Detailed information of component protein


Summary

Component ID T6CP000336
Component protein type TssC
T6SS ID (Type) T6SS00041 insolico (Type i1)
Strain Pseudomonas syringae pv. tomato str. DC3000
Replicon chromosome
Sequence Protein sequence (492 a.a.); Nucleotide sequence (1476 bp)
Reference
[1] Haapalainen M, Mosorin H, Dorati F, et al. Hcp2, a secreted protein of the phytopathogen Pseudomonas syringae pv. tomato DC3000, is required for fitness for competition against bacteria and yeasts. J Bacteriol. 2012 Sep;194(18):4810-22. doi: 10.1128/JB.00611-12. Epub 2012 Jun 29. PMID: 22753062
[2] Sarris PF, Skandalis N, Kokkinidis M, et al. In silico analysis reveals multiple putative type VI secretion systems and effector proteins in Pseudomonas syringae pathovars. Mol Plant Pathol. 2010 Nov;11(6):795-804. doi: 10.1111/j.1364-3703.2010.00644.x. PMID: 21091602
[3] Boyer F, Fichant G, Berthod J, et al. Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? BMC Genomics. 2009 Mar 12;10:104. doi: 10.1186/1471-2164-10-104. PMID: 19284603
[4] Barret M, Egan F, Fargier E, et al. Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology (Reading). 2011 Jun;157(Pt 6):1726-1739. doi: 10.1099/mic.0.048645-0. Epub 2011 Apr 7. PMID: 21474537
insolico Bioinformatics investigation has been performed on this T6SS
External database links

Locus tag (Gene) PSPTO_RS13175
Coordinate (Strand) 2808195..2809670 (+)
NCBI ID WP_011104072.1
RefSeq NC_004578
Uniprot ID -
KEGG ID -
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
VipB PF05943.14 6.7e-127 65..364
VipB_2 PF18945.2 2e-44 378..488
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-491 MTSKAMQQGTVSEFQHGILDQIIAETRLSPDDDAYEIAKRGVAAFIEELLKPHNSNEPVKKALVDRMITEIDAKLSQQMDEIIHHAEFQALEASWRGLQLLIDRTDFRENIKIELLSISRQDLLEDFEDSPEVVQSGLYKHVYTAEYGQFGGNPVGAIIANYFFSPSAPDVKTMQYVSSVACMAHAPFIAAAGPNFFGLEQFTGLPDLKDLRDHFEGPQFAKWQSFRQQEDARYLALTVPRFLLRSPYEPEENPVKTFAYKENVANSHEHYLWGNTAYAFATKLTDSFAKFRWCPNIIGPLSGGAVEDLPLHHFHSMGEIETKIPTEVLVSDRREYELAEEGFIALTMRKGSDNAAFFSASSVQKPKFFGNSPEGKTAELNYRLGTQLPYMMVVNRLAHYLKVLQREQIGSWKERADLEAQLNKWIRQYIADQENPSSEVRGRRPLRSAQIIVSDVEGDPGWYRVSLNVRPHFKYMGADFTLSLVGKMDKE


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 0.9951 - -


  Protein sequence: 492 a.a.    

>T6CP000336 NC_004578:2808195-2809670 [Pseudomonas syringae pv. tomato str. DC3000] [TssC]
MTSKAMQQGTVSEFQHGILDQIIAETRLSPDDDAYEIAKRGVAAFIEELLKPHNSNEPVKKALVDRMITEIDAKLSQQMD
EIIHHAEFQALEASWRGLQLLIDRTDFRENIKIELLSISRQDLLEDFEDSPEVVQSGLYKHVYTAEYGQFGGNPVGAIIA
NYFFSPSAPDVKTMQYVSSVACMAHAPFIAAAGPNFFGLEQFTGLPDLKDLRDHFEGPQFAKWQSFRQQEDARYLALTVP
RFLLRSPYEPEENPVKTFAYKENVANSHEHYLWGNTAYAFATKLTDSFAKFRWCPNIIGPLSGGAVEDLPLHHFHSMGEI
ETKIPTEVLVSDRREYELAEEGFIALTMRKGSDNAAFFSASSVQKPKFFGNSPEGKTAELNYRLGTQLPYMMVVNRLAHY
LKVLQREQIGSWKERADLEAQLNKWIRQYIADQENPSSEVRGRRPLRSAQIIVSDVEGDPGWYRVSLNVRPHFKYMGADF
TLSLVGKMDKE*

  Nucleotide sequence: 1476 bp    

>T6CP000336 NC_004578:2808195-2809670 [Pseudomonas syringae pv. tomato str. DC3000] [TssC]
ATGACCAGCAAAGCTATGCAACAGGGTACTGTCAGCGAATTTCAGCACGGAATCCTTGATCAGATCATCGCAGAAACCAG
GCTGAGCCCGGATGATGATGCCTATGAAATTGCCAAGCGTGGTGTTGCTGCGTTTATCGAAGAACTGCTCAAGCCGCACA
ACAGCAACGAGCCAGTAAAAAAGGCCTTGGTCGATCGAATGATCACGGAAATTGACGCCAAACTGAGTCAGCAGATGGAT
GAGATCATTCACCATGCAGAATTTCAGGCATTGGAGGCGTCCTGGCGCGGACTGCAGTTACTGATTGATCGAACAGATTT
TCGCGAAAATATCAAAATCGAATTGTTGAGCATCTCCAGGCAGGACCTTCTGGAGGATTTTGAGGACTCCCCCGAAGTGG
TCCAGTCGGGACTTTACAAGCACGTCTACACCGCTGAATACGGCCAGTTTGGTGGCAATCCGGTTGGTGCAATCATTGCC
AACTATTTCTTTTCCCCAAGCGCTCCCGATGTCAAGACCATGCAGTACGTTTCAAGTGTTGCCTGTATGGCACACGCACC
ATTTATCGCGGCGGCGGGGCCCAATTTTTTCGGGCTTGAGCAGTTCACCGGTCTGCCTGACCTCAAAGACTTGAGAGATC
ATTTCGAAGGCCCACAGTTCGCCAAATGGCAGAGCTTCCGCCAGCAAGAAGACGCTCGATACCTGGCACTGACAGTGCCA
CGTTTTCTTTTGCGCAGCCCTTACGAGCCCGAGGAAAATCCGGTTAAAACGTTTGCCTACAAGGAGAATGTTGCGAACAG
TCACGAGCACTATCTGTGGGGGAACACGGCGTATGCATTCGCGACGAAGCTGACAGACAGCTTCGCCAAATTCCGCTGGT
GTCCTAACATCATCGGGCCGTTGAGCGGCGGTGCCGTCGAAGATCTTCCTTTGCATCACTTCCACAGCATGGGCGAGATC
GAGACCAAGATCCCGACTGAAGTGCTGGTCTCTGATCGTCGTGAGTACGAGCTGGCCGAGGAAGGGTTCATTGCATTGAC
CATGCGCAAAGGAAGCGACAACGCCGCCTTTTTCTCGGCGAGCTCAGTGCAGAAGCCGAAGTTTTTCGGCAACAGCCCGG
AAGGTAAGACAGCCGAACTCAATTACAGGCTGGGTACTCAACTGCCGTACATGATGGTGGTCAACCGACTGGCGCATTAT
CTCAAGGTCTTGCAGCGGGAACAGATAGGCTCCTGGAAAGAACGAGCGGATCTCGAGGCTCAACTCAATAAATGGATTCG
CCAGTATATTGCAGACCAGGAAAATCCAAGTTCTGAAGTACGTGGACGGCGTCCGTTACGCTCTGCGCAAATCATCGTCA
GTGACGTGGAAGGTGATCCTGGCTGGTACCGGGTCAGTTTGAATGTTCGTCCTCATTTTAAATACATGGGCGCTGATTTC
ACCTTGTCTCTGGTCGGCAAGATGGACAAGGAATAG