Detailed information of component protein


Summary

Component ID T6CP004915
Component protein type PdpB
T6SS ID (Type) T6SS00158 experimental (Type ii)
Strain Francisella tularensis subsp. novicida U112
Replicon chromosome
Sequence Protein sequence (1094 a.a.); Nucleotide sequence (3282 bp)
Reference
[1] de Bruin OM, Duplantis BN, Ludu JS, et al. The biochemical properties of the Francisella pathogenicity island (FPI)-encoded proteins IglA, IglB, IglC, PdpB and DotU suggest roles in type VI secretion. Microbiology (Reading). 2011 Dec;157(Pt 12):3483-3491. doi: 10.1099/mic.0.052308-0. Epub 2011 Oct 6. PMID: 21980115
[2] Robb CS, Nano FE, Boraston AB. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of intracellular growth locus E (IglE) protein from Francisella tularensis subsp. novicida. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Dec 1;66(Pt 12):1596-8. doi: 10.1107/S1744309110034378. Epub 2010 Nov 25. PMID: 21139203
[3] Nano FE, Schmerk C. The Francisella pathogenicity island. Ann N Y Acad Sci. 2007 Jun;1105:122-37. Epub 2007 Mar 29. PMID: 17395722
[4] Bröms JE, Meyer L, Sun K, et al. Unique substrates secreted by the type VI secretion system of Francisella tularensis during intramacrophage infection. PLoS One. 2012;7(11):e50473. doi: 10.1371/journal.pone.0050473. Epub 2012 Nov 20. PMID: 23185631
[5] Barker JR, Chong A, Wehrly TD, et al. The Francisella tularensis pathogenicity island encodes a secretion system that is required for phagosome escape and virulence. Mol Microbiol. 2009 Dec;74(6):1459-70. PMID: 20054881
[6] Hare RF, Hueffer K. Francisella novicida pathogenicity island encoded proteins were secreted during infection of macrophage-like cells. PLoS One. 2014 Aug 26;9(8):e105773. doi: 10.1371/journal.pone.0105773. eCollection 2014. PMID: 25158041
experimental Experimental investigation has been performed on this T6SS
External database links

Locus tag (Gene) FTN_RS06710
Coordinate (Strand) 1380761..1384042 (+)
NCBI ID WP_003040112.1
RefSeq NC_008601
Uniprot ID A0A6I4RUA1_FRATU, A0Q7H1_FRATN
KEGG ID ftn:FTN_1310, ftx:AW25_694
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-9 MNFIKNHQI
Transmembrane helix 10-29 LIISLTIAIIVLSVLGIFII
Inside 30-272 KKWLKTSRNPNKKSASKTIKNAKSLIKKNKVKNNLSELYIFYGDYLAAKDYITKIKPQAQIIDNNELPLIAIDKNNTSLVFANNEFSYLYKLKKKLNLQFYKLNFCFDISDDYYHENIKISEIYKELLKLRLKNFIISFYTLSEHTRSYNNAIDKKSIFKLTSDADTNHKAEEEILSKILSSKDDVNNKYNNVRILNQIRRLLKNIYPQLKSINKEIFFNFGLNIPDNIIAKKDTIFFSSSPK
Transmembrane helix 273-292 GIIINLISLLFSFIFIINIF
Outside 293-1093 QEINIKEKLSIQELNQLHESDSNKIIKEARKKIDDAILLDILYPKSIKYHFIYEQYADTLLKNVILPKYNDTYDLSMITSFLIFFEYLDNKITNQHTNRILKIISSITNLSEKQLDIVIKYTTPSIRTEMIKSAINRANKLYTNRLIVVGEDSESYLSTKGFNAEYLGISNTKRAKVINNIYIQYLYKCATDNAILDLNDNYIIPTEVNNIFKMYQEQFDTSSKKLCNSSYINSITKSVSLILNQEENKRKFKSFSDMLDHIYYLVKSLEKNAKDVADDGKEQTSSITVSLINYVINSVVNPTYNKNELPLISPVSKNLYMEFAPNFYSKRILISPIYSKEYIKDNIDPINKKFNRLVNNLKNNFNIEPDFMIAIYKSSINNYIEKYIGSYNKMIDSLNNDSEFNKNISNKGALKLYLLAMSSKDSSFNSLIEFYSTNTDLITNESETNSSKKINKLQHFYGEITKLNKQNNTNDPNDKSLWEPIDNYFKENDKYLESKSYADYKNIFKQLNNLIIEQGYSSTYKNIKQGYEPLQKVYSELSKINNHQGNNNLYKLLKKHLDIAINAIKTIAIQDAITKLNNTVNIEYEYINNQFPFNKDSNSAATNEAITKDFDNNGYIYSGFIEQLSPLLSYNKTDDRWESKDFSKPEEIDYLNKFNKVYLLNKLLWDDKRNPKAIKFDITPIPNKDNDYTFFSIILDKQNYVNSLNIKYSDSIEVLYNWNSLESTTITIKFEDGSNEQISYQGKWSILKAIKDANCDQNNICTWVIKHKGKTYPVSFKIKSKFLQVLGWQKQGEVNVQ


Signal peptides
  • Sec/SPI: "standard" secretory signal peptides transported by the Sec translocon and cleaved by Signal Peptidase I (Lep).
  • Sec/SPII: lipoprotein signal peptides transported by the Sec translocon and cleaved by Signal Peptidase II (Lsp).
  • Tat/SPI: Tat signal peptides transported by the Tat translocon and cleaved by Signal Peptidase I (Lep).
Prediction        Probability Cleavage site Signal peptide sequence
Other 0.9961 - -


  Protein sequence: 1094 a.a.    

>T6CP004915 NC_008601:1380761-1384042 [Francisella tularensis subsp. novicida U112] [PdpB]
MNFIKNHQILIISLTIAIIVLSVLGIFIIKKWLKTSRNPNKKSASKTIKNAKSLIKKNKVKNNLSELYIFYGDYLAAKDY
ITKIKPQAQIIDNNELPLIAIDKNNTSLVFANNEFSYLYKLKKKLNLQFYKLNFCFDISDDYYHENIKISEIYKELLKLR
LKNFIISFYTLSEHTRSYNNAIDKKSIFKLTSDADTNHKAEEEILSKILSSKDDVNNKYNNVRILNQIRRLLKNIYPQLK
SINKEIFFNFGLNIPDNIIAKKDTIFFSSSPKGIIINLISLLFSFIFIINIFQEINIKEKLSIQELNQLHESDSNKIIKE
ARKKIDDAILLDILYPKSIKYHFIYEQYADTLLKNVILPKYNDTYDLSMITSFLIFFEYLDNKITNQHTNRILKIISSIT
NLSEKQLDIVIKYTTPSIRTEMIKSAINRANKLYTNRLIVVGEDSESYLSTKGFNAEYLGISNTKRAKVINNIYIQYLYK
CATDNAILDLNDNYIIPTEVNNIFKMYQEQFDTSSKKLCNSSYINSITKSVSLILNQEENKRKFKSFSDMLDHIYYLVKS
LEKNAKDVADDGKEQTSSITVSLINYVINSVVNPTYNKNELPLISPVSKNLYMEFAPNFYSKRILISPIYSKEYIKDNID
PINKKFNRLVNNLKNNFNIEPDFMIAIYKSSINNYIEKYIGSYNKMIDSLNNDSEFNKNISNKGALKLYLLAMSSKDSSF
NSLIEFYSTNTDLITNESETNSSKKINKLQHFYGEITKLNKQNNTNDPNDKSLWEPIDNYFKENDKYLESKSYADYKNIF
KQLNNLIIEQGYSSTYKNIKQGYEPLQKVYSELSKINNHQGNNNLYKLLKKHLDIAINAIKTIAIQDAITKLNNTVNIEY
EYINNQFPFNKDSNSAATNEAITKDFDNNGYIYSGFIEQLSPLLSYNKTDDRWESKDFSKPEEIDYLNKFNKVYLLNKLL
WDDKRNPKAIKFDITPIPNKDNDYTFFSIILDKQNYVNSLNIKYSDSIEVLYNWNSLESTTITIKFEDGSNEQISYQGKW
SILKAIKDANCDQNNICTWVIKHKGKTYPVSFKIKSKFLQVLGWQKQGEVNVQ*

  Nucleotide sequence: 3282 bp    

>T6CP004915 NC_008601:1380761-1384042 [Francisella tularensis subsp. novicida U112] [PdpB]
ATGAATTTTATTAAAAATCATCAAATATTAATAATTTCACTAACTATAGCAATAATTGTTTTATCAGTACTTGGTATTTT
TATAATTAAAAAATGGCTTAAAACATCAAGAAATCCTAACAAAAAATCTGCCTCAAAGACCATAAAAAATGCAAAATCAT
TGATCAAAAAGAATAAAGTAAAAAACAACTTAAGTGAATTGTATATTTTCTATGGGGACTATCTGGCAGCTAAAGATTAT
ATAACAAAGATAAAGCCTCAAGCTCAAATCATTGATAATAATGAACTCCCTTTAATAGCTATTGATAAAAACAATACATC
TCTCGTATTTGCAAATAATGAATTTTCGTACCTATATAAGTTAAAAAAGAAACTAAATCTACAATTTTATAAGCTTAACT
TTTGCTTCGATATATCCGATGATTACTACCATGAAAATATCAAAATTAGTGAAATCTATAAAGAACTATTAAAATTAAGA
TTAAAAAACTTCATAATATCTTTTTACACCTTATCTGAGCATACTAGAAGCTATAATAATGCAATTGATAAAAAATCAAT
ATTTAAATTAACTTCTGATGCGGATACAAATCATAAAGCTGAAGAGGAAATATTATCAAAAATTCTTAGCTCTAAAGATG
ATGTTAATAATAAATACAATAATGTTAGGATATTAAATCAAATAAGAAGGTTGCTAAAAAACATCTACCCTCAATTAAAA
TCTATAAATAAAGAAATATTCTTTAATTTTGGGCTAAACATACCAGATAATATTATAGCAAAGAAAGATACAATATTTTT
TAGCAGCTCTCCAAAAGGTATTATTATAAACTTAATATCTTTGTTATTTAGTTTTATATTTATCATTAATATTTTTCAAG
AAATTAACATTAAAGAAAAACTCTCTATACAAGAGCTTAATCAACTACATGAAAGCGACTCTAATAAAATAATAAAAGAA
GCTAGAAAAAAAATTGATGATGCTATACTTCTAGACATCCTATATCCAAAATCGATAAAATATCATTTCATATACGAACA
ATATGCTGATACTCTCCTAAAGAATGTAATCCTACCAAAATATAATGATACATATGACTTATCAATGATTACATCATTTT
TAATATTTTTTGAGTATTTGGATAACAAAATTACTAACCAACATACGAATAGAATACTTAAAATAATAAGCAGTATCACC
AACCTATCTGAAAAGCAGCTAGATATCGTGATCAAGTATACGACCCCAAGTATAAGAACTGAAATGATTAAGTCAGCCAT
CAACAGAGCAAATAAACTTTATACAAATCGTTTAATAGTTGTAGGTGAAGACTCCGAAAGTTACTTAAGTACTAAAGGAT
TTAATGCTGAATACTTAGGGATTTCAAATACTAAAAGAGCGAAGGTCATAAATAATATTTATATACAATACCTATATAAA
TGTGCTACAGATAATGCAATTTTAGATTTAAACGATAACTACATAATACCAACAGAAGTAAATAATATCTTCAAGATGTA
TCAAGAGCAATTTGACACATCATCTAAAAAGCTATGTAATTCATCATATATTAACTCTATTACAAAGAGTGTTTCTTTGA
TACTTAATCAAGAGGAAAATAAAAGAAAATTTAAAAGCTTCAGTGATATGCTAGACCATATCTATTATTTAGTAAAATCA
TTAGAAAAAAATGCTAAAGATGTCGCAGATGATGGTAAAGAACAAACTAGCTCGATAACAGTATCGCTTATAAATTACGT
TATAAATAGTGTTGTCAACCCTACTTATAATAAAAATGAGCTCCCACTAATAAGTCCAGTAAGTAAAAACCTATATATGG
AGTTTGCTCCTAATTTCTATAGTAAAAGAATACTTATCTCCCCAATATACTCAAAAGAATATATTAAAGATAATATAGAT
CCTATAAATAAAAAGTTTAATAGACTCGTCAATAATCTAAAGAATAACTTCAATATAGAACCCGACTTTATGATTGCTAT
CTATAAAAGTTCTATAAACAACTACATTGAGAAATATATAGGATCCTATAATAAGATGATTGATAGCCTTAATAATGACT
CTGAATTTAACAAAAATATATCTAACAAGGGTGCTCTTAAATTATATTTGCTAGCAATGTCATCAAAGGATTCTTCCTTT
AATAGCCTAATAGAGTTTTATAGCACTAATACAGACCTAATAACTAATGAATCCGAAACCAATTCATCTAAAAAGATAAA
TAAGCTTCAACATTTTTATGGAGAAATAACTAAATTAAACAAACAAAACAATACTAATGATCCAAATGATAAGTCATTGT
GGGAGCCTATAGATAACTACTTTAAAGAAAACGATAAATATCTTGAGTCTAAGAGTTATGCCGACTATAAAAACATATTT
AAACAGTTAAATAATCTAATAATAGAACAAGGCTATTCAAGTACATATAAAAATATCAAACAAGGATATGAACCACTACA
AAAAGTTTACTCTGAACTTTCTAAGATAAATAATCATCAAGGTAATAATAACTTATATAAACTGCTGAAGAAACATCTAG
ATATTGCCATTAATGCTATAAAAACTATCGCGATACAAGATGCTATAACTAAACTTAATAATACTGTCAATATTGAGTAC
GAATATATAAATAATCAATTCCCTTTTAATAAGGATAGTAACTCGGCTGCAACAAATGAAGCTATAACCAAAGACTTTGA
TAACAATGGTTATATATACTCTGGATTTATAGAGCAGCTATCTCCACTACTTTCTTATAATAAAACAGATGATAGATGGG
AAAGTAAAGATTTTTCAAAACCTGAGGAAATAGACTATCTAAACAAATTCAATAAGGTATATCTTTTAAATAAGCTACTA
TGGGATGATAAAAGAAATCCAAAAGCTATAAAATTTGATATAACTCCTATACCAAACAAAGATAATGATTATACATTTTT
TAGCATAATCCTCGATAAGCAAAACTATGTAAACTCATTAAACATAAAATATTCAGATAGTATTGAAGTTTTGTACAACT
GGAATTCACTTGAGTCAACAACTATTACCATAAAATTTGAGGATGGTAGTAATGAGCAAATAAGCTATCAAGGAAAATGG
TCTATATTAAAAGCAATTAAAGACGCAAATTGTGATCAAAACAATATTTGTACCTGGGTAATCAAGCACAAAGGTAAAAC
ATATCCTGTAAGCTTCAAAATAAAATCAAAATTCTTACAAGTATTAGGATGGCAAAAACAAGGAGAAGTTAATGTACAAT
AA