Detailed information of component protein


Summary

Component ID T6CP000778
Component protein type TssD
T6SS ID (Type) T6SS00086 experimental (Type i4b)
Strain Pseudomonas syringae pv. syringae B728a
Replicon chromosome
Sequence Protein sequence (173 a.a.); Nucleotide sequence (519 bp)
Reference
[1] Records AR, Gross DC. Sensor kinases RetS and LadS regulate Pseudomonas syringae type VI secretion and virulence factors. J Bacteriol. 2010 Jul;192(14):3584-96. doi: 10.1128/JB.00114-10. Epub 2010 May 14. PMID: 20472799
[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
experimental Experimental investigation has been performed on this T6SS
External database links

Locus tag (Gene) PSYR_RS25780
Coordinate (Strand) 5889737..5890255 (+)
NCBI ID WP_003318810.1
RefSeq NC_007005
Uniprot ID A0A1H0KR64_9PSED, Q4ZLI0_PSEU2, A0A326SQ33_9PSED, A0A2V3Q9T7_9PSED, A0A1G9X8C5_PSESX, A0A2S4J456_PSESY, A0A0W0IMK8_9PSED
KEGG ID psb:Psyr_4965
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
T6SS_HCP PF05638.14 1.4e-40 6..145
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-172 MAFDAYIQIDGIPGEVLDDKHKDWIEVLGYEFGATQATSATASSSGGASSERVALSDFSIRKSVDKASAKLFEACCKGTHIAKIQLNVNRAGGDKLTYLTINLEEVVVSSVKAVAGGSQKGEDNAVSDLPIEEISFNFARIKTTYTQQSRSDGQGGGNVTGGWDRTANKVFA


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 0.9477 - -


  Protein sequence: 173 a.a.    

>T6CP000778 NC_007005:5889737-5890255 [Pseudomonas syringae pv. syringae B728a] [TssD]
MAFDAYIQIDGIPGEVLDDKHKDWIEVLGYEFGATQATSATASSSGGASSERVALSDFSIRKSVDKASAKLFEACCKGTH
IAKIQLNVNRAGGDKLTYLTINLEEVVVSSVKAVAGGSQKGEDNAVSDLPIEEISFNFARIKTTYTQQSRSDGQGGGNVT
GGWDRTANKVFA*

  Nucleotide sequence: 519 bp    

>T6CP000778 NC_007005:5889737-5890255 [Pseudomonas syringae pv. syringae B728a] [TssD]
ATGGCATTTGACGCATACATCCAAATCGATGGCATCCCAGGCGAAGTTCTGGACGACAAGCACAAGGACTGGATCGAAGT
GTTGGGCTACGAGTTCGGCGCTACCCAGGCCACCTCGGCGACCGCCAGTTCTTCGGGCGGTGCTTCGTCCGAGCGCGTTG
CACTGAGCGACTTCAGCATCCGCAAGTCTGTGGACAAGGCTTCCGCCAAGCTGTTCGAAGCGTGCTGCAAGGGCACTCAC
ATCGCCAAGATCCAGCTGAACGTCAACCGTGCAGGCGGCGACAAGCTGACCTACCTGACCATCAACCTGGAAGAAGTGGT
TGTGTCTTCCGTGAAGGCGGTTGCTGGCGGTAGCCAGAAAGGCGAAGACAACGCAGTCAGCGATCTGCCGATTGAAGAAA
TCAGCTTCAACTTCGCTCGCATCAAGACCACCTACACCCAGCAGAGCCGTTCCGATGGCCAGGGTGGCGGTAACGTCACT
GGCGGCTGGGACCGCACTGCGAACAAAGTATTCGCATAA