Detailed information of regulator
Summary
| Regulator ID | REG0117  |
| Regulator type | protein |
| Regulatory pathway (from literatures) | c-di-GMP regulatory pathway |
| KEGG pathway (determined by BlastKOALA) | - |
| Related T6SS | T6SS00043 (Type i1) |
| Strain | Vibrio parahaemolyticus RIMD 2210633 |
| Replicon | chromosome |
| Sequence | Protein sequence (457 a.a.); Nucleotide sequence (1371 bp) |
| Description | c-di-GMP-producing diguanylate cyclase. |
| Reference |
External database links
| Locus tag (Gene) | VPA0739 (vdcA) |
| Coordinates (Strand) | 772439..773809 (+) |
| NCBI ID | 28900594 |
| RefSeq | NC_004605 |
| Uniprot ID | Q87I67_VIBPA |
| KEGG ID | vpa:VPA0739 |
| KEGG pathway (determined by BlastKOALA) | - |
| PDB ID | - |
Target
| Target | Regulation (↓/↑) | Target sequence |
|---|---|---|
| VP1028 (TfoY) | ↓ | - |
Pfam domain hit(s) of regulator
| Domain | Pfam ID | E-value | Aligned region |
|---|---|---|---|
| GGDEF | PF00990.23 | 2.4e-33 | 307..453 |
Transmembrane helices
- Transmembrane helices are predicted using TMHMM 2.0 software.
| Prediction | Region | Sequence |
|---|---|---|
| Inside | 1-6 | MTFKSI |
| Transmembrane helix | 7-29 | ALSFFVATLLFATSTMMIGAVLI |
| Outside | 30-265 | SYEVKQFNTYANNLAKIKQKVILMGLLTEAKLEQYKGLSVDEVEAQTEFSFQDAIYSLSPYEKLNYVEAVARKSLHQAEAYLSNAFNRQNAIMYFRSYTGSKLILERPIKALEGVKATFDVDWCKSNYSCVLAAWKEQLTDRVLFSLPFKTTYSDDMAISIMSPVYFQGELVGEFSEQLYLSSLYNEGKAVDVQISNGNKQMVIYFSGYPWPSFAYTQSFVADNNNLIVYMYPFSK |
| Transmembrane helix | 266-285 | VMVDYSFLFVIFFLATLAYY |
| Inside | 286-456 | NKAHESKESKLRLATALTNVTKDDLTGLLNRRVFKDSEFKRRLKTAPYSVIAIDGDRIKRINDRYGHHVGDEVIEIIADAMRKVFRTSDYLVRTGGDEFIAILPGCSISQSSMLAKKLRSFVKDNRLKTLDIEVSVSTGVAANESHESLQDVIVRADEDLYEMKKRRQHSQ |
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 | 0.8201 | - | - |
Protein sequence of regulator: 457 a.a. .
>REG0117 NC_004605:772439-773809 [Vibrio parahaemolyticus RIMD 2210633]
MTFKSIALSFFVATLLFATSTMMIGAVLISYEVKQFNTYANNLAKIKQKVILMGLLTEAKLEQYKGLSVDEVEAQTEFSF
QDAIYSLSPYEKLNYVEAVARKSLHQAEAYLSNAFNRQNAIMYFRSYTGSKLILERPIKALEGVKATFDVDWCKSNYSCV
LAAWKEQLTDRVLFSLPFKTTYSDDMAISIMSPVYFQGELVGEFSEQLYLSSLYNEGKAVDVQISNGNKQMVIYFSGYPW
PSFAYTQSFVADNNNLIVYMYPFSKVMVDYSFLFVIFFLATLAYYNKAHESKESKLRLATALTNVTKDDLTGLLNRRVFK
DSEFKRRLKTAPYSVIAIDGDRIKRINDRYGHHVGDEVIEIIADAMRKVFRTSDYLVRTGGDEFIAILPGCSISQSSMLA
KKLRSFVKDNRLKTLDIEVSVSTGVAANESHESLQDVIVRADEDLYEMKKRRQHSQ*
MTFKSIALSFFVATLLFATSTMMIGAVLISYEVKQFNTYANNLAKIKQKVILMGLLTEAKLEQYKGLSVDEVEAQTEFSF
QDAIYSLSPYEKLNYVEAVARKSLHQAEAYLSNAFNRQNAIMYFRSYTGSKLILERPIKALEGVKATFDVDWCKSNYSCV
LAAWKEQLTDRVLFSLPFKTTYSDDMAISIMSPVYFQGELVGEFSEQLYLSSLYNEGKAVDVQISNGNKQMVIYFSGYPW
PSFAYTQSFVADNNNLIVYMYPFSKVMVDYSFLFVIFFLATLAYYNKAHESKESKLRLATALTNVTKDDLTGLLNRRVFK
DSEFKRRLKTAPYSVIAIDGDRIKRINDRYGHHVGDEVIEIIADAMRKVFRTSDYLVRTGGDEFIAILPGCSISQSSMLA
KKLRSFVKDNRLKTLDIEVSVSTGVAANESHESLQDVIVRADEDLYEMKKRRQHSQ*
Nucleotide sequence of regulator: 1371 bp .
>REG0117 NC_004605:772439-773809 [Vibrio parahaemolyticus RIMD 2210633]
ATGACATTTAAAAGCATCGCGCTGTCTTTCTTTGTGGCGACGTTACTGTTTGCGACTTCAACAATGATGATAGGCGCTGT
GTTGATTTCTTATGAAGTAAAGCAGTTCAACACCTACGCAAATAACCTAGCCAAAATAAAGCAAAAAGTCATTTTAATGG
GGCTGCTGACGGAAGCGAAGCTTGAACAATACAAAGGCTTGAGCGTGGATGAAGTAGAAGCTCAAACTGAGTTCAGCTTC
CAAGACGCGATTTACTCGCTGTCACCGTACGAAAAGCTGAATTACGTTGAAGCCGTCGCACGCAAATCGCTGCATCAAGC
CGAAGCGTATTTATCGAATGCGTTTAATCGACAAAATGCCATTATGTACTTTCGCTCTTATACTGGGAGCAAGTTGATTT
TAGAGCGACCAATCAAAGCGTTAGAAGGTGTGAAGGCCACATTCGATGTCGATTGGTGCAAGAGCAACTACTCTTGCGTT
CTGGCTGCGTGGAAAGAACAACTGACTGATCGCGTGTTGTTTTCTCTGCCGTTTAAAACCACCTACTCGGATGACATGGC
AATAAGCATCATGAGCCCGGTTTATTTCCAAGGTGAGCTAGTCGGCGAGTTTTCAGAACAGCTCTATCTTTCATCACTTT
ATAACGAAGGGAAAGCCGTCGACGTACAGATCTCCAATGGTAACAAGCAAATGGTGATCTATTTTTCGGGTTATCCGTGG
CCATCGTTCGCGTACACCCAATCTTTTGTGGCAGACAACAACAACTTGATTGTCTACATGTACCCGTTTAGTAAAGTGAT
GGTGGATTACAGCTTTCTGTTTGTTATTTTCTTTTTGGCAACCTTGGCGTATTACAACAAAGCGCATGAATCCAAAGAGA
GCAAACTTCGTCTGGCGACGGCACTGACGAATGTGACAAAAGACGATTTAACCGGGTTACTTAACCGCAGAGTCTTTAAA
GATAGCGAATTCAAACGCCGCTTGAAAACGGCCCCTTATTCCGTCATTGCCATTGATGGCGACAGGATCAAGCGAATCAA
TGATCGCTATGGTCATCACGTTGGGGACGAGGTTATCGAGATCATTGCCGATGCGATGCGTAAAGTGTTCAGAACCAGCG
ATTATCTCGTCCGAACTGGGGGCGATGAGTTTATCGCAATCTTGCCGGGGTGCAGCATCAGTCAGTCTTCGATGTTGGCG
AAAAAGTTACGTAGCTTTGTCAAAGACAACCGACTTAAAACGTTAGACATTGAAGTCAGCGTAAGCACTGGCGTTGCGGC
AAACGAATCACACGAATCACTGCAAGATGTTATCGTTCGAGCAGATGAAGATCTCTATGAGATGAAAAAACGCAGACAAC
ACTCACAGTAA
ATGACATTTAAAAGCATCGCGCTGTCTTTCTTTGTGGCGACGTTACTGTTTGCGACTTCAACAATGATGATAGGCGCTGT
GTTGATTTCTTATGAAGTAAAGCAGTTCAACACCTACGCAAATAACCTAGCCAAAATAAAGCAAAAAGTCATTTTAATGG
GGCTGCTGACGGAAGCGAAGCTTGAACAATACAAAGGCTTGAGCGTGGATGAAGTAGAAGCTCAAACTGAGTTCAGCTTC
CAAGACGCGATTTACTCGCTGTCACCGTACGAAAAGCTGAATTACGTTGAAGCCGTCGCACGCAAATCGCTGCATCAAGC
CGAAGCGTATTTATCGAATGCGTTTAATCGACAAAATGCCATTATGTACTTTCGCTCTTATACTGGGAGCAAGTTGATTT
TAGAGCGACCAATCAAAGCGTTAGAAGGTGTGAAGGCCACATTCGATGTCGATTGGTGCAAGAGCAACTACTCTTGCGTT
CTGGCTGCGTGGAAAGAACAACTGACTGATCGCGTGTTGTTTTCTCTGCCGTTTAAAACCACCTACTCGGATGACATGGC
AATAAGCATCATGAGCCCGGTTTATTTCCAAGGTGAGCTAGTCGGCGAGTTTTCAGAACAGCTCTATCTTTCATCACTTT
ATAACGAAGGGAAAGCCGTCGACGTACAGATCTCCAATGGTAACAAGCAAATGGTGATCTATTTTTCGGGTTATCCGTGG
CCATCGTTCGCGTACACCCAATCTTTTGTGGCAGACAACAACAACTTGATTGTCTACATGTACCCGTTTAGTAAAGTGAT
GGTGGATTACAGCTTTCTGTTTGTTATTTTCTTTTTGGCAACCTTGGCGTATTACAACAAAGCGCATGAATCCAAAGAGA
GCAAACTTCGTCTGGCGACGGCACTGACGAATGTGACAAAAGACGATTTAACCGGGTTACTTAACCGCAGAGTCTTTAAA
GATAGCGAATTCAAACGCCGCTTGAAAACGGCCCCTTATTCCGTCATTGCCATTGATGGCGACAGGATCAAGCGAATCAA
TGATCGCTATGGTCATCACGTTGGGGACGAGGTTATCGAGATCATTGCCGATGCGATGCGTAAAGTGTTCAGAACCAGCG
ATTATCTCGTCCGAACTGGGGGCGATGAGTTTATCGCAATCTTGCCGGGGTGCAGCATCAGTCAGTCTTCGATGTTGGCG
AAAAAGTTACGTAGCTTTGTCAAAGACAACCGACTTAAAACGTTAGACATTGAAGTCAGCGTAAGCACTGGCGTTGCGGC
AAACGAATCACACGAATCACTGCAAGATGTTATCGTTCGAGCAGATGAAGATCTCTATGAGATGAAAAAACGCAGACAAC
ACTCACAGTAA