Detailed information of component protein


Summary

Component ID T6CP008396
Component protein type TssD
T6SS ID (Type) T6SS00041 insolico (Type i1)
Strain Pseudomonas syringae pv. tomato str. DC3000
Replicon chromosome
Sequence Protein sequence (172 a.a.); Nucleotide sequence (516 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_RS13150
Coordinate (Strand) 2803874..2804389 (-)
NCBI ID WP_007246961.1
RefSeq NC_004578
Uniprot ID -
KEGG ID -
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
T6SS_HCP PF05638.14 7.1e-34 18..154
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-171 MPTPAFLSVTGTKQGHITEQAGSIDSLGGHGQIDHPDESIVHAFSHEIISPYDAQSGEITGRRRHNAICITKVFDRASPLLLEALCRGEKLTDVVINWYRTNDGKEQNYYRTTLHGALIVAIKDHMPTCDDPNNSHAIHLQDVHFTYRQIRWDHVIATSSGSYDLDDLGLD


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 0.9359 - -


  Protein sequence: 172 a.a.    

>T6CP008396 NC_004578:c2804389-2803874 [Pseudomonas syringae pv. tomato str. DC3000] [TssD]
MPTPAFLSVTGTKQGHITEQAGSIDSLGGHGQIDHPDESIVHAFSHEIISPYDAQSGEITGRRRHNAICITKVFDRASPL
LLEALCRGEKLTDVVINWYRTNDGKEQNYYRTTLHGALIVAIKDHMPTCDDPNNSHAIHLQDVHFTYRQIRWDHVIATSS
GSYDLDDLGLD*

  Nucleotide sequence: 516 bp    

>T6CP008396 NC_004578:c2804389-2803874 [Pseudomonas syringae pv. tomato str. DC3000] [TssD]
ATGCCTACACCCGCATTTCTATCTGTCACAGGGACCAAACAAGGTCATATTACAGAACAGGCTGGTTCCATTGACTCTTT
AGGCGGCCATGGCCAGATAGATCATCCTGACGAATCAATTGTTCACGCATTCAGTCACGAAATCATATCCCCTTACGACG
CTCAGTCAGGCGAAATTACTGGTCGACGCAGGCATAACGCAATTTGTATCACAAAAGTATTTGACCGGGCATCGCCATTA
CTTCTGGAAGCGTTATGCAGGGGCGAAAAACTAACTGACGTTGTGATAAATTGGTACCGCACTAACGACGGCAAGGAGCA
AAACTACTATAGAACAACACTTCATGGGGCGCTTATTGTGGCTATAAAAGACCACATGCCAACCTGCGACGATCCAAATA
ACTCGCATGCCATCCATCTGCAGGATGTGCACTTTACCTACCGTCAAATAAGATGGGATCACGTGATAGCTACTTCATCC
GGATCATACGACCTGGACGACTTAGGTCTGGACTGA