Family Search for PF04241 (DUF423)

PF04241 hits 13 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

EQ812_08585 DUF423 domain-containing protein from Staphylococcus lugdunensis
Aligns to 18:103 / 122 (70.5%), covers 98.9% of PF04241, 109.3 bits

• Comparative proteomics analysis of biofilms and planktonic cells of Enterococcus faecalis and Staphylococcus lugdunensis with contrasting biofilm-forming ability
  Cho, PloS one 2024
  • “.... lugdunensis 9 495 5.347593583 Transmembrane helix EQ812_05590 EQ812_06165 EQ812_06755 EQ812_02465 EQ812_07275 EQ812_03435 EQ812_04050 EQ812_09000 EQ812_08585 9 498 5.315379164 Transmembrane EQ812_05590 EQ812_06165 EQ812_06755 EQ812_02465 EQ812_07275 EQ812_03435 EQ812_04050 EQ812_09000 EQ812_08585 9 525 5.042016807 Membrane EQ812_05590 EQ812_06165 EQ812_06755 EQ812_02465 EQ812_07275 EQ812_03435 EQ812_04050 EQ812_09000 EQ812_08585 Another analysis using STRING-db...”

SA0540 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAOUHSC_00567 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0565 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
Aligns to 18:103 / 122 (70.5%), covers 98.9% of PF04241, 107.4 bits

• Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
  Scherr, Infection and immunity 2013
  • “...SA1569 SA1794 SA1285 SA1205 SA0563 SA1495 SA0432 SA1107 SA0540 SA0970 SA1839 SA1523 SA0513 SA1752 SA2131 SA0314 SA1323 SA1832 SA1065 SA1954 SA2634 SA1637 SA1966...”
• 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
  • “...SA1778 tyrosyl-tRNA synthetase sa_c2972s2529_a_at 11.7 2.5 2.5 valS SA1710 valyl-tRNA synthetase sa_c7499s6519_a_at 3.2 2.5 2.5 SA0540 putative endoribonuclease L-PSP sa_c7535s6554_a_at 2.2 2.5 2.5 SA0552 hypothetical protein sa_c7597s6610_a_at 2.5 2.5 5 SA0578 RNA methyltransferase, sa_c7641s6656_a_at * 3.9 15 15 SA0590 30S ribosomal protein L7 Ae-like sa_c8103s7087_a_at 2.7...”
• Genome-wide CRISPRi screens for high-throughput fitness quantification and identification of determinants for dalbavancin susceptibility in Staphylococcus aureus
  Liu, mSystems 2024
  • “...which governs metabolic regulation ), three target tRNAs, and two target genes of unknown function (SAOUHSC_00567 and SAOUHSC_00685). The growth defect resulting from knockdown of these last two genes was confirmed by individually constructed CRISPRi mutants ( Fig. 3D ). We note that we cannot exclude...”
• Genome-wide CRISPRi screens reveal the essentialome and determinants for susceptibility to dalbavancin inStaphylococcus aureus
  Liu, 2023
• Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
  Xiao, Antibiotics (Basel, Switzerland) 2022
  • “...24.52 10.68 SAUSA300_0566 hypothetical amino acid permease 24.49 5.06 SAUSA300_0871 hypothetical hypothetical protein 24.49 12.19 SAUSA300_0565 hypothetical conserved hypothetical protein 24.43 5.34 SAUSA300_0391 hypothetical hypothetical protein 24.38 0.45 SAUSA300_1328 hypothetical putative drug transporter 24.10 7.38 SAUSA300_2279 hypothetical LysR family regulatory protein 23.92 10.37 SAUSA300_0505 hypothetical glutamine...”

WP_042478071 DUF423 domain-containing protein from Bacillus ndiopicus
Aligns to 18:108 / 123 (74.0%), covers 100.0% of PF04241, 104.9 bits

• Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures
  Gupta, Frontiers in microbiology 2019
  • “...pathway activation protein a WP_057986232 Supplementary Figure 14 3 aa ins 153196 DUF423 domain-containing protein WP_042478071 Supplementary Figure 15 24 aa ins 3992 a Minor exceptions or anomalies present (refer to figure for details). Conserved Signature Indels Specific for the Lysinibacillus sensu stricto Clade The Lysinibacillus...”

lmo0666 similar to unknown protein from Listeria monocytogenes EGD-e
LMRG_00353 hypothetical protein from Listeria monocytogenes 10403S
Aligns to 18:103 / 125 (68.8%), covers 100.0% of PF04241, 102.2 bits

• Listeria monocytogenes σ^A Is Sufficient to Survive Gallbladder Bile Exposure
  Boonmee, Frontiers in microbiology 2019
  • “...lmo0399 PTS system, IIB component 3.52 0.00 LMRG_00352 lmo0665 LMRG_00351-LMRG_00353 Hypothetical protein 2.32 0.01 LMRG_00353 lmo0666 Domain-containing protein 2.12 0.01 LMRG_00369 lmo0681 Flagellar biosynthesis regulator FlhF 2.01 0.00 LMRG_00373 lmo0685 motA motAB Flagellar motor rotation protein MotA 2.43 0.00 LMRG_00852 lmo1400 LMRG_00852-LMRG_00854 phosphinothricin N-acetyltransferase 2.06 0.00...”
• Listeria monocytogenes σ^A Is Sufficient to Survive Gallbladder Bile Exposure
  Boonmee, Frontiers in microbiology 2019
  • “...LMRG_00092 lmo0399 PTS system, IIB component 3.52 0.00 LMRG_00352 lmo0665 LMRG_00351-LMRG_00353 Hypothetical protein 2.32 0.01 LMRG_00353 lmo0666 Domain-containing protein 2.12 0.01 LMRG_00369 lmo0681 Flagellar biosynthesis regulator FlhF 2.01 0.00 LMRG_00373 lmo0685 motA motAB Flagellar motor rotation protein MotA 2.43 0.00 LMRG_00852 lmo1400 LMRG_00852-LMRG_00854 phosphinothricin N-acetyltransferase 2.06...”

KZA74_06265 DUF423 domain-containing protein from Acinetobacter baumannii
Aligns to 16:102 / 121 (71.9%), covers 100.0% of PF04241, 94.8 bits

• DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978
  Cook, Frontiers in cellular and infection microbiology 2023
  • “...NSC KZA74_06130 NSC R 17 A1S_2266/KZA74_06250 NSC R KZA74_06250 NSC R 18 A1S_2263/KZA74_06265 NSC R KZA74_06265 NSC R 19 A1S_2241/KZA74_06380 NSC R KZA74_06380 NSC NSC 20 A1S_2204/KZA 74_06585 NSC R KZA74_06585 NSC R 21 A1S_2200/KZA74_06610 NSC R KZA74_06610 NSC R 22 A1S_2192/KZA74_06650 NSC R KZA74_06650 NSC...”

HI1073 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 19:104 / 124 (69.4%), covers 100.0% of PF04241, 90.2 bits

• Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae
  Gladitz, Nucleic acids research 2005
  • “...strains) HI1058 40 195 51.88 GF2 9.9 88.85 Conserved hypothetical protein (homology to membrane protein) HI1073 38 125 49.31 HF 0 52.46 Conserved hypothetical GTP-binding protein (predicted GTPase) HI1118 40 206 37.32 HP2 0 65.19 Conserved hypothetical protein HI1150 34 210 38.9 HFDY 0 68.94 Conserved...”

YgdD / b2807 DUF423 domain-containing inner membrane protein YgdD from Escherichia coli K-12 substr. MG1655 (see 4 papers)
YGDD_ECOLI / P0ADR2 UPF0382 inner membrane protein YgdD from Escherichia coli (strain K12) (see paper)
Aligns to 20:106 / 131 (66.4%), covers 100.0% of PF04241, 84.3 bits

• function: May be a peptide transporter or a protein that facilitates peptide internalization (PubMed:26860543).
  disruption phenotype: Mutants show a slight decrease in the internalization level of some proline-rich antimicrobial peptides of eukaryotic origin.

orf2 / AAC13743.1 unknown from Escherichia coli (see paper)
Aligns to 20:106 / 131 (66.4%), covers 100.0% of PF04241, 83.5 bits

YLKC_SCHPO / Q9P7G8 UPF0382 membrane protein C1782.12c from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
Aligns to 17:106 / 118 (76.3%), covers 100.0% of PF04241, 82.9 bits

AT2G04900 hypothetical protein from Arabidopsis thaliana
Aligns to 37:116 / 128 (62.5%), covers 100.0% of PF04241, 81.4 bits

• Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis
  Chai, PeerJ 2020
  • “...the transcription factor TFIIIC (tau55-related protein); (3) AT1G14800 encodes a nucleic acid-binding, OB-fold-like protein; (4) AT2G04900 encodes an unknown protein; (5) AT3G10070 encodes one of two Arabidopsis proteins with similarity to the TBP-associated factor, TAF12; (6) AT1G15060 encodes an alpha/beta hydrolase family protein; (7) AT3G54620 encodes...”
  • “...(GAUT14) BnaA02g03080D AT3G15420 Transcription factor TFIIIC, Tau55-related protein BnaA04g16220D AT1G14800 Nucleic acid-binding, OB-fold-like protein BnaA07g04500D AT2G04900 Unknown protein BnaA09g45000D AT3G10070 TBP-ASSOCIATED FACTOR 12 (TAF12) BnaA09g45260D AT1G15060 Uncharacterized conserved protein UCP031088, alpha/beta hydrolase BnaAnng30260D AT3G54620 BASIC LEUCINE ZIPPER 25 (BZIP25) BnaC02g06440D AT5G16210 HEAT repeat-containing protein BnaC06g16950D AT3G59000...”
• The Receptor for Activated C Kinase in Plant Signaling: Tale of a Promiscuous Little Molecule
  Islas-Flores, Frontiers in plant science 2015
  • “...phosphatase 2C 15 family protein Unknown c A. thaliana Klopffleisch et al., 2011 112 AtRACK1A AT2G04900 Uncharacterized protein Unknown e A. thaliana Kundu et al., 2013 113 AtRACK1A AT2G10940 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein Lipid transport e A. thaliana Kundu et al., 2013...”
• Synergistic use of plant-prokaryote comparative genomics for functional annotations
  Gerdes, BMC genomics 2011
  • “...COG3146 Pterin-dependent enzyme Xanthomonas campestris protein lacks benzoate hydroxylase activity in complementation assay 236 22 At2g04900 2363 ywdK COG2363 Thiamine-related transporter E. coli protein does not mediate uptake of thiazole or hydroxymethylpyrminidine 221 23 At1g09150 2016 rRNA modification Archaea; DOE-COG2016 Ribosome assembly/translation termination In progress in...”

Q8N2U0 Transmembrane protein 256 from Homo sapiens
NP_689979 transmembrane protein 256 precursor from Homo sapiens
Aligns to 22:101 / 113 (70.8%), covers 98.9% of PF04241, 69.5 bits

• Molecular Network Analysis of the Urinary Proteome of Alzheimer's Disease Patients.
  Watanabe, Dementia and geriatric cognitive disorders extra 2019
  • “...(n = 18) P02042 16.0 Hemoglobin subunit (HBD) 17.59 0.0001 19.7571 0 10 0.032 0.166 Q8N2U0 11.7 Transmembrane protein 256 (TMEM256) 10.53 0.0001 0.1478 0 9 0.006 0.068 A0AVF1 64.1 Intraflagellar transport protein 56 (TTC26) 10.49 0.0001 0.1440 0 12 0.023 0.138 P81605-2 12.4 Isoform 2...”
• Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import.
  Nguyen, Nature communications 2018
  • “...LWGLLFLSAALSL WPTSG + + 26.7 0.404 P08572 * COL4A2 MGRDQRAVAGPALRRW LLLGTVTVGFLA QSVLA + 20.0 0.04 Q8N2U0 * TMEM256 MAGPAAAFRR LGALSGAAALGF ASYGAHG + 24.1 0.292 Q9UBV2 * SEL1L MRVR IGLTLLLCAVLL SLASA + + 4.8 1.651 Q969V3 NCLN MLEEAGEVLENMLKASCLPLGFIVFLPAVLLLVAPPLPAADA + + 16.7 1.038 O14672 * ADAM10 M VLLRVLILLLSW...”
• Identification of prostate cancer biomarkers in urinary exosomes
  Øverbye, Oncotarget 2015
  • “...specificity #PAT at 100% specificity Validated iBAQ ratio PAT:CTR Abundance (ppm of total proteome) 1 Q8N2U0 Transmembrane protein 256 5 16 94% 15 140.39 4324 2 Q15847 Adipogenesis regulatory factor 4 15 81% 13 18.99 369 3 Q6IAA8 Ragulator complex protein LAMTOR1 4 16 81% 13...”
• Mitochondrial proteomic approach reveals galectin-7 as a novel BCL-2 binding protein in human cells
  Villeneuve, Molecular biology of the cell 2011
  • “...P04040 Catalase Human 3 7 P10606 Cytochrome c oxidase subunit, mitochondrial precursor Human 5 30.2 Q8N2U0 UPF0451 protein C17orf61 precursor Human 1 24.8 Q9NVH1 DnaJ homologue subfamily C member 11 Human 7 10.4 Q96LJ7 Dehydrogenase/reductase SDR family member 1 Human 4 12.1 P43003 Excitatory amino acid...”
• Long-term functional improvement and gene expression changes after bone marrow-derived multipotent progenitor cell transplantation in myocardial infarction
  Jameel, American journal of physiology. Heart and circulatory physiology 2010
  • “...0.51 ANAPC11 BLOC1S1 CALM2 MAGM_HUMAN 0.56 0.53 0.54 0.55 Q8N2U0 0.56 0.57 Q8NAX4 TRAPPC5 MRPS18A DUT OLFM1 0.56 0.58 0.56 0.54 0.56 Q69YN4 ZFP91 GMDS ERO1L...”
• Exosomal proteins as prostate cancer biomarkers in urine: From mass spectrometry discovery to immunoassay-based validation.
  Wang, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences 2017 (PubMed)
  • GeneRIF: Western blot experiments designed to detect flotillin 2, TMEM256, Rab3B and LAMTOR1 showed that the level of these proteins was higher in urinary exosomes from prostate cancer patients compared to healthy males

F1LYI7 Transmembrane protein 256 from Rattus norvegicus
Aligns to 22:101 / 113 (70.8%), covers 100.0% of PF04241, 69.1 bits

• iTRAQ-based proteomics analysis on insomnia rats treated with Mongolian medical warm acupuncture
  Xu, Bioscience reports 2020
  • “...0.012393709 A0A0G2K4U7 Protein Mtus2 1.232703408 0.01391488 D4A1U8 Protein RGD1311744 1.277139639 0.014144665 P24090 Alpha-2-HS-glycoprotein 1.296358037 0.01441777 F1LYI7 Protein Tmem256 1.207978689 0.015866603 D3ZA53 Protein Pnmal1 1.421893598 0.016281749 Q9EQP5 Prolargin 1.273012448 0.017232379 M0RA79 Protein LOC691828 1.273971816 0.019054036 Q95571 RT1.A(U) alpha chain (Fragment) 1.266842428 0.019175113 M0R6Y8 Phosphoglycerate kinase 1.22539767 0.024665028...”

NGR_c24510 hypothetical protein from Rhizobium sp. NGR234
NGR_c24510 DUF423 domain-containing protein from Sinorhizobium fredii NGR234
Aligns to 24:101 / 130 (60.0%), covers 98.9% of PF04241, 26.6 bits

• Calcium Induces the Cleavage of NopA and Regulates the Expression of Nodulation Genes and Secretion of T3SS Effectors in Sinorhizobium fredii NGR234
  Kim, International journal of molecular sciences 2024
  • “...4.686157099 hypothetical protein NGR_c03900 0.265386827 hypothetical protein NGR_c17840 4.790515014 hypothetical protein NGR_c20330 4.411039572 hypothetical protein NGR_c24510 0.322154807 conserved hypothetical protein NGR_c31210 0.106635366 hypothetical protein Other functions NGR_a01890 0.252290146 putative transposase of undefined mobile element NGR_b05010 3.132126719 conserved hypothetical protein (rotamase, protein folding) NGR_b12570 0.302431844 catalase-peroxidase protein...”

Or search for genetic data about PF04241 in the Fitness Browser