Detailed information of regulator
Summary
| Regulator ID | REG0083  |
| Regulator type | protein |
| Regulatory pathway (from literatures) | c-di-GMP regulatory pathway |
| KEGG pathway (determined by BlastKOALA) | - |
| Related T6SS | T6SS00016 (Type i5) |
| Strain | Agrobacterium fabrum str. C58 |
| Replicon | chromosome |
| Sequence | Protein sequence (380 a.a.); Nucleotide sequence (1140 bp) |
| Description | High levels of c-di-GMP are capable of down-regulating the T9SS, as seen by monitoring Hcp, ClpV and TssB production. |
| Reference |
External database links
| Locus tag (Gene) | Atu2179 (DgcC) |
| Coordinates (Strand) | 2154605..2155744 (-) |
| NCBI ID | 159185090 |
| RefSeq | NC_003062 |
| Uniprot ID | Q7CXP3_AGRFC |
| KEGG ID | atu:Atu2179 |
| KEGG pathway (determined by BlastKOALA) | - |
| PDB ID | - |
Target
| Target | Regulation (↓/↑) | Target sequence |
|---|---|---|
| the levels of c-di-GMP | ↑ | - |
Pfam domain hit(s) of regulator
| Domain | Pfam ID | E-value | Aligned region |
|---|---|---|---|
| GGDEF | PF00990.23 | 2.2e-41 | 221..371 |
Transmembrane helices
- Transmembrane helices are predicted using TMHMM 2.0 software.
| Prediction | Region | Sequence |
|---|---|---|
| Outside | 1-9 | MLGELDLAT |
| Transmembrane helix | 10-28 | VILMQKCSYIVGLLSFIYL |
| Inside | 29-34 | KMSNRG |
| Transmembrane helix | 35-57 | LPGPVHLAAGFAAMTVGSTLAGY |
| Outside | 58-66 | GEWKILSPA |
| Transmembrane helix | 67-87 | LWELGSVLFGIAGYALIWLGL |
| Inside | 88-99 | KTLSDGRFVNRK |
| Transmembrane helix | 100-119 | TILFTCLVALLAIGVALQVA |
| Outside | 120-123 | GNNT |
| Transmembrane helix | 124-146 | FRAALFNGCAALAYLGGAGVLFA |
| Inside | 147-152 | RWRKEP |
| Transmembrane helix | 153-172 | LLSRLALGAITGVSGLISLA |
| Outside | 173-186 | VMKSVLFPGYASIN |
| Transmembrane helix | 187-209 | LVTAFFFIIMLNFAISLFVMMLV |
| Inside | 210-379 | AERSERKLLVLANTDPLTGVKNRRFFFQTMPAAPDPADAAMLLDIDHFKSINDRFGHAVGDSVLQEVARRISGSIRGGDVLARYGGEEFIIFLPGAGVDKACMIGERIRDAVAINEVDCGGLRVGVTISIGVATTGDMRCDLQMLAEKADRALYRAKTEGRNCVREALAA |
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 | 0.9839 | - | - |
Protein sequence of regulator: 380 a.a. .
>REG0083 NC_003062:c2155744-2154605 [Agrobacterium fabrum str. C58]
MLGELDLATVILMQKCSYIVGLLSFIYLKMSNRGLPGPVHLAAGFAAMTVGSTLAGYGEWKILSPALWELGSVLFGIAGY
ALIWLGLKTLSDGRFVNRKTILFTCLVALLAIGVALQVAGNNTFRAALFNGCAALAYLGGAGVLFARWRKEPLLSRLALG
AITGVSGLISLAVMKSVLFPGYASINLVTAFFFIIMLNFAISLFVMMLVAERSERKLLVLANTDPLTGVKNRRFFFQTMP
AAPDPADAAMLLDIDHFKSINDRFGHAVGDSVLQEVARRISGSIRGGDVLARYGGEEFIIFLPGAGVDKACMIGERIRDA
VAINEVDCGGLRVGVTISIGVATTGDMRCDLQMLAEKADRALYRAKTEGRNCVREALAA*
MLGELDLATVILMQKCSYIVGLLSFIYLKMSNRGLPGPVHLAAGFAAMTVGSTLAGYGEWKILSPALWELGSVLFGIAGY
ALIWLGLKTLSDGRFVNRKTILFTCLVALLAIGVALQVAGNNTFRAALFNGCAALAYLGGAGVLFARWRKEPLLSRLALG
AITGVSGLISLAVMKSVLFPGYASINLVTAFFFIIMLNFAISLFVMMLVAERSERKLLVLANTDPLTGVKNRRFFFQTMP
AAPDPADAAMLLDIDHFKSINDRFGHAVGDSVLQEVARRISGSIRGGDVLARYGGEEFIIFLPGAGVDKACMIGERIRDA
VAINEVDCGGLRVGVTISIGVATTGDMRCDLQMLAEKADRALYRAKTEGRNCVREALAA*
Nucleotide sequence of regulator: 1140 bp .
>REG0083 NC_003062:c2155744-2154605 [Agrobacterium fabrum str. C58]
ATGCTGGGTGAACTCGACCTTGCAACAGTCATACTGATGCAAAAATGTTCTTACATCGTTGGGCTGTTGAGTTTTATCTA
CCTGAAGATGAGTAATCGCGGTTTGCCCGGCCCCGTTCATCTTGCGGCGGGTTTCGCGGCGATGACGGTCGGCTCTACGC
TTGCCGGTTACGGCGAATGGAAGATACTTTCGCCGGCGCTGTGGGAGCTTGGCAGCGTTTTGTTCGGTATTGCCGGATAT
GCGCTGATCTGGCTTGGGCTGAAGACGTTGAGCGACGGACGCTTTGTCAATCGCAAAACCATCTTGTTTACCTGTCTTGT
CGCCCTGCTGGCGATTGGCGTTGCGCTGCAGGTGGCCGGCAACAATACGTTTCGCGCGGCGCTTTTTAATGGCTGTGCGG
CTCTGGCCTATCTTGGCGGGGCGGGCGTGCTTTTTGCCCGGTGGCGGAAAGAGCCGCTTCTTTCCCGGCTGGCTCTCGGT
GCGATTACAGGCGTTTCCGGTCTGATATCGCTGGCGGTGATGAAAAGCGTGCTTTTCCCTGGTTACGCCAGCATCAATCT
GGTCACTGCGTTTTTCTTCATTATCATGCTCAACTTCGCCATCTCGCTCTTTGTGATGATGCTGGTAGCGGAGCGGTCCG
AACGGAAATTGCTGGTTCTGGCGAATACCGATCCACTGACGGGCGTCAAGAACCGGCGTTTCTTCTTCCAGACCATGCCC
GCAGCCCCCGATCCCGCTGATGCGGCCATGTTGCTTGACATTGACCACTTCAAGTCGATCAATGACCGTTTCGGCCACGC
TGTCGGCGACAGCGTGCTGCAGGAAGTGGCAAGGCGCATCAGCGGCAGCATCCGTGGCGGCGATGTGCTGGCGCGTTACG
GCGGCGAGGAATTCATCATTTTCCTGCCGGGTGCCGGTGTGGACAAGGCTTGCATGATCGGCGAGCGCATTCGCGACGCG
GTTGCGATAAATGAGGTCGATTGCGGCGGTCTGCGTGTCGGGGTGACCATCAGCATCGGCGTTGCCACCACAGGCGATAT
GCGCTGCGATCTCCAGATGCTCGCCGAAAAGGCGGATCGAGCGCTTTACCGGGCAAAGACCGAAGGGCGCAATTGCGTTC
GCGAGGCGCTGGCCGCGTAA
ATGCTGGGTGAACTCGACCTTGCAACAGTCATACTGATGCAAAAATGTTCTTACATCGTTGGGCTGTTGAGTTTTATCTA
CCTGAAGATGAGTAATCGCGGTTTGCCCGGCCCCGTTCATCTTGCGGCGGGTTTCGCGGCGATGACGGTCGGCTCTACGC
TTGCCGGTTACGGCGAATGGAAGATACTTTCGCCGGCGCTGTGGGAGCTTGGCAGCGTTTTGTTCGGTATTGCCGGATAT
GCGCTGATCTGGCTTGGGCTGAAGACGTTGAGCGACGGACGCTTTGTCAATCGCAAAACCATCTTGTTTACCTGTCTTGT
CGCCCTGCTGGCGATTGGCGTTGCGCTGCAGGTGGCCGGCAACAATACGTTTCGCGCGGCGCTTTTTAATGGCTGTGCGG
CTCTGGCCTATCTTGGCGGGGCGGGCGTGCTTTTTGCCCGGTGGCGGAAAGAGCCGCTTCTTTCCCGGCTGGCTCTCGGT
GCGATTACAGGCGTTTCCGGTCTGATATCGCTGGCGGTGATGAAAAGCGTGCTTTTCCCTGGTTACGCCAGCATCAATCT
GGTCACTGCGTTTTTCTTCATTATCATGCTCAACTTCGCCATCTCGCTCTTTGTGATGATGCTGGTAGCGGAGCGGTCCG
AACGGAAATTGCTGGTTCTGGCGAATACCGATCCACTGACGGGCGTCAAGAACCGGCGTTTCTTCTTCCAGACCATGCCC
GCAGCCCCCGATCCCGCTGATGCGGCCATGTTGCTTGACATTGACCACTTCAAGTCGATCAATGACCGTTTCGGCCACGC
TGTCGGCGACAGCGTGCTGCAGGAAGTGGCAAGGCGCATCAGCGGCAGCATCCGTGGCGGCGATGTGCTGGCGCGTTACG
GCGGCGAGGAATTCATCATTTTCCTGCCGGGTGCCGGTGTGGACAAGGCTTGCATGATCGGCGAGCGCATTCGCGACGCG
GTTGCGATAAATGAGGTCGATTGCGGCGGTCTGCGTGTCGGGGTGACCATCAGCATCGGCGTTGCCACCACAGGCGATAT
GCGCTGCGATCTCCAGATGCTCGCCGAAAAGGCGGATCGAGCGCTTTACCGGGCAAAGACCGAAGGGCGCAATTGCGTTC
GCGAGGCGCTGGCCGCGTAA