Detailed information of regulator


Summary

Regulator ID REG0367 experimental
Regulator type protein
Regulatory pathway (from literatures) QS regulatory pathway
KEGG pathway (determined by BlastKOALA) RNA degradation (map03018); Quorum sensing (map02024); Biofilm formation - Vibrio cholerae (map05111)
Related T6SS -
Strain Pseudomonas protegens strain H78
Replicon chromosome
Sequence Protein sequence (87 a.a.); Nucleotide sequence (261 bp)
Description The RNA-Seq analysis results showed that all genes within the H1-T6SS gene cluster were significantly down-regulated by 2.1- to 10.6-fold in the hfq mutant relative to the wild-type strain H78 and lacZ reporter showed the expression of the tssA, tssE, and fha genes was significantly down-regulated in the hfq mutant compared with its parental strain H78.
Reference

External database links

Locus tag (Gene) H78_RS02920 (Hfq)
Coordinates (Strand) 662937..663197 (+)
NCBI ID 495196588
RefSeq NZ_CP013184
Uniprot ID A0A2C9EFF6_PSEPH, A0A285F4U6_9PSED, A0A0D6BAQ2_9PSED, A0A1H3QCX2_9PSED, A0A0C5E255_9PSED, A0A2S8YL97_9PSED, A0A1T1IC49_9PSED, A0A2W0FHS1_9PSED, A0A2N8B207_9PSED, A0A2N8BHS8_9PSED, HFQ_PSEF5, A0A2J7U1R6_9PSED, A0A1H4W9Z1_9PSED, A0A0E1DXN8_9PSED, A0A1E1FPX8_9PSED
KEGG ID pcz:PCL1606_55230, pch:EY04_02165, pcp:JM49_27550, pprc:PFLCHA0_c05750, psem:TO66_02715, psos:POS17_0559, pfl:PFL_0566
KEGG pathway (determined by BlastKOALA) map03018; map02024; map05111
PDB ID -

  Target
Target Regulation (↓/↑) Target sequence
T6SS transcription level -

Pfam domain hit(s) of regulator

Domain Pfam ID E-value Aligned region
Hfq PF17209.5 5.4e-30 7..68

Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-86 MSKGHSLQDPYLNTLRKEKVGVSIYLVNGIKLQGTIESFDQFVILLKNTVSQMVYKHAISTVVPVRPIRLPSASESEQGDAEPGNA



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 0.9963 - -



  Protein sequence of regulator: 87 a.a.    .

>REG0367 NZ_CP013184:662937-663197 [Pseudomonas protegens]
MSKGHSLQDPYLNTLRKEKVGVSIYLVNGIKLQGTIESFDQFVILLKNTVSQMVYKHAISTVVPVRPIRLPSASESEQGD
AEPGNA*

  Nucleotide sequence of regulator: 261 bp    .

>REG0367 NZ_CP013184:662937-663197 [Pseudomonas protegens]
ATGTCAAAAGGGCATTCGCTACAAGACCCTTACTTGAATACATTGCGTAAAGAGAAGGTTGGGGTTTCCATCTATCTGGT
CAACGGGATCAAGCTGCAAGGTACGATCGAGTCTTTCGACCAGTTCGTCATCCTGCTGAAGAACACCGTCAGCCAAATGG
TTTACAAGCACGCTATCTCGACAGTGGTTCCAGTTCGCCCGATTCGCCTGCCTAGCGCTTCCGAATCCGAACAGGGTGAC
GCTGAGCCAGGTAACGCCTGA