Detailed information of component protein


Summary

Component ID T6CP012428
Component protein type TagQ
T6SS ID (Type) T6SS00035 experimental (Type i3)
Strain Pseudomonas protegens Pf-5
Replicon chromosome
Sequence Protein sequence (310 a.a.); Nucleotide sequence (930 bp)
Reference
[1] Loper JE, Hassan KA, Mavrodi DV, et al. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet. 2012 Jul;8(7):e1002784. doi: 10.1371/journal.pgen.1002784. Epub 2012 Jul 5. PMID: 22792073
[2] Russell AB, Singh P, Brittnacher M, et al. A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe. 2012 May 17;11(5):538-49. doi: 10.1016/j.chom.2012.04.007. PMID: 22607806
[3] Hassan KA, Johnson A, Shaffer BT, et al. Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environ Microbiol. 2010 Apr;12(4):899-915. doi: 10.1111/j.1462-2920.2009.02134.x. Epub 2010 Jan 18. PMID: 20089046
[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
[5] Whitney JC, Chou S, Russell AB, et al. Identification, structure, and function of a novel type VI secretion peptidoglycan glycoside hydrolase effector-immunity pair. J Biol Chem. 2013 Sep 13;288(37):26616-24. doi: 10.1074/jbc.M113.488320. Epub 2013 Jul 22. PMID: 23878199
experimental Experimental investigation has been performed on this T6SS
External database links

Locus tag (Gene) PFL_RS30790
Coordinate (Strand) 6895202..6896131 (-)
NCBI ID WP_011064242.1
RefSeq NC_004129
Uniprot ID A0A1K2A8L7_9PSED, A0A2T0Z745_9PSED, Q4K3Q1_PSEF5, A0A7U9LBC8_PSEFL
KEGG ID pfl:PFL_6074
PDB ID -
Pfam domain hit(s)

Domain Pfam ID E-value Aligned region
Gly-zipper_YMGG PF13441.8 3.9e-10 67..113
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-309 MLFSRNPFASTSKRHLLLVAAGFSTVLTGCATSPVSKVASTTKVEYYPSCYEPVQHLRATDSDMTKSVVTGAALGAAGGALLGALTGDGDHRGRNAAIGAAGGALAGGAAGYYTERQKQIADDNQRIASYAADVNKSAADIDRSTAYARASQTCYQRAFDSLISSRKANTINDVEGRKRLAEIVSGLKESNDLITAVNGRASEDLSKYNQAYEQDLQQVGVQRTDVVKVATADTTTVTTGGKRKQPQKVKQPKLPTVPQEAVSTERSIQDAKIKQAESNKVATTGQTQVNSMCKNPDLGDWAPVPCPNV


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
LIPO(Sec/SPII) 0.9793 pos: 29-30. LTG-CA. MLFSRNPFASTSKRHLLLVAAGFSTVLTG


  Protein sequence: 310 a.a.    

>T6CP012428 NC_004129:c6896131-6895202 [Pseudomonas protegens Pf-5] [TagQ]
MLFSRNPFASTSKRHLLLVAAGFSTVLTGCATSPVSKVASTTKVEYYPSCYEPVQHLRATDSDMTKSVVTGAALGAAGGA
LLGALTGDGDHRGRNAAIGAAGGALAGGAAGYYTERQKQIADDNQRIASYAADVNKSAADIDRSTAYARASQTCYQRAFD
SLISSRKANTINDVEGRKRLAEIVSGLKESNDLITAVNGRASEDLSKYNQAYEQDLQQVGVQRTDVVKVATADTTTVTTG
GKRKQPQKVKQPKLPTVPQEAVSTERSIQDAKIKQAESNKVATTGQTQVNSMCKNPDLGDWAPVPCPNV*

  Nucleotide sequence: 930 bp    

>T6CP012428 NC_004129:c6896131-6895202 [Pseudomonas protegens Pf-5] [TagQ]
ATGCTTTTTTCCCGCAACCCATTTGCTTCAACGTCCAAGCGTCACCTGCTGTTGGTTGCCGCCGGGTTCAGCACCGTATT
GACCGGTTGCGCGACCTCTCCGGTGTCCAAGGTCGCCTCGACCACCAAGGTCGAGTACTACCCGAGCTGCTACGAGCCGG
TGCAGCACCTGCGCGCCACGGATTCGGACATGACCAAGTCGGTGGTCACCGGTGCTGCCCTGGGCGCTGCCGGCGGCGCT
TTGCTCGGTGCCCTGACCGGTGACGGCGACCACCGTGGCCGCAACGCCGCCATCGGTGCCGCAGGCGGTGCCCTGGCCGG
TGGCGCAGCCGGTTACTACACCGAGCGCCAGAAGCAGATCGCCGACGATAACCAGCGCATCGCTTCCTACGCTGCCGACG
TCAACAAGAGCGCGGCCGACATCGACCGCAGCACGGCCTATGCCCGCGCTTCCCAGACCTGCTACCAGCGCGCCTTCGAC
AGCCTGATCAGCTCCCGCAAGGCCAACACCATCAATGACGTGGAAGGGCGCAAGCGCCTGGCGGAAATCGTCAGCGGCCT
GAAGGAGTCCAACGACCTGATCACCGCGGTGAACGGCCGTGCCAGCGAAGACCTGAGCAAGTACAACCAGGCCTACGAGC
AGGATCTGCAGCAAGTGGGCGTGCAGCGTACCGACGTGGTGAAAGTCGCCACCGCCGATACCACCACGGTGACCACCGGT
GGCAAGAGAAAACAGCCACAGAAGGTCAAGCAGCCCAAGCTGCCGACCGTGCCTCAGGAAGCGGTGAGCACCGAGAGGTC
GATCCAGGATGCCAAGATCAAGCAGGCCGAGAGCAACAAGGTCGCGACCACCGGCCAGACCCAGGTCAACAGCATGTGCA
AGAACCCGGACCTGGGTGACTGGGCACCGGTGCCTTGCCCTAACGTCTGA