Family Search for PF13910 (DUF4209)

Running HMMer for PF13910

PF13910 hits 10 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

NP_001265460 endoplasmic reticulum membrane-associated RNA degradation protein isoform 2 from Homo sapiens
Aligns to 133:214 / 631 (13.0%), covers 98.9% of PF13910, 106.4 bits

• Periventricular heterotopia in 6q terminal deletion syndrome: role of the C6orf70 gene.
  Conti, Brain : a journal of neurology 2013 (PubMed)
  • GeneRIF: C6orf70 plays a major role in the control of neuronal migration; its haploinsufficiency or mutation causes periventricular nodular heterotopia.

EMARD_HUMAN / Q5T6L9 Endoplasmic reticulum membrane-associated RNA degradation protein; ER membrane-associated RNA degradation protein from Homo sapiens (Human) (see paper)
Aligns to 133:214 / 678 (12.1%), covers 98.9% of PF13910, 106.2 bits

• function: May play a role in neuronal migration during embryonic development.
• Quantitative gingival crevicular fluid proteome in health and periodontal disease using stable isotope chemistries and mass spectrometry
  Carneiro, Journal of clinical periodontology 2014
  • “...SNS 1.59 0.33 SNS 9 9 Q6IQ55 Tau-tubulin kinase 2 0.95 0.33 SNS 5 3 Q5T6L9 Transmembrane protein C6orf70 1.55 0.65 SNS 3 2 Q6ZXV5 Transmembrane and TPR repeat-containing protein 3 8.68 6.6 SNS 3 2 Q0VAA2 Uncharacterized protein C14orf166B 1.24 0.06 SNS 3 2 Q15878...”
• Genetic and functional evidence implicating DLL1 as the gene that influences susceptibility to visceral leishmaniasis at chromosome 6q27.
  Fakiola, The Journal of infectious diseases 2011

EMARD_RAT / Q3B8R1 Endoplasmic reticulum membrane-associated RNA degradation protein; ER membrane-associated RNA degradation protein from Rattus norvegicus (Rat) (see paper)
Aligns to 133:214 / 678 (12.1%), covers 98.9% of PF13910, 97.6 bits

• function: May play a role in neuronal migration during embryonic development.
  disruption phenotype: RNAi-mediated knockdown of the protein, performed in utero by electroporation in lateral ventricle of 15 dpc embryos, results in a massive neuronal migration defect and in the development of heterotopic nodules along the walls of the lateral ventricles. At 20 dpc, a significant arrest of cells within the ventricular zone is observed, while, at this stage in control embryos, cells have reached the cortical plate.

PFCIRM129_12290 DUF4209 domain-containing protein from Propionibacterium freudenreichii subsp. freudenreichii
Aligns to 484:575 / 614 (15.0%), covers 98.9% of PF13910, 82.0 bits

• Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129
  do, Frontiers in microbiology 2018
  • “...Glutamyl-tRNA(Gln) amidotransferase subunit C (Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C) 1.71 0.045 Translation, ribosomal structure and biogenesis PFCIRM129_12290 113.782 Hypothetical protein 1.73 0.023 Translation, ribosomal structure and biogenesis PFCIRM129_02880 157.3643 Zn dependant peptidase 1.82 0.002 General function prediction only PFCIRM129_01675 171.214 Flavin-containing amine oxidase 1.82 0.013 Amino acid...”

SMUL_0516 DUF4209 domain-containing protein from Sulfurospirillum multivorans DSM 12446
Aligns to 491:582 / 592 (15.5%), covers 98.9% of PF13910, 58.1 bits

• Conditional essentiality of the 11-subunit complex I-like enzyme in strict anaerobes: the case of Desulfitobacterium hafniense strain DCB-2
  Willemin, Frontiers in microbiology 2024
  • “...the presence of additional genes of various functions within the nuo transcriptional unit. Note that SMUL_0516 (indicated by an asterisk) is a gene of unknown function that is not predicted to be part of any S. multivorans nuo operons. The double asterisk indicates a nuoCD fused...”

XAC1509 hypothetical protein from Xanthomonas axonopodis pv. citri str. 306
Aligns to 520:610 / 636 (14.3%), covers 96.6% of PF13910, 57.4 bits

• Interaction network and mass spectrometry data of Xanthomonas citri subsp. citri surface proteins from differential proteomic analysis of infectious and non-infectious cells
  Carnielli, Data in brief 2016
  • “...chaperone DnaK Not defined GO:0005524 ATP binding GO:0006457 protein folding GO:0006950 response to stress Q8PMC2 XAC1509 Not defined No hits found No hits found No hits found Not defined Not defined Not defined Q8PML3 oma Not defined Outer membrane protein assembly factor BamA OS= Edwardsiella ictaluri...”
• Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges
  Gordon, BMC genomics 2015
  • “...citri pv.bilvae Island1 4 1253042-1259543 1272074-1278440 XAC1101 XAC1107 A* Unknown Island2 5 1729051-1743732 1758692-1774868 XAC1497 XAC1509 Aw Unknown Island3 6 2931468-2932633 3000594-3001946 XAC2505 XAC2506 LE3-1, LE20-1 Unknown 7 3256265-3256278 3344395-3344409 Intergenic Intergenic JJ10-1, C40 Unknown 8 3525240-3525417 3615434-3615613 XAC3016 XAC3016 JS581, JS582, JS584, JK48, JK2-10 Unknown...”
  • “...and A w strain Xcaw12879 [ 12 ]), and xrvA , mobL, XAC1496, XAC1499 and XAC1509 on Island 3 that are absent from A*. Islands 24 all contain at least one gene that is usually plasmid-associated indicating their probable origin as plasmidic. Table 3 Gene islands...”
• Genome-wide mutagenesis of Xanthomonas axonopodis pv. citri reveals novel genetic determinants and regulation mechanisms of biofilm formation
  Li, PloS one 2011
  • “...68.81.9* 89.12.7* 92.82.8 XAC1469 bdp3 hypothetical protein, similar to TatD-related DNase 270H4 78.82.6* 93.33.9 94.12.3 XAC1509 bdp4 hypothetical protein 411F5 65.12.1* 92.12.3 62.71.1* XAC1923 bdp5 hypothetical protein 288D11 92.83.8 92.73.6 92.42.2 XAC2018 bdp6 hypothetical protein, predicted transcriptional regulator containing an XRE-like HTH domain 290E7 103.94.6 79.71.6*...”
  • “...a hypothetical protein without any conserved domains. The closest homolog (80% amino acid identity) to XAC1509 was found in X. campestris pv. campestris strain B100 with a protein of unknown function. The putative 363 amino acid XAC2848 protein contains a predicted DUF3616 domain (Pfam entry PF12275)....”

SAPIG0067 DUF4209 domain-containing protein from Staphylococcus aureus subsp. aureus ST398
Aligns to 496:587 / 596 (15.4%), covers 96.6% of PF13910, 50.7 bits

• Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild and Captive Macaques
  Monecke, International journal of molecular sciences 2022
  • “...19 72,372 72,390 19 N/A D2N3A7 putative protein Forward 81,084 82,875 1792 72,448 74,238 1791 SAPIG0067 F8WKF7 putative protein Forward, truncated in AM990992 82,916 84,073 1158 74,279 74,897 619 SAPIG0068...”

BHWA1_01317 hypothetical protein from Brachyspira hyodysenteriae WA1
Aligns to 473:568 / 584 (16.4%), covers 98.9% of PF13910, 50.2 bits

• Absence of a set of plasmid-encoded genes is predictive of reduced pathogenic potential in Brachyspira hyodysenteriae
  La, Veterinary research 2014
  • “...the WA1 genes. Only five genes (of unknown function) were specific to B. hyodysenteriae WA1 (BHWA1_01317, BHWA1_00005, BHWA1_00006, BHWA1_01358 and BHWA1_00574). The data from the CGH analysis have been deposited at the Gene Expression Omnibus public repository [ 14 ]. The CGH analysis identified four genes...”

Q8YCT2 DUF4209 domain-containing protein from Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)
Aligns to 521:615 / 631 (15.1%), covers 98.9% of PF13910, 23.9 bits

• Identification of a gene encoding a functional reverse transcriptase within a highly variable locus in the P2-like coliphages
  Odegrip, Journal of bacteriology 2006
  • “...Q858T3 Q7Y487 Q06426 Q6K1F0 Q6D3W7 1.5E63 2.3E36 5.9E36 Q913X4 Q8YCT2 Q578W9 tin (253 aa) old (587 aa) 3,033 67 orf555 orf333 P2-EC30 P2-EC31 1,806 954 66 51...”

BruAb2_0386 hypothetical protein from Brucella abortus biovar 1 str. 9-941
Q578W9 DUF4209 domain-containing protein from Brucella abortus biovar 1 (strain 9-941)
Aligns to 521:615 / 631 (15.1%), covers 98.9% of PF13910, 23.9 bits

• Identification of a gene encoding a functional reverse transcriptase within a highly variable locus in the P2-like coliphages
  Odegrip, Journal of bacteriology 2006
  • “...aaa Brucella melitensis, BMEIl1446, 631 aaa Brucella abortus, BruAb2_0386, 631 aaa P2-EC58 2,203 62 orf86 orf544 No significant hits Synechocystis sp. strain...”
• Identification of a gene encoding a functional reverse transcriptase within a highly variable locus in the P2-like coliphages
  Odegrip, Journal of bacteriology 2006
  • “...Q7Y487 Q06426 Q6K1F0 Q6D3W7 1.5E63 2.3E36 5.9E36 Q913X4 Q8YCT2 Q578W9 tin (253 aa) old (587 aa) 3,033 67 orf555 orf333 P2-EC30 P2-EC31 1,806 954 66 51 orf570...”

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