Detailed information of regulator


Summary

Regulator ID REG0116 experimental
Regulator type protein
Regulatory pathway (from literatures) c-di-GMP regulatory pathway
KEGG pathway (determined by BlastKOALA) Biofilm formation - Vibrio cholerae (map05111)
Related T6SS T6SS00043 experimental (Type i1)
Strain Vibrio parahaemolyticus RIMD 2210633
Replicon chromosome
Sequence Protein sequence (788 a.a.); Nucleotide sequence (2364 bp)
Description A phosphodiesterase keeps c-di-GMP in low levels.
Reference
External database links

Locus tag (Gene) VPA1088 (cdpA)
Coordinates (Strand) 1147728..1150091 (+)
NCBI ID 28900943
RefSeq NC_004605
Uniprot ID Q87H77_VIBPA
KEGG ID vpa:VPA1088
KEGG pathway (determined by BlastKOALA) map05111
PDB ID -
  Target
Target Regulation (↓/↑) Target sequence
VP1028 (TfoY) ↑ -
Pfam domain hit(s) of regulator

Domain Pfam ID E-value Aligned region
EAL PF00563.22 2.8e-60 522..754
GGDEF PF00990.23 3.9e-35 340..502
Transmembrane helices

  • Transmembrane helices are predicted using TMHMM 2.0 software.

Prediction                 Region     Sequence
Outside 1-4 MKLS
Transmembrane helix 5-27 NRVILLVAPVIILSALVSSYIIY
Inside 28-257 SIQKVTLIKREDSYIQLQMEKLAGQFRQANIFLNSYAYTLSKSDVLQDYFINHDNPYRERVLFSRLDETADVLSHGYKGDASMAILDGKQNLLYYTENQYYESSGVVDPKVLEYIATSFAARGEYSHTGFIYNSSGQSILLRYELIDKRTGAPPVSFDPSNVFFVVVSVSLEVFNDIKHDVEFDTHSVITFADKPIYLDIPLAQTIELLPHFYAVLSPAEYLMWNKVDKV
Transmembrane helix 258-280 WLELALSFGIAAFCTITLIVLVL
Outside 281-787 YRYVLHPVSRLDKQLSELESNQRDNIEKLGTNDEIGRLSSRFFDMYEELNVIYKKTKRLAETDHLTQLANRHRFHQLATRELASPPSHLWVIYVDLDNFKYVNDKYGHELGDNLLKVFSTHIKNACQKFSQQYDSPCFGARLSGDEFAILLSSNKDVGSIPDLLAKELLKPISNLSQTWANAFPVTASVGIAQYPQDGQDIAKLLSNADAAMYQAKRAGKNQYAYYSAELNLESQRRSQIERALRKSNVEDEFRLVFQPYMNNKDNEIEGLEVLLRWDAEGLGPVPPTEFIPIAEQAGLFDRIDRWVFANATEEYHHLRSIFGKDIVLSINLSSAELNSLEMAQFIHKHVTRNGIKPECIELEITETFAAEQQGTALLDELSKLGYRLAIDDFGSGYTSLTQLVQYPVQKIKFDREFLLTLMNTNNGHVIKPIIELCHAQNKTVTAEGIEHDVMHKWLSAYRCDFMQGYLFGKPMDKEQLSLWWKSANDDNRFSQPLTTKLAAEGGI


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 0.8597 - -


  Protein sequence of regulator: 788 a.a.    .

>REG0116 NC_004605:1147728-1150091 [Vibrio parahaemolyticus RIMD 2210633]
MKLSNRVILLVAPVIILSALVSSYIIYSIQKVTLIKREDSYIQLQMEKLAGQFRQANIFLNSYAYTLSKSDVLQDYFINH
DNPYRERVLFSRLDETADVLSHGYKGDASMAILDGKQNLLYYTENQYYESSGVVDPKVLEYIATSFAARGEYSHTGFIYN
SSGQSILLRYELIDKRTGAPPVSFDPSNVFFVVVSVSLEVFNDIKHDVEFDTHSVITFADKPIYLDIPLAQTIELLPHFY
AVLSPAEYLMWNKVDKVWLELALSFGIAAFCTITLIVLVLYRYVLHPVSRLDKQLSELESNQRDNIEKLGTNDEIGRLSS
RFFDMYEELNVIYKKTKRLAETDHLTQLANRHRFHQLATRELASPPSHLWVIYVDLDNFKYVNDKYGHELGDNLLKVFST
HIKNACQKFSQQYDSPCFGARLSGDEFAILLSSNKDVGSIPDLLAKELLKPISNLSQTWANAFPVTASVGIAQYPQDGQD
IAKLLSNADAAMYQAKRAGKNQYAYYSAELNLESQRRSQIERALRKSNVEDEFRLVFQPYMNNKDNEIEGLEVLLRWDAE
GLGPVPPTEFIPIAEQAGLFDRIDRWVFANATEEYHHLRSIFGKDIVLSINLSSAELNSLEMAQFIHKHVTRNGIKPECI
ELEITETFAAEQQGTALLDELSKLGYRLAIDDFGSGYTSLTQLVQYPVQKIKFDREFLLTLMNTNNGHVIKPIIELCHAQ
NKTVTAEGIEHDVMHKWLSAYRCDFMQGYLFGKPMDKEQLSLWWKSANDDNRFSQPLTTKLAAEGGI*

  Nucleotide sequence of regulator: 2364 bp    .

>REG0116 NC_004605:1147728-1150091 [Vibrio parahaemolyticus RIMD 2210633]
ATGAAATTAAGCAATCGAGTTATCTTGCTTGTCGCACCCGTGATCATTTTGAGTGCGCTGGTATCGAGTTACATCATCTA
TAGCATTCAAAAAGTAACACTCATCAAGCGCGAAGATAGCTACATACAACTTCAGATGGAAAAACTGGCGGGGCAATTTC
GACAAGCCAATATTTTTCTTAACAGCTATGCGTACACGCTGAGTAAAAGTGATGTGCTGCAGGACTATTTTATTAATCAC
GACAATCCCTACCGTGAGCGAGTGCTTTTTAGCCGCTTGGATGAAACTGCTGATGTCCTGAGTCATGGCTATAAAGGGGA
TGCGAGCATGGCGATCCTCGACGGCAAGCAAAATCTGCTTTATTACACCGAAAACCAATATTATGAATCGTCCGGCGTTG
TTGACCCAAAGGTGCTGGAGTACATAGCAACCAGCTTCGCGGCTCGTGGTGAATACAGTCACACAGGGTTCATTTATAAC
TCCAGTGGCCAAAGCATCTTGTTGCGATACGAACTCATTGACAAACGAACGGGCGCACCGCCAGTTAGCTTCGATCCTAG
CAACGTGTTTTTTGTTGTCGTGTCCGTATCTTTAGAAGTGTTTAACGACATCAAACACGACGTCGAATTTGATACTCATA
GTGTGATTACGTTTGCCGATAAACCCATTTATCTAGACATCCCTCTTGCGCAAACCATTGAACTTCTGCCCCACTTTTAT
GCGGTGCTCTCCCCTGCGGAGTATCTGATGTGGAACAAAGTGGACAAAGTATGGCTAGAGCTTGCACTTTCTTTTGGTAT
CGCGGCATTTTGTACCATCACGCTGATCGTCTTAGTGCTCTATCGTTACGTTTTGCATCCAGTCTCTCGCCTCGATAAAC
AACTCAGCGAGCTAGAATCGAATCAGCGAGACAACATCGAAAAGCTCGGAACCAATGATGAAATTGGCCGTCTTTCATCA
CGCTTTTTTGATATGTACGAAGAGCTCAACGTCATTTACAAAAAGACCAAACGTCTCGCAGAAACTGATCACCTTACTCA
GCTGGCAAACCGTCATCGATTCCACCAACTTGCCACGCGTGAACTAGCCTCGCCACCTTCTCATTTGTGGGTGATTTATG
TCGATCTGGATAACTTCAAGTACGTGAACGATAAATATGGTCATGAACTTGGCGACAACCTGCTAAAGGTCTTCTCGACT
CACATTAAAAACGCCTGTCAAAAGTTCTCTCAGCAATACGACAGCCCTTGTTTTGGCGCGCGTTTATCTGGTGACGAGTT
CGCCATCCTACTCAGCTCCAATAAAGACGTAGGCAGCATCCCAGATTTACTCGCCAAAGAACTATTAAAACCAATTAGCA
ACCTCAGCCAAACTTGGGCGAACGCCTTCCCGGTGACCGCCAGTGTTGGCATCGCTCAGTACCCGCAAGATGGGCAAGAC
ATCGCGAAACTGTTGTCCAATGCAGACGCAGCAATGTACCAAGCCAAACGTGCTGGAAAAAATCAGTACGCGTACTACTC
AGCAGAGCTAAATTTGGAATCTCAGCGACGCAGTCAGATCGAACGTGCACTGCGTAAAAGCAACGTTGAAGATGAGTTTA
GGCTTGTGTTTCAACCTTACATGAATAACAAAGACAACGAAATTGAAGGCTTGGAAGTGCTTCTACGTTGGGACGCAGAA
GGCTTGGGGCCAGTGCCACCAACCGAATTTATTCCAATCGCCGAGCAAGCTGGGTTGTTTGACAGAATAGACCGTTGGGT
GTTTGCCAATGCAACCGAGGAATACCATCATTTAAGAAGCATTTTTGGCAAAGACATTGTCCTGTCCATCAACCTTTCAT
CGGCCGAATTAAACTCGTTAGAAATGGCGCAATTTATTCATAAACACGTAACGAGAAATGGCATCAAACCAGAATGTATC
GAACTAGAAATTACCGAGACGTTTGCCGCGGAACAGCAAGGCACGGCATTGCTTGATGAGCTTTCGAAACTGGGTTATCG
ACTTGCGATTGATGATTTCGGCTCTGGCTACACGTCGCTCACTCAACTTGTTCAATACCCAGTACAAAAGATTAAGTTTG
ACCGAGAGTTTCTACTGACGTTAATGAATACCAATAATGGACACGTGATCAAACCGATCATTGAGCTGTGCCATGCCCAA
AACAAAACCGTGACCGCCGAAGGCATTGAACACGACGTTATGCACAAATGGTTGTCCGCTTATCGATGTGATTTCATGCA
AGGATACTTGTTCGGAAAGCCAATGGACAAAGAGCAACTTAGCTTGTGGTGGAAATCGGCCAACGATGACAATCGATTCT
CTCAGCCGCTTACAACCAAACTCGCGGCTGAGGGTGGAATTTGA