Family Search for PF05656 (DUF805)

PF05656.14 hits 30 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

YhaH / b3103 putative inner membrane protein from Escherichia coli K-12 substr. MG1655 (see paper)
b3103 predicted inner membrane protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
Aligns to 11:117 / 121 (88.4%), covers 100.0% of PF05656, 120.6 bits

• luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
  Wang, Journal of bacteriology 2005
  • “...b2406 b3939 b3945 b0648 b1680 b0823 b1112 b4288 b4310 b3103 b0621 b1407 b0076 b2723 b3683 b3028 b2968 b0579 b3220 b0260 b3046 b2919 b3906 b2060 b0790 b1720...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b1421 b1610 b3453 b1183 b3495 b1521 b0422 b4031 b2605 b3073 b3103 b3877 b0058 b0105 b0119 b0163 b0233 b0286 b0288 Fold induction 2.1 4.7 4.3 2.8 2.2 2.3 3.4 3.8...”

STM3234 putative inner membrane protein (NCBI ptt file) from Salmonella typhimurium LT2
Aligns to 11:117 / 121 (88.4%), covers 100.0% of PF05656, 118.6 bits

• Selection-Driven Gene Inactivation in Salmonella
  Cherry, Genome biology and evolution 2020
  • “...STM1227 STM3739 STM3114 STM0807 STM1148 STM0130 STM2238 STM0826 STM3234 STM3026 STM0239 STM0839 STM2742 STM0295 cyuP cysK pepT ligB speC ybhL clsC ddlB -- rlmF...”
• The target spectrum of SdsR small RNA in Salmonella
  Fröhlich, Nucleic acids research 2016
  • “..., 17 ) mopA STM4329 4,26 co-chaperonin GroES (72 to +45 in mopB)::gfp nc yhaH STM3234 3,70 putative inner membrane protein (43 to +45 in yhaH)::gfp FC yes yes ( 14 , 15 ) yhcB STM3347 3,46 cytochrome d ubiquinol oxidase subunit III (59 to +45...”

PMI1438 hypothetical protein (RefSeq) from Proteus mirabilis HI4320
Aligns to 12:125 / 127 (89.8%), covers 100.0% of PF05656, 114.4 bits

• Transcriptome of swarming Proteus mirabilis
  Pearson, Infection and immunity 2010
  • “...PMI1629 PMI2898 PMI1654 PMI1617 PMI1653 PMI3460 PMI2057 PMI1438 PMI1650 PMI1637 PMI1442 PMI0993 PMI1649 PMI1647 PMI1644 PMI1961 PMI0182 PMI1621 PMI3036 PMI2496...”

YhaI / b3104 putative inner membrane protein from Escherichia coli K-12 substr. MG1655 (see paper)
b3104 predicted inner membrane protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
Z4458 putative cytochrome (NCBI ptt file) from Escherichia coli O157:H7 EDL933
Aligns to 11:113 / 118 (87.3%), covers 100.0% of PF05656, 113.9 bits

• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b1129 b3666 b1444 b1601 b0696 b4017 b0188 b2578 b1749 b3242 b3104 b1736 b3299 b0011 b1447 b3302 b1451 b2261 b0285 b1600 b0174 b2534 b0154 b3312 b1400 82 77 59...”
• Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
  Wei, Infection and immunity 2003
  • “...b4207 b3420 b1737 b3683 b1229 b2622 b0569 b0404 b2138 b3104 b0042 b0419 b0496 b0520 b0837 b1168 b1494 b1498 b1587 b1729 b2055 b2057 b2269 b2430 b2519 b2657...”
• Microarray analysis of the Ler regulon in enteropathogenic and enterohaemorrhagic Escherichia coli strains
  Bingle, PloS one 2014
  • “...secretion system for StcE pO157 Z0955 5 - systemic factor protein A homologue PP (OI#36) Z4458 36 yhaI putative cytochrome Z5100 7 espF LEE-encoded effector EspF LEE (OI#148) Z5102 24 orf29 component of T3SS, SsaH family LEE (OI#148) Z5103 14 escF T3SS structure protein EscF LEE...”

PA0563 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 12:113 / 117 (87.2%), covers 100.0% of PF05656, 112.8 bits

• Transcriptional Responses of Pseudomonas aeruginosa to Inhibition of Lipoprotein Transport by a Small Molecule Inhibitor
  Lorenz, Journal of bacteriology 2020 (no snippet)
• Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures
  Chan, PeerJ 2016
  • “...10.9322 1.89052 2.53173 2.42142 0.00025 0.00268304 gene4330 rplV 73.7324 13.723 2.4257 2.23755 0.0036 0.0243101 gene568 PA0563 74.2912 14.1381 2.39361 2.52297 0.00425 0.0258005 gene4663 PA4571 13.6487 2.62789 2.37679 3.4702 5.00E-05 0.00069884 gene4324 rplX 126.547 24.3781 2.37602 2.89574 0.0001 0.00130652 gene4331 rpsS 993.38 192.891 2.36456 3.71984 5.00E-05 0.00069884...”

plu2346 No description from Photorhabdus luminescens subsp. laumondii TTO1
Aligns to 11:118 / 122 (88.5%), covers 99.0% of PF05656, 104.8 bits

• Txp40, a ubiquitous insecticidal toxin protein from Xenorhabdus and Photorhabdus bacteria
  Brown, Applied and environmental microbiology 2006
  • “...proteins, particularly downstream of the toxin gene (plu2327 to plu2346). The only annotated open reading frames in this region are upstream of the toxin gene...”

BC2001 Integral membrane protein (NCBI ptt file) from Bacillus cereus ATCC 14579
Aligns to 11:112 / 120 (85.0%), covers 100.0% of PF05656, 100.7 bits

• Continuing towards optimization of bladder cancer care in Canada: Summary of the third Bladder Cancer Canada-Canadian Urological Association-Canadian Urologic Oncology Group (BCC-CUA-CUOG) bladder cancer quality of care consensus meeting
  Kassouf, Canadian Urological Association journal = Journal de l'Association des urologues du Canada 2020
• Development and validation of a follow-up methodology for a randomised controlled trial, utilising routine clinical data as an alternative to traditional designs: a pilot study to assess the feasibility of use for the BladderPath trial
  Mintz, Pilot and feasibility studies 2020
  • “...score Charlson Comorbidity Index score NIHR National Institute for Health Research MRI Magnetic resonance imaging BC2001 Bladder Cancer 2001 HR Hazard ratio CI Confidence interval PPV Positive predictive value BCG Bacillus Calmette-Gurin TURBT Transurethral resection of bladder tumour MIBC Muscle invasive bladder cancer LINAC Linear accelerator...”
• A Festschrift in Honor of Edward M. Messing, MD, FACS
  Joseph, Bladder cancer (Amsterdam, Netherlands) 2018
  • “...up to 50%. The importance of concurrent chemotherapy with surgery was emphasized in the randomized BC2001 trial, [ 22 ] with an improvement in 5 year overall survival from 35% to 48% when chemotherapy was added to radiation. There is a low incidence of late side...”
• Bladder preservation in non-metastatic muscle-invasive bladder cancer (MIBC): a single-institution experience
  Gerardi, Ecancermedicalscience 2016
  • “...haematological, gastrointestinal, and genitourinary. Neuropathy may be reported in cases of cisplatin-based concurrent chemotherapy. The BC2001 trial reported neither an increase in G3G4 toxicity with concurrent chemotherapy compared with radiotherapy alone nor a decrease in radiotherapy completion rates caused by toxicity [ 25 ]. In the...”
• Trimodality therapy in bladder cancer: who, what, and when?
  Premo, The Urologic clinics of North America 2015
  • “...response to induction therapy may not always be known, as many recent trials, such as BC2001 and RTOG 0926, do not include cystoscopic reassessment after induction. For these studies, careful patient selection becomes increasingly important as a full radiotherapy dose will be delivered before response to...”
  • “...the delivery of concurrent cisplatin, and a number of studies have evaluated alternative regimens. The BC2001 trial tested the use of 5-FU with mitomycin-C (MMC) concurrently with radiotherapy with excellent response rates and impressive tolerability. ( 19 ) This regimen can be particularly useful in those...”
• Chemical- and radiation-induced haemorrhagic cystitis: current treatments and challenges
  Payne, BJU international 2013
  • “...RT has ended, from 2 months to 15 years later [ 41 ]. In the BC2001 study, late toxicity was measured with the Radiation Therapy Oncology Group (RTOG) and Late Effects of Normal Tissue (Subjective, Objective, and Management elements) (LENT/SOM) criteria in 360 patients with muscle-invasive...”

PG0198 conserved hypothetical protein (NCBI) from Porphyromonas gingivalis W83
Aligns to 11:164 / 179 (86.0%), covers 100.0% of PF05656, 97.2 bits

• Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis
  Klein, Mobile DNA 2015
  • “...family transcriptional regulator - BrickBuilt_3 PGN_0303 PG0196 PGTDC60_0466 EG14_04795 Zinc protease (Peptidase M16) + PGN_0306 PG0198 PGTDC60_0471 EG14_04805 PF05656 family protein (DUF 805) + BrickBuilt_4 PGN_0336 NP PGTDC60_1661 EG14_04940 Immunoreactive antigen/PorSS CTD - PGN_0340 NP PGTDC60_1665 EG14_04960 Peptidase S41/PorSS CTD + BrickBuilt_5 PGN_0361 PG0264 PGTDC60_0543 EG14_05065...”

PGN_0306 hypothetical protein (RefSeq) from Porphyromonas gingivalis ATCC 33277
Aligns to 112:265 / 280 (55.0%), covers 100.0% of PF05656, 96.0 bits

• Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis
  Klein, Mobile DNA 2015
  • “...AraC family transcriptional regulator - BrickBuilt_3 PGN_0303 PG0196 PGTDC60_0466 EG14_04795 Zinc protease (Peptidase M16) + PGN_0306 PG0198 PGTDC60_0471 EG14_04805 PF05656 family protein (DUF 805) + BrickBuilt_4 PGN_0336 NP PGTDC60_1661 EG14_04940 Immunoreactive antigen/PorSS CTD - PGN_0340 NP PGTDC60_1665 EG14_04960 Peptidase S41/PorSS CTD + BrickBuilt_5 PGN_0361 PG0264 PGTDC60_0543...”
• Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis
  Hirano, Molecular oral microbiology 2013
  • “...0.02 PGN_1290 hypothetical protein 0.81 0.03 PGN_0531 putative von Willebrand factor type A 0.82 0.03 PGN_0306 hypothetical protein 0.85 0.02 PGN_1278 partial transposase in ISPg3 0.85 0.03 PGN_1911 transposase in ISPg3 0.87 0.00 PGN_1591 hypothetical protein 0.87 0.05 PGN_1586 hypothetical protein 0.96 0.03 PGN_0860 hypothetical protein...”

lmo0672 similar to unknown protein (NCBI ptt file) from Listeria monocytogenes EGD-e
Aligns to 14:135 / 142 (85.9%), covers 98.1% of PF05656, 93.6 bits

• Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation
  Vivant, Applied and environmental microbiology 2015
  • “...lmo2761 lmo0412 lmo0471 lmo0471 lmo0471 lmo0518 lmo0559 lmo0561 lmo0672 lmo0830 lmo0867 lmo0919 togenes to the soil environment. It is interesting to notice...”
• The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages
  Mraheil, Nucleic acids research 2011
  • “...of mgtA . Interestingly, a putative sRNA located in the intergenic region between lmo0671 and lmo0672 was previously reported as rli33 encoding a transcript of 534nt in length ( 31 ). However, our RNA-seq revealed two smaller fragments of 186nt ( rli33-1 ) and 274nt (...”
• Amplified intergenic locus polymorphism as a basis for bacterial typing of Listeria spp. and Escherichia coli
  Somer, Applied and environmental microbiology 2005
  • “...or species Lmo1430 clpE BetL ATTM ltrC cheR lisR Lmo0672 Lmo0196 Lmo0075 Lin0694 Lmo0023 gid fhuB Lmo0042 Lmo0176 abc gbuA Allelea at following locus: LM6-4b...”

YiiR / b3921 DUF805 domain-containing protein YiiR from Escherichia coli K-12 substr. MG1655 (see paper)
Aligns to 7:133 / 146 (87.0%), covers 98.1% of PF05656, 77.3 bits

ACICU_03432 hypothetical protein (RefSeq) from Acinetobacter baumannii ACICU
Aligns to 4:118 / 171 (67.3%), covers 98.1% of PF05656, 75.6 bits

• Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment
  Wright, mBio 2017 (no snippet)

lp_1702 integral membrane protein (NCBI ptt file) from Lactobacillus plantarum WCFS1
Aligns to 12:121 / 121 (90.9%), covers 91.4% of PF05656, 75.4 bits

• Genomic Evidence for Bacterial Determinants Influencing Obesity Development
  Isokpehi, International journal of environmental research and public health 2017
  • “...neighbors. Using the genome of L. plantarum WCFS1 as the reference, the genes tagged as lp_1702 and lp_1703 and respectively annotated as membrane protein and diacylglycerol kinase family protein were in the same transcription direction as the two-gene operon. 3.4. Gene Neighborhood of Gene for the...”

M3Q_3669 DUF805 domain-containing protein from Acinetobacter baumannii TYTH-1
Aligns to 15:129 / 182 (63.2%), covers 98.1% of PF05656, 75.3 bits

• Transcriptome Remodeling of Acinetobacter baumannii during Infection and Treatment
  Wright, mBio 2017 (no snippet)

PA0659 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 174:277 / 358 (29.1%), covers 99.0% of PF05656, 74.8 bits

• Isolation and characterization of Pseudomonas aeruginosa R' plasmids constructed by interspecific mating
  Morgan, Journal of bacteriology 1982
  • “...trpF leu-10 phe-2 amiE200 PAO114 PA0505 PA0473 PA0905 PA0659 PA0505 PA0904 PA0305 PA0897 argF1O argG27 pMO757 pMO758 Wild-type alleles carried by R'pMO778...”

LSA1296 Hypothetical integral membrane protein (NCBI) from Lactobacillus sakei subsp. sakei 23K
Aligns to 12:120 / 121 (90.1%), covers 90.5% of PF05656, 70.9 bits

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...1.7 1.4 LSA1189 lsa1189 Hypothetical integral membrane protein -1.6 -1.1 LSA1282 lsa1282 Hypothetical protein -0.5 LSA1296 lsa1296 Hypothetical integral membrane protein -1.2 -0.8 LSA1342 lsa1342 Hypothetical protein -0.7 LSA1346 lsa1346 Hypothetical protein 0.8 LSA1350 lsa1350 Hypothetical protein -0.6 -1.0 LSA1353 lsa1353 Hypothetical integral membrane protein -0.9...”

SACOL2338 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus COL
Q2FVS2 Uncharacterized protein from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SAOUHSC_02620 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2289 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus USA300_FPR3757
Aligns to 20:180 / 215 (74.9%), covers 100.0% of PF05656, 67.4 bits

• Identification of Staphylococcus aureus Cellular Pathways Affected by the Stilbenoid Lead Drug SK-03-92 Using a Microarray
  Schwan, Antibiotics (Basel, Switzerland) 2017
  • “...2.5 succinate dehydrogenase, cytochrome b558 subunit ( sdhC ) SACOL1604 2.1 glucokinase ( glk ) SACOL2338 3.5 hypothetical protein (putative oxidoreductase) SACOL1713 2.3 hypothetical protein, putative ammonia monooxygenase Unknown SACOL0089 4.4 myosin-reactive antigen, 67 kDa SACOL2315 3.8 conserved hypothetical protein SACOL2338 3.4 conserved hypothetical protein SACOL2491...”
• A Small Membrane Stabilizing Protein Critical to the Pathogenicity of Staphylococcus aureus
  Duggan, Infection and immunity 2020
  • “...Q2G294 Acetyl-coenzyme A synthetase 2.1 0.001 Q2FZI6 purH Bifunctional purine biosynthesis protein PurH 2.2 <0.0001 Q2FVS2 Uncharacterized protein 2.2 0.001 Q2G2P7 hutH Histidine ammonia-lyase 2.2 0.006 Q2FW51 Truncated major histocompatibility complex class II analog protein 2.2 0.015 Q2FVQ4 l -Lactate permease 2.2 0.006 Q2FV59 crtM Dehydrosqualene...”
• Lysogenization of Staphylococcus aureus RN450 by phages ϕ11 and ϕ80α leads to the activation of the SigB regulon
  Fernández, Scientific reports 2018
  • “...SAOUHSC_02451 0.44 0.49 SAOUHSC_02452 lacD 0.38 0.45 SAOUHSC_02453 lacC 0.39 0.49 SAOUHSC_02597 2.12 2.90 Up SAOUHSC_02620 0.45 0.24 Down SAOUHSC_02729 2.20 3.14 Up SAOUHSC_02771 2.96 5.46 Up SAOUHSC_02772 2.32 6.49 Up SAOUHSC_02812 3.00 7.98 Up SAOUHSC_02815 2.63 4.38 Up SAOUHSC_02822 fbp 2.31 3.17 Up SAOUHSC_02848 glcB...”
• Prediction driven functional annotation of hypothetical proteins in the major facilitator superfamily of S. aureus NCTC 8325
  Marklevitz, Bioinformation 2016
  • “...well-defined function is more likely related. SAOUHSC_02307, SAOUHSC_02309, and ABD31816.1 hit several general membrane proteins. SAOUHSC_02620 and SAOUHSC_02866 matched several hypothetical proteins as well as general membrane proteins. This indicates these hypothetical proteins may not be in the MFS. Table 5 lists the physiochemical parameters calculated...”
  • “...Four of the five hypothetical proteins that had ambiguous membrane protein BLASTP hits, SAOUHSC_02307, SAOUHSC_02309, SAOUHSC_02620, and SAOUHSC_02866, came up outside this size range. Examination of other physiochemical calculations failed to be consistent in predicting MFS proteins among hypotheticals though some proteins outside this size range...”
• Staphylococcus aureus ClpX localizes at the division septum and impacts transcription of genes involved in cell division, T7-secretion, and SaPI5-excision
  Jensen, Scientific reports 2019
  • “...toxin-antitoxin system (type VII secretion locus) 0,6 4,6E-03 SAUSA300_0271 ABC transporter ATP-binding protein 0,6 5,2E-03 SAUSA300_2289 hypothetical protein 0,6 4,5E-04 copZ copper chaperone copZ 0,6 7,3E-05 esxC EsxC toxin (type VII secretion locus) 0,6 6,2E-03 SAUSA300_0273 hypothetical protein 0,6 6,7E-08 nrdD anaerobic ribonucleoside triphosphate reductase 0,6...”
• VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
  Boyle-Vavra, Antimicrobial agents and chemotherapy 2013
  • “...Transporter Hypothetical Transporter Membrane spanning SAUSA300_2288 SAUSA300_2289 SAUSA300_2453 SAUSA300_2454 SA2132 SA2133 SA2302 SA2303 2.2 4.3 2.2 2.4 3.5...”

SA2133 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus N315
Aligns to 20:180 / 206 (78.2%), covers 100.0% of PF05656, 67.3 bits

• What Happens in the Staphylococcal Nucleoid under Oxidative Stress?
  Morikawa, Microorganisms 2019
  • “...4.04 mrgA(dps) SA1941 MrgA, Dps family protein 2.07 lrgB SA0253 antiholin-like protein LrgB 1.86 / SA2133 hypothetical protein 1.65 oppB SA0853 oligopeptide ABC transporter permease 1.59 arcB SA2427 ornithine carbamoyltransferase 1.54 sen SA1643 enterotoxin SeN (in pathogenicity island, SaPIn3) 1.53 / SA2470 histidinol dehydrogenase 1.51 /...”
• VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
  Boyle-Vavra, Antimicrobial agents and chemotherapy 2013
  • “...Membrane spanning SAUSA300_2288 SAUSA300_2289 SAUSA300_2453 SAUSA300_2454 SA2132 SA2133 SA2302 SA2303 2.2 4.3 2.2 2.4 3.5 2.7 2.3 3.6 2.5 Hypothetical...”
• 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
  • “...2.5 SA2108 hypothetical protein sa_c4480s3823_a_at 4.7 2.5 2.5 SA2118 hypothetical protein sa_c4519s3864_a_at 2.6 2.5 2.5 SA2133 hypothetical protein sa_c10171s8867_at 8.2 2.5 2.5 SA2134 hypothetical protein sa_c10176s10598_s_at 4.8 2.5 5 SA2140 hypothetical protein sa_c4593s3925_a_at * 2.2 2.5 2.5 SA2152 hypothetical protein sa_c4635s3957_a_at 11.9 2.5 2.5 SA2164 hypothetical...”
• Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome
  Ben, Journal of bacteriology 2008
  • “...Similar to unknown proteins PD PD PD SA2133 SA2143 SA2190 Membrane Secreted/SP Cytoplasm Conserved hypothetical protein Conserved hypothetical protein Conserved...”
• Differential gene expression profiling of Staphylococcus aureus cultivated under biofilm and planktonic conditions
  Resch, Applied and environmental microbiology 2005
  • “...with Tn554 0.166 0.099 0.162 5.108 3.375 5.768 SA0271 SA2133 SA0412 SA2143 SA0292 SA0509 SA0082 SA2378 SA0739 4.664 3.315 3.278 3.148 3.147 2.906 2.878 2.742...”
  • “...SA0292 SA0609 SA0890 SA1403 SA0588 SA1053 SA1472 SA1419 SA2133 SA1944 SA1056 SA0412 SA1402 SA0291 SA1971 SAS048 SA2378 SA2143 SA1293 SA1912 SA0975 7.686 4.76...”
• Global regulation of Staphylococcus aureus genes by Rot
  Saïd-Salim, Journal of bacteriology 2003
  • “...SAS013 SA0739 SA0651 SA1613 SA0428 SA2378 SA1717 SA0523 SA2133 SA0682 SA2261 SAS088 SA2007 SA0620 SA2284 SA2170 SA2171 SA0914 SA0407 SA0408 SA2303 SA0439 SA1059...”

MW2263 conserved hypothetical protein (NCBI ptt file) from Staphylococcus aureus subsp. aureus MW2
Aligns to 20:180 / 206 (78.2%), covers 100.0% of PF05656, 67.2 bits

• Rsp inhibits attachment and biofilm formation by repressing fnbA in Staphylococcus aureus MW2
  Lei, Journal of bacteriology 2011
  • “...MW0267 COL-SA1165 MW1410 MW1405 MW1406 MW1408 MW1427 MW1969 MW2260 MW2263 MW2560 MW2573 MW2600 Fold change VOL. 193, 2011 BIOFILM REGULATION BY Rsp IN S. AUREUS...”

SAR2428 putative membrane protein (NCBI) from Staphylococcus aureus subsp. aureus MRSA252
Aligns to 20:180 / 215 (74.9%), covers 100.0% of PF05656, 66.9 bits

• Response of Staphylococcus aureus to subinhibitory concentrations of a sequence-selective, DNA minor groove cross-linking pyrrolobenzodiazepine dimer
  Doyle, The Journal of antimicrobial chemotherapy 2009
  • “...SAR1423 0.46 Hypothetical protein femA 0.49 Peptidogylcan biosynthesis and methicillin resistance murF 0.49 Peptidogylcan biosynthesis SAR2428 0.49 Putative membrane protein Table 4 Comparison of microarray, proteomic and qRT-PCR data after addition of ELB-21 (0.5 MIC) to cultures of EMRSA-16 Gene Microarray Proteomics qRT-PCR a recA 5.24...”
• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...protein 2.04 3.47E-03 SAR2369 putative acyl-CoA dehydrogenase 2.86 1.94E-03 SAR2425 putative membrane protein 2.13 5.63E-03 SAR2428 putative membrane protein 2.00 3.23E-03 SAR2435 putative acyl hydrolase 2.50 3.02E-02 SAR2439 tetR family regulatory protein 2.22 3.23E-03 SAR2473 putative exported protein 3.85 3.97E-03 SAR2500 putative lipoprotein 2.86 8.48E-04 SAR2546...”
  • “...2.38 3.02E-03 SAR2426 putative membrane protein 2.09 2.11E-03 SAR2427 ABC transporter ATP-binding protein 2.14 4.82E-03 SAR2428 putative membrane protein 3.73 1.21E-05 SAR2569 hypothetical protein 6.01 4.75E-02 10.1371/journal.pone.0004344.t004 Table 4 MRSA252 genes down-regulated during growth in the presence of linoleic acid (0.01mM ) (linoleic acid growth exposure)....”

LF82_004 DUF805 domain-containing protein from Escherichia coli LF82
Aligns to 14:121 / 121 (89.3%), covers 93.3% of PF05656, 65.5 bits

• A multi-phenotypic imaging screen to identify bacterial effectors by exogenous expression in a HeLa cell line
  Collins, Scientific data 2018
  • “...LF82_259 1.61 0.18 Set3_Part2 F08 LF82_266 1.61 0.04 Set3_Part2 E08 LF82_121 1.60 0.05 Set3_Part1 E09 LF82_004 1.60 0.20 Set3_Part1 C10 LF82_441 1.59 0.04 Set3_Part2 D06 LF82_347 1.59 0.18 Set3_Part1 F03 LF82_539 1.59 0.09 Set3_Part1 F09 LF82_772 1.59 0.21 Set3_Part1 E10 LF82_772 1.58 0.16 Set3_Part1 F10 LF82_793...”

PMT1567 conserved hypothetical protein (NCBI) from Prochlorococcus marinus str. MIT 9313
Aligns to 14:107 / 108 (87.0%), covers 91.4% of PF05656, 62.8 bits

• Identification of cyanobacterial non-coding RNAs by comparative genome analysis
  Axmann, Genome biology 2005
  • “...purK MIT 9313 yfr1 257 1220973..1221029 57 guaB and trxA yfr2 NP Complement (1667304..1667390) 87 PMT1567 and PMT1568 yfr7 NP 727045..727219 (complementary to PMT0670 ) 175 purK and PMT0671 WH 8102 yfr1 257 Complement (706826..706881) 56 trxA and guaB yfr2 NP 1127972..1128056 NT Overlapping SYNW1139 yfr3...”

EF1089 conserved hypothetical protein (NCBI ptt file) from Enterococcus faecalis V583
Aligns to 12:124 / 131 (86.3%), covers 88.6% of PF05656, 62.4 bits

• Conservation of Ebp-type pilus genes among Enterococci and demonstration of their role in adherence of Enterococcus faecalis to human platelets
  Nallapareddy, Infection and immunity 2011
  • “...The deleted region corresponds to 9 complete genes in V583 (ef1089 to ef1097), including the ebp locus (ef1090 to ef1094), as well as the 3 end of ef1088. (iii)...”

SSA_0718 Conserved uncharacterized protein (NCBI) from Streptococcus sanguinis SK36
Aligns to 12:165 / 364 (42.3%), covers 98.1% of PF05656, 61.0 bits

• Streptococcus sanguinis Noncoding cia-Dependent Small RNAs Negatively Regulate Expression of Type IV Pilus Retraction ATPase PilT and Biofilm Formation
  Ota, Infection and immunity 2018
  • “...11.39 SSA_1820 Hypothetical protein csRNA1-1 37 (8) 11.59 SSA_0718 Hypothetical protein csRNA1-2 9 (9) 11.36 SSA_1632 Surface protein csRNA1-1 10 11.16 SSA_0991...”
  • “...4 AUAGGGGGA 12 23 UUCAAUCCUCCAGA 10 |||||||| ||: SSA_0718 78 CAGUUAGGAAGUUA 65 59 CCCUCUAAUAAUACUU 44 |||||||| ||| | SSA_1632 11 AGGAGAUUAAAAUG-A 4 SSA_0991...”

A1S_3236 hypothetical protein (RefSeq) from Acinetobacter baumannii ATCC 17978
Aligns to 2:84 / 137 (60.6%), covers 59.0% of PF05656, 58.6 bits

• An ribonuclease T2 family protein modulates Acinetobacter baumannii abiotic surface colonization
  Jacobs, PloS one 2014
  • “...pilN/comN fibrial assembly protein gi-126643206 3.5 11.9 A1S_3195 comM competence protein A gi-126643244 2.8 4 A1S_3236 hypothetical protein gi-126643330 2.3 10.7 A1S_3323 putative flavoprotein 1 ATCC17978 locus tag; adjacent loci are highlighted in grey; loci associated with pili formation and motility are bolded. To further verify...”
  • “...RNA binding/nucleotide hydrolase), A1S_1476 (tautomerase/hydrolase), A1S_2787 (limited homology to Bartonella cell invasion associated protein) and A1S_3236 (homology to tRNA transferase/hydrolase) did not provide additional insight regarding how A1S_3026 modulates abiotic surface colonization. Thus, we surmise that the RNase T2 family protein-associated biofilm formation phenotype is predominately...”

LSA1480 Hypothetical membrane protein (NCBI) from Lactobacillus sakei subsp. sakei 23K
Aligns to 24:159 / 168 (81.0%), covers 85.7% of PF05656, 46.2 bits

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...Hypothetical protein 0.6 LSA1464 lsa1464 Hypothetical protein -0.6 LSA1478 lsa1478 Hypothetical protein -0.7 -0.6 -0.6 LSA1480 lsa1480 Hypothetical membrane protein 0.5 D LSA1524 lsa1524 Hypothetical protein 0.8 LSA1539 lsa1539 Hypothetical protein 0.9 LSA1713 lsa1713 Hypothtical small peptide -0.6 LSA1787 lsa1787 Hypothetical cell surface protein precursor -0.5...”

llmg_1683 hypothetical protein (NCBI) from Lactococcus lactis subsp. cremoris MG1363
Aligns to 12:166 / 173 (89.6%), covers 74.3% of PF05656, 43.6 bits

• The transcriptional and gene regulatory network of Lactococcus lactis MG1363 during growth in milk
  de, PloS one 2013
  • “...two putative ABC transporters ( llmg_1973 and llmg_0341 ) and two putative membrane proteins ( llmg_1683 and llmg_2454 ), all of which have no known functions. General stress protein genes are overrepresented in cluster 49 according to the FIVA analysis but no common motif could be...”

YPO0751 putative membrane protein (NCBI ptt file) from Yersinia pestis CO92
Aligns to 1:92 / 93 (98.9%), covers 83.8% of PF05656, 42.9 bits

• Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics
  Califf, Microbial genomics 2015
  • “...protein MotA YPO0746 motB Hypothetical protein YPO0747 YPO0749 Hypothetical protein YPO0749 YPO0750 Hypothetical protein YPO0750 YPO0751 Hypothetical protein YPO0751 YPO0754 Hypothetical protein YPO0754 YPO1380 MFS family transporter protein YPO1380 YPO2315 Hypothetical protein YPO2315 Pcp Lipoprotein YPO2373 YPO2375 Aldo/keto reductase YPO2375 YPO2376 Hypothetical protein YPO2376 sepC Insecticial...”

LAS9267_02046 DUF805 domain-containing protein from Lactobacillus sakei
Aligns to 10:110 / 110 (91.8%), covers 89.5% of PF05656, 40.2 bits

• Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705
  Terán, PloS one 2020
  • “...SPE23715.1 7 4221 4553 +3 110 Putative membrane protein of unknown function 100% hypothetical protein LAS9267_02046 [ L . sakei ] SPE23716.1 8 4606 5406 -2 266 Transposase (IS150 family) 98% IS3 family transposase [ L . curvatus ] ASN62826.1 9 5448 5606 -3 52 Transposase...”

WP_019293277 DUF805 domain-containing protein from Lactococcus garvieae 8831
Aligns to 12:128 / 129 (90.7%), covers 94.3% of PF05656, 37.3 bits

• Characterization of prophages of Lactococcus garvieae
  Eraclio, Scientific reports 2017
  • “...20 10180 9791 129 15 9.2 AGGtaAatATG Membrane prot. L. garvieae 121/129 (94%) 2.0E-83 129 WP_019293277 21 + 10373 10579 68 7 4.8 AGGAGAataaaacATG L. lactis 52/68 (76%) 5.0E-25 68 WP_012897654 22 + 10585 10818 77 9 10.6 tGGAGAataagtcaaATG L . garvieae 32/52 (62%) 2.0E-10 73...”

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