.7% of PF09972, 77.9 bits

• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013

Bbr_0376 DUF2207 domain-containing protein from Bifidobacterium breve UCC2003
Aligns to 9:167 / 486 (32.7%), covers 63.4% of PF09972, 69.9 bits

• Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure
  Kelly, Scientific reports 2020
  • “...0.5% (w/v) porcine bile. Locus tag Putative Function Fold change in expression (Up regulation) P-value Bbr_0376 Hypothetical protein 10.08 9.18E14 Bbr_1594 PTS system fructose/glucose ( fruA ) 6.09 4.99E15 Bbr_0925 Permease MFS superfamily 5.49 0.000125407 Bbr_0204 Multi-domain protein fatty acids or polyketide synthesis 4.33 1.79E10 Bbr_1558...”

MAB_2776 hypothetical protein from Mycobacterium abscessus ATCC 19977
Aligns to 37:201 / 549 (30.1%), covers 95.3% of PF09972, 38.8 bits

• Use of epigenetically modified bacteriophage and dual beta-lactams to treat a Mycobacterium abscessus sternal wound infection
  Cristinziano, Nature communications 2024
  • “...has a single base insertion in an intergenic region between divergently transcribed genes (MAB_2775c and MAB_2776 in the ATCC19977 reference strain), and presumably influences the expression of one or both genes. Phage-resistant mutations have not previously been reported at this locus, and the functions of both...”

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