Detailed information of component protein


Summary

Component ID T6CP000342
Component protein type TssL
T6SS ID (Type) T6SS00041 insolico (Type i1)
Strain Pseudomonas syringae pv. tomato str. DC3000
Replicon chromosome
Sequence Protein sequence (297 a.a.); Nucleotide sequence (891 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_RS13215
Coordinate (Strand) 2819138..2820028 (+)
NCBI ID WP_046463302.1
RefSeq NC_004578
Uniprot ID -
KEGG ID -
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
DotU PF09850.11 7.1e-65 69..271
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-250 MGDQKLMNELNDEQGRREDSTIDYGWVDAARGDDLFTDVNDTNIPEGPTARRVQNSGRTDERFNIHVNPLVAAASGLLAQVARLPVADEVGDIHFLNVQLSDQVKLFEAEARKRAIDNDQLLAARYVLCTVVDEAVLNTRWGSASDWSKISLLSRFHKETFGGEKFFQLLERLSTNPFKHLPMLELMYLCLALGFEGKYRSTRRNSSELEDIRDSLYRQIRHLRGDVSRTLSPHWQGAESSRNGPLRIVP
Transmembrane helix 251-273 IWLIVLFTFTSLTVLYSGFAWVL
Inside 274-296 SEQREAVLTPYRSALSTVLEPRS


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 0.9868 - -


  Protein sequence: 297 a.a.    

>T6CP000342 NC_004578:2819138-2820028 [Pseudomonas syringae pv. tomato str. DC3000] [TssL]
MGDQKLMNELNDEQGRREDSTIDYGWVDAARGDDLFTDVNDTNIPEGPTARRVQNSGRTDERFNIHVNPLVAAASGLLAQ
VARLPVADEVGDIHFLNVQLSDQVKLFEAEARKRAIDNDQLLAARYVLCTVVDEAVLNTRWGSASDWSKISLLSRFHKET
FGGEKFFQLLERLSTNPFKHLPMLELMYLCLALGFEGKYRSTRRNSSELEDIRDSLYRQIRHLRGDVSRTLSPHWQGAES
SRNGPLRIVPIWLIVLFTFTSLTVLYSGFAWVLSEQREAVLTPYRSALSTVLEPRS*

  Nucleotide sequence: 891 bp    

>T6CP000342 NC_004578:2819138-2820028 [Pseudomonas syringae pv. tomato str. DC3000] [TssL]
TTGGGCGATCAGAAACTGATGAACGAATTGAACGATGAGCAAGGCCGTCGCGAAGACAGCACTATTGACTATGGCTGGGT
TGATGCCGCCCGGGGCGATGACCTGTTTACCGACGTCAACGACACGAATATCCCTGAGGGCCCAACGGCGCGACGGGTCC
AGAACTCCGGGAGAACAGACGAGCGCTTCAATATTCATGTCAATCCGCTGGTTGCAGCGGCAAGCGGGCTGCTTGCTCAG
GTAGCGAGGCTGCCTGTTGCAGACGAAGTTGGCGATATTCATTTTCTCAACGTACAGCTGTCGGACCAGGTAAAGCTGTT
CGAGGCCGAGGCCCGCAAGCGCGCAATCGATAACGATCAGCTACTCGCCGCACGCTATGTGTTGTGCACGGTGGTGGACG
AAGCTGTTTTGAATACGCGCTGGGGCAGCGCAAGTGACTGGTCGAAGATCAGCCTGCTGAGCCGCTTTCACAAGGAAACA
TTCGGCGGGGAAAAGTTCTTTCAATTGCTCGAAAGACTTTCCACCAACCCGTTCAAACACTTGCCGATGCTTGAGTTGAT
GTACCTGTGTCTGGCACTCGGGTTTGAAGGGAAATACCGCTCGACCCGCCGTAATAGCAGTGAACTGGAAGATATCCGGG
ACAGCCTTTACCGGCAGATAAGGCACCTCAGAGGCGACGTCTCTCGAACCCTTTCACCTCACTGGCAGGGCGCGGAGTCA
TCACGTAACGGTCCGCTGCGTATTGTGCCGATATGGCTGATTGTGCTGTTCACCTTTACCAGTCTGACAGTGCTGTATTC
GGGGTTCGCCTGGGTGCTGAGCGAGCAGCGTGAGGCTGTACTCACACCTTATCGGTCAGCACTTTCGACAGTGCTCGAGC
CTCGATCCTGA