Detailed information of component protein


Summary

Component ID T6CP012438
Component protein type Sfa2
T6SS ID (Type) T6SS00042 experimental (Type i1)
Strain Pseudomonas syringae pv. tomato str. DC3000
Replicon chromosome
Sequence Protein sequence (506 a.a.); Nucleotide sequence (1518 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
experimental Experimental investigation has been performed on this T6SS
External database links

Locus tag (Gene) PSPTO_RS28060
Coordinate (Strand) 6165047..6166564 (-)
NCBI ID WP_011105485.1
RefSeq NC_004578
Uniprot ID Q87U83_PSESM
KEGG ID pst:PSPTO_5424
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
Sigma54_activat PF00158.28 1.7e-69 196..363
HTH_8 PF02954.21 1.6e-10 456..495
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-505 MFTQMPQPLAYAQALLAQFASLARAVNGAQLLGDFVRSLAELSGCELSQLYLLDATHKCLKMRAECLDGTLQPREAASLPVDYNGEQLLQFALCQNRVVCLGELSGSLHETSFLPTQSTPWQSLLCVPVVNHQQAVEGLLLCASRRHVDLQGFADSLGQFGSFALGQLNLLQRLHKPADEVRPAGITMPSVSGYGLIGKSASMRQTYTMISKVLHSPYTVLLRGETGTGKEVVARAIHDFGPRRSQPFIVQNCAAFPEHLLESELFGYRKGAFTGADSDRTGLFEAANGGTLLLDEIGDIPLPLQAKLLRVLQEGEIRPLGCNDTRKIDVRILAATHRDLSAMVSEGKFREDLYYRLAQFPIELPALRNREGDILDLARHFVDKTCAFLQRSPLRWSDAALDLLSGYTFPGNVRELKGLVERAVLLCEGSELLVEHFSLRPEVVPEGSSLNLRERLEQVERSLLLDCLRKNDGNQTLSARELGLPRRTLLYRLGRLNINLGDLNG


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
SP(Sec/SPI) 0.6156 pos: 25-26. ARA-VN. MFTQMPQPLAYAQALLAQFASLARA


  Protein sequence: 506 a.a.    

>T6CP012438 NC_004578:c6166564-6165047 [Pseudomonas syringae pv. tomato str. DC3000] [Sfa2]
MFTQMPQPLAYAQALLAQFASLARAVNGAQLLGDFVRSLAELSGCELSQLYLLDATHKCLKMRAECLDGTLQPREAASLP
VDYNGEQLLQFALCQNRVVCLGELSGSLHETSFLPTQSTPWQSLLCVPVVNHQQAVEGLLLCASRRHVDLQGFADSLGQF
GSFALGQLNLLQRLHKPADEVRPAGITMPSVSGYGLIGKSASMRQTYTMISKVLHSPYTVLLRGETGTGKEVVARAIHDF
GPRRSQPFIVQNCAAFPEHLLESELFGYRKGAFTGADSDRTGLFEAANGGTLLLDEIGDIPLPLQAKLLRVLQEGEIRPL
GCNDTRKIDVRILAATHRDLSAMVSEGKFREDLYYRLAQFPIELPALRNREGDILDLARHFVDKTCAFLQRSPLRWSDAA
LDLLSGYTFPGNVRELKGLVERAVLLCEGSELLVEHFSLRPEVVPEGSSLNLRERLEQVERSLLLDCLRKNDGNQTLSAR
ELGLPRRTLLYRLGRLNINLGDLNG*

  Nucleotide sequence: 1518 bp    

>T6CP012438 NC_004578:c6166564-6165047 [Pseudomonas syringae pv. tomato str. DC3000] [Sfa2]
ATGTTCACTCAGATGCCGCAGCCTCTGGCATATGCCCAAGCCTTGTTGGCGCAATTCGCCAGCTTGGCGCGGGCGGTGAA
TGGTGCCCAATTGCTGGGTGATTTTGTACGTAGCCTCGCTGAGCTCAGCGGCTGCGAGCTGTCGCAGCTTTATCTGCTGG
ACGCCACTCATAAGTGTTTGAAGATGAGAGCCGAGTGCCTGGACGGCACGCTGCAACCGCGGGAAGCGGCAAGCCTGCCG
GTGGATTACAACGGCGAACAGCTGTTGCAATTTGCCCTTTGTCAGAATCGTGTGGTTTGCCTTGGCGAACTGAGCGGCAG
CCTGCACGAAACCAGTTTTCTGCCGACGCAAAGTACGCCGTGGCAGTCGCTGCTTTGTGTCCCGGTCGTCAACCATCAGC
AAGCCGTCGAAGGCTTGTTGTTGTGCGCAAGTCGCCGACATGTCGATCTGCAGGGTTTTGCTGATTCTCTCGGTCAGTTC
GGCTCGTTCGCACTGGGTCAACTCAACCTGCTGCAACGTTTGCATAAGCCTGCGGATGAGGTACGACCGGCAGGGATCAC
TATGCCAAGCGTCAGCGGATACGGTTTGATCGGAAAAAGCGCAAGCATGCGTCAGACCTACACGATGATCAGCAAGGTGC
TGCACAGCCCGTACACTGTGTTGCTGCGGGGAGAGACAGGCACCGGCAAAGAAGTCGTTGCCCGGGCGATTCACGACTTC
GGTCCGCGTCGCTCTCAGCCTTTCATTGTTCAGAACTGTGCGGCATTTCCAGAGCACCTGCTTGAAAGCGAGCTTTTCGG
CTATCGCAAAGGAGCCTTTACAGGTGCCGACAGTGATCGTACCGGGCTGTTCGAGGCTGCCAATGGCGGCACACTGTTGC
TCGACGAAATCGGCGACATTCCCCTGCCGCTGCAAGCCAAGCTGCTGCGCGTGCTGCAAGAGGGCGAGATTCGCCCATTG
GGTTGCAACGATACGCGCAAGATCGACGTGCGTATTCTTGCAGCAACGCATCGTGACCTGTCGGCGATGGTCAGCGAAGG
CAAATTCCGCGAGGACTTGTATTACCGTCTTGCGCAATTTCCCATTGAGCTGCCTGCCCTGCGCAATCGAGAGGGTGACA
TTCTCGACCTGGCGCGGCACTTCGTCGACAAGACGTGTGCGTTCTTGCAACGTAGCCCTTTGCGCTGGTCGGACGCAGCT
CTTGATCTCCTGTCCGGTTATACGTTTCCCGGCAATGTGCGCGAACTCAAAGGCCTGGTCGAGCGTGCTGTCCTGCTCTG
CGAGGGCAGCGAGTTGCTTGTGGAGCATTTCTCTCTGCGCCCGGAAGTTGTGCCTGAAGGCAGCAGCCTCAATCTGCGCG
AGCGGCTGGAGCAGGTGGAGCGCAGCCTGTTGCTTGATTGCCTGCGCAAGAACGACGGCAACCAGACTCTTTCCGCGCGT
GAACTCGGCCTGCCGAGGCGCACGCTGCTTTACCGTTTGGGACGCCTGAATATCAACCTGGGTGACTTAAATGGTTAG