Detailed information    

insolico Bioinformatically predicted

Overview

Name   rpoS   Type   Regulator
Locus tag   GPW86_RS14995 Genome accession   NZ_CP046742
Coordinates   1942839..1943846 (+) Length   335 a.a.
NCBI ID   WP_123011330.1    Uniprot ID   -
Organism   Vibrio cholerae strain 3523-03     
Function   regulation of chitinases (predicted from homology)   
Competence regulation

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
Prophage 1903053..1958894 1942839..1943846 within 0


Gene organization within MGE regions


Location: 1903053..1958894
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GPW86_RS14790 - 1903053..1903430 (-) 378 WP_071179079.1 hypothetical protein -
  GPW86_RS14795 - 1903402..1903971 (-) 570 WP_071179080.1 GNAT family N-acetyltransferase -
  GPW86_RS14800 - 1903971..1905161 (-) 1191 WP_071179081.1 hypothetical protein -
  GPW86_RS14805 - 1905391..1905746 (-) 356 Protein_1644 tyrosine-type recombinase/integrase -
  GPW86_RS14810 - 1906598..1907818 (-) 1221 WP_071187285.1 hypothetical protein -
  GPW86_RS14815 - 1908323..1908958 (+) 636 WP_071187946.1 inovirus Gp2 family protein -
  GPW86_RS14820 - 1909023..1909691 (+) 669 WP_123011317.1 inovirus Gp2 family protein -
  GPW86_RS14825 - 1909752..1910348 (+) 597 WP_123011318.1 inovirus-type Gp2 protein -
  GPW86_RS14830 - 1910413..1910613 (+) 201 WP_001211744.1 AlpA family transcriptional regulator -
  GPW86_RS14835 - 1911355..1913907 (+) 2553 WP_123011319.1 LysM peptidoglycan-binding domain-containing protein -
  GPW86_RS14840 - 1914407..1914634 (-) 228 WP_123011320.1 hypothetical protein -
  GPW86_RS14845 - 1914682..1915050 (-) 369 WP_123011321.1 hypothetical protein -
  GPW86_RS14850 - 1915081..1915815 (-) 735 WP_119788842.1 WYL domain-containing protein -
  GPW86_RS14855 - 1915954..1916130 (-) 177 WP_114729912.1 hypothetical protein -
  GPW86_RS14860 - 1916134..1916577 (-) 444 WP_123011322.1 DUF2787 domain-containing protein -
  GPW86_RS14865 - 1916628..1917065 (-) 438 WP_184476174.1 DUF2787 domain-containing protein -
  GPW86_RS14870 radC 1917062..1917535 (-) 474 WP_123011324.1 DNA repair protein RadC -
  GPW86_RS14875 - 1917727..1919223 (+) 1497 WP_001961454.1 ATP-binding protein -
  GPW86_RS14880 - 1919220..1921931 (+) 2712 WP_123011325.1 Z1 domain-containing protein -
  GPW86_RS14885 - 1921924..1922874 (+) 951 WP_123011326.1 PD-(D/E)XK motif protein -
  GPW86_RS14890 - 1922877..1924943 (+) 2067 WP_001961449.1 AIPR family protein -
  GPW86_RS14895 - 1925076..1926620 (+) 1545 WP_123011327.1 DNA cytosine methyltransferase -
  GPW86_RS14900 - 1926887..1928128 (-) 1242 WP_123011328.1 integrase domain-containing protein -
  GPW86_RS14910 rpoD 1928514..1930391 (-) 1878 WP_000372618.1 RNA polymerase sigma factor RpoD -
  GPW86_RS14915 dnaG 1930490..1932253 (-) 1764 WP_123011329.1 DNA primase -
  GPW86_RS14920 - 1932343..1932786 (-) 444 WP_001173892.1 GatB/YqeY domain-containing protein -
  GPW86_RS14925 rpsU 1932816..1933031 (-) 216 WP_001145625.1 30S ribosomal protein S21 -
  GPW86_RS14930 tsaD 1933272..1934290 (+) 1019 Protein_1668 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD -
  GPW86_RS14935 - 1934444..1935255 (+) 812 Protein_1669 alpha/beta fold hydrolase -
  GPW86_RS14940 plsY 1935304..1935930 (-) 627 WP_033933160.1 glycerol-3-phosphate 1-O-acyltransferase PlsY -
  GPW86_RS14945 folB 1936119..1936472 (+) 354 WP_000361952.1 bifunctional dihydroneopterin aldolase/7,8-dihydroneopterin epimerase -
  GPW86_RS14950 folK 1936469..1936975 (+) 507 WP_000627006.1 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase -
  GPW86_RS14955 - 1936972..1937775 (+) 804 WP_000119813.1 undecaprenyl-diphosphate phosphatase -
  GPW86_RS14960 ftsB 1937890..1938174 (+) 285 WP_033933161.1 cell division protein FtsB -
  GPW86_RS14965 ispD 1938171..1938869 (+) 699 WP_033933162.1 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase -
  GPW86_RS14970 ispF 1938866..1939342 (+) 477 WP_033933163.1 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase -
  GPW86_RS14975 truD 1939372..1940457 (+) 1086 WP_069212455.1 tRNA pseudouridine(13) synthase TruD -
  GPW86_RS14980 surE 1940459..1941211 (+) 753 WP_000698379.1 5'/3'-nucleotidase SurE -
  GPW86_RS14985 - 1941204..1941830 (+) 627 WP_057550676.1 protein-L-isoaspartate(D-aspartate) O-methyltransferase -
  GPW86_RS14990 nlpD 1941830..1942765 (+) 936 WP_095461793.1 murein hydrolase activator NlpD -
  GPW86_RS14995 rpoS 1942839..1943846 (+) 1008 WP_123011330.1 RNA polymerase sigma factor RpoS Regulator
  GPW86_RS15000 mutS 1943940..1946528 (-) 2589 WP_001934677.1 DNA mismatch repair protein MutS -
  GPW86_RS15005 cysM 1946796..1947683 (-) 888 WP_123011331.1 cysteine synthase CysM -
  GPW86_RS15010 cysP 1948066..1949067 (+) 1002 WP_123011332.1 thiosulfate ABC transporter substrate-binding protein CysP -
  GPW86_RS15015 cysT 1949144..1949995 (+) 852 WP_123011333.1 sulfate/thiosulfate ABC transporter permease CysT -
  GPW86_RS15020 cysW 1950007..1950870 (+) 864 WP_123011334.1 sulfate ABC transporter permease subunit CysW -
  GPW86_RS15025 - 1950867..1951997 (+) 1131 WP_002051153.1 sulfate/molybdate ABC transporter ATP-binding protein -
  GPW86_RS15030 pncC 1952164..1952670 (+) 507 WP_123011335.1 nicotinamide-nucleotide amidase -
  GPW86_RS15035 recA 1952804..1953868 (+) 1065 WP_000344154.1 recombinase RecA Machinery gene
  GPW86_RS15040 recX 1954001..1954459 (+) 459 WP_123011336.1 recombination regulator RecX -
  GPW86_RS15045 alaS 1954632..1957214 (+) 2583 WP_000481019.1 alanine--tRNA ligase -
  GPW86_RS15050 - 1957418..1958605 (+) 1188 WP_001885701.1 aspartate kinase -
  GPW86_RS15055 csrA 1958697..1958894 (+) 198 WP_000906485.1 carbon storage regulator CsrA -

Sequence

Protein


Download         Length: 335 a.a.        Molecular weight: 38564.42 Da        Isoelectric Point: 4.3648

>NTDB_id=406976 GPW86_RS14995 WP_123011330.1 1942839..1943846(+) (rpoS) [Vibrio cholerae strain 3523-03]
MSVSNTVTKVEEFDFEDEALEVLETDTELASDEELVAVEGTSEDVREEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLY
ARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALM
NQTRTIRLPIHVVKELNIYLRTARELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISSVDTPIGGDGDKALLDILP
DSHNADPEFSTQDDDIRESLLNWLDELNPKQKEVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVK
QGLNMEALFNVEYDN

Nucleotide


Download         Length: 1008 bp        

>NTDB_id=406976 GPW86_RS14995 WP_123011330.1 1942839..1943846(+) (rpoS) [Vibrio cholerae strain 3523-03]
ATGAGTGTCAGCAATACCGTAACCAAAGTAGAAGAGTTCGATTTTGAAGATGAAGCACTGGAAGTGCTAGAAACTGATAC
CGAGCTCGCCAGTGATGAAGAATTAGTTGCTGTTGAAGGGACAAGTGAAGACGTTCGTGAAGAGTTTGATGCTTCTGCGA
AAAGTCTTGATGCGACCCAGATGTATCTCAGCGAAATTGGTTTTTCACCGCTCCTTACTGCCGAAGAAGAAGTGCTTTAT
GCTCGTCGTGCCTTACGTGGTGATGAAGCCGCACGTAAACGCATGATTGAAAGTAACTTGCGTCTGGTGGTAAAAATTTC
ACGCCGTTACAGCAACCGAGGATTAGCACTGCTCGATCTGATTGAAGAAGGTAATCTTGGTCTGATCCGTGCGGTTGAGA
AATTCGATCCAGAACGCGGTTTCCGCTTCTCTACCTACGCAACATGGTGGATCCGTCAAACCATTGAACGTGCGCTGATG
AACCAAACACGCACCATTCGTCTACCGATCCATGTCGTCAAAGAACTGAACATTTATTTGCGTACTGCTCGCGAATTATC
ACAGCGCCTTGACCACGAACCTACGCCAGAAGAAATTGCTCTTGAGTTAGATCGACCTGTCGATGATGTGACTAAGATGC
TGCGTCTTAACGAACGGATCAGCTCAGTGGATACGCCAATTGGTGGTGATGGAGATAAGGCACTGCTGGATATTTTGCCA
GACTCACACAATGCCGATCCTGAGTTTTCAACTCAAGATGATGACATTCGTGAATCGCTGCTCAACTGGTTGGATGAACT
TAATCCAAAGCAAAAAGAAGTGCTTGCTCGTCGCTTTGGGCTTCTTGGCTATGAACCATCGACCTTGGAAGAAGTGGGTC
GTGAGATCAATCTCACTCGTGAGCGTGTTCGCCAAATCCAAGTGGAAGGTCTACGTCGTCTGCGTGAGATTTTGGTGAAA
CAAGGTTTGAATATGGAAGCTCTGTTTAACGTCGAATACGACAACTAA

Domains

Predicted by InterproScan.

Sigma-70 region 3 (Sigma70_r3)

(175-249)

Sigma-70 factor, region 1.2 (Sigma70_r1_2)

(57-90)

Sigma-70 region 2 (Sigma70_r2)

(95-164)

Sigma-70, region 4 (Sigma70_r4)

(263-316)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  rpoS Vibrio cholerae O1 biovar El Tor strain E7946

99.104

100

0.991

Multiple sequence alignment