Detailed information of regulator
Summary
| Regulator ID | REG0367  |
| 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, A0A2V3Z790_9PSED, A0A285F4U6_9PSED, A0A0D6BAQ2_9PSED, A0A1X7Q6U7_9PSED, A0A1H7YQX6_9PSED, A0A1K2AZ71_9PSED, A0A2T0Z468_9PSED, A0A1H3QCX2_9PSED, A0A0C5E255_9PSED, A0A2S8YL97_9PSED, A0A1T1IC49_9PSED, A0A2W0FHS1_9PSED, A0A2N8B207_9PSED, A0A2N8BHS8_9PSED, A0A2K4IZ77_9PSED, HFQ_PSEF5, A0A2J7U1R6_9PSED, A0A1H4W9Z1_9PSED, A0A0E1DXN8_9PSED, A0A1E1FPX8_9PSED |
| KEGG ID | pcp:JM49_27550, psem:TO66_02715, pcz:PCL1606_55230, pch:EY04_02165, pprc:PFLCHA0_c05750, pfl:PFL_0566, psos:POS17_0559 |
| 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*
MSKGHSLQDPYLNTLRKEKVGVSIYLVNGIKLQGTIESFDQFVILLKNTVSQMVYKHAISTVVPVRPIRLPSASESEQGD
AEPGNA*
Nucleotide sequence of regulator: 261 bp .
>REG0367 NZ_CP013184:662937-663197 [Pseudomonas protegens]
ATGTCAAAAGGGCATTCGCTACAAGACCCTTACTTGAATACATTGCGTAAAGAGAAGGTTGGGGTTTCCATCTATCTGGT
CAACGGGATCAAGCTGCAAGGTACGATCGAGTCTTTCGACCAGTTCGTCATCCTGCTGAAGAACACCGTCAGCCAAATGG
TTTACAAGCACGCTATCTCGACAGTGGTTCCAGTTCGCCCGATTCGCCTGCCTAGCGCTTCCGAATCCGAACAGGGTGAC
GCTGAGCCAGGTAACGCCTGA
ATGTCAAAAGGGCATTCGCTACAAGACCCTTACTTGAATACATTGCGTAAAGAGAAGGTTGGGGTTTCCATCTATCTGGT
CAACGGGATCAAGCTGCAAGGTACGATCGAGTCTTTCGACCAGTTCGTCATCCTGCTGAAGAACACCGTCAGCCAAATGG
TTTACAAGCACGCTATCTCGACAGTGGTTCCAGTTCGCCCGATTCGCCTGCCTAGCGCTTCCGAATCCGAACAGGGTGAC
GCTGAGCCAGGTAACGCCTGA