Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   DN399_RS18745 Genome accession   NZ_CP031062
Coordinates   3657291..3658070 (-) Length   259 a.a.
NCBI ID   WP_000421290.1    Uniprot ID   A0A9W5VKA1
Organism   Bacillus sp. AR4-2     
Function   repression of comK (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)
ICE 3631995..3693757 3657291..3658070 within 0


Gene organization within MGE regions


Location: 3631995..3693757
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DN399_RS18635 (DN399_18635) - 3632566..3633465 (-) 900 WP_000868224.1 polysaccharide deacetylase family protein -
  DN399_RS18640 (DN399_18640) pnp 3633619..3635757 (-) 2139 WP_000076737.1 polyribonucleotide nucleotidyltransferase -
  DN399_RS18645 (DN399_18645) rpsO 3635918..3636187 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  DN399_RS18650 (DN399_18650) ribF 3636288..3637259 (-) 972 WP_000766706.1 bifunctional riboflavin kinase/FAD synthetase -
  DN399_RS18655 (DN399_18655) truB 3637303..3638226 (-) 924 WP_000399350.1 tRNA pseudouridine(55) synthase TruB -
  DN399_RS18660 (DN399_18660) rbfA 3638313..3638669 (-) 357 WP_000776437.1 30S ribosome-binding factor RbfA -
  DN399_RS18665 (DN399_18665) - 3638685..3638966 (-) 282 WP_000582363.1 DUF503 family protein -
  DN399_RS18670 (DN399_18670) infB 3638963..3641023 (-) 2061 WP_000036343.1 translation initiation factor IF-2 -
  DN399_RS18675 (DN399_18675) - 3641028..3641339 (-) 312 WP_001286523.1 YlxQ family RNA-binding protein -
  DN399_RS18680 (DN399_18680) - 3641340..3641612 (-) 273 WP_000071127.1 YlxR family protein -
  DN399_RS18685 (DN399_18685) nusA 3641624..3642730 (-) 1107 WP_000102604.1 transcription termination factor NusA -
  DN399_RS18690 (DN399_18690) rimP 3642748..3643218 (-) 471 WP_000359096.1 ribosome maturation factor RimP -
  DN399_RS18695 (DN399_18695) - 3643555..3647856 (-) 4302 WP_000060005.1 PolC-type DNA polymerase III -
  DN399_RS18700 (DN399_18700) - 3647981..3649681 (-) 1701 WP_000814300.1 proline--tRNA ligase -
  DN399_RS18705 (DN399_18705) rseP 3649791..3651047 (-) 1257 WP_140159289.1 RIP metalloprotease RseP -
  DN399_RS18710 (DN399_18710) dxr 3651065..3652207 (-) 1143 WP_000790373.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  DN399_RS18715 (DN399_18715) cdsA 3652231..3653022 (-) 792 WP_000813594.1 phosphatidate cytidylyltransferase -
  DN399_RS18720 (DN399_18720) uppS 3653040..3653816 (-) 777 WP_000971296.1 isoprenyl transferase -
  DN399_RS18725 (DN399_18725) frr 3653902..3654459 (-) 558 WP_000531501.1 ribosome recycling factor -
  DN399_RS18730 (DN399_18730) pyrH 3654462..3655184 (-) 723 WP_000042668.1 UMP kinase -
  DN399_RS18735 (DN399_18735) tsf 3655251..3656138 (-) 888 WP_001018578.1 translation elongation factor Ts -
  DN399_RS18740 (DN399_18740) rpsB 3656242..3656943 (-) 702 WP_000111485.1 30S ribosomal protein S2 -
  DN399_RS18745 (DN399_18745) codY 3657291..3658070 (-) 780 WP_000421290.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  DN399_RS18750 (DN399_18750) hslU 3658148..3659539 (-) 1392 WP_000550078.1 ATP-dependent protease ATPase subunit HslU -
  DN399_RS18755 (DN399_18755) hslV 3659562..3660104 (-) 543 WP_000526272.1 ATP-dependent protease proteolytic subunit HslV -
  DN399_RS18760 (DN399_18760) xerC 3660147..3661046 (-) 900 WP_001101243.1 tyrosine recombinase XerC -
  DN399_RS18765 (DN399_18765) trmFO 3661112..3662416 (-) 1305 WP_000213002.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  DN399_RS18770 (DN399_18770) topA 3662465..3664543 (-) 2079 WP_001286963.1 type I DNA topoisomerase -
  DN399_RS18775 (DN399_18775) dprA 3664688..3665557 (-) 870 WP_000818043.1 DNA-processing protein DprA -
  DN399_RS18780 (DN399_18780) sucD 3665646..3666548 (-) 903 WP_000115178.1 succinate--CoA ligase subunit alpha -
  DN399_RS18785 (DN399_18785) sucC 3666568..3667728 (-) 1161 WP_001020791.1 ADP-forming succinate--CoA ligase subunit beta -
  DN399_RS18790 (DN399_18790) - 3667923..3668696 (-) 774 WP_001194265.1 ribonuclease HII -
  DN399_RS18795 (DN399_18795) ylqF 3668753..3669643 (-) 891 WP_000236704.1 ribosome biogenesis GTPase YlqF -
  DN399_RS18800 (DN399_18800) lepB 3669664..3670215 (-) 552 WP_000711853.1 signal peptidase I -
  DN399_RS18805 (DN399_18805) rplS 3670317..3670661 (-) 345 WP_001186516.1 50S ribosomal protein L19 -
  DN399_RS18810 (DN399_18810) trmD 3670808..3671542 (-) 735 WP_000686903.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  DN399_RS18815 (DN399_18815) rimM 3671542..3672057 (-) 516 WP_000170278.1 ribosome maturation factor RimM -
  DN399_RS18820 (DN399_18820) - 3672179..3672406 (-) 228 WP_000737401.1 KH domain-containing protein -
  DN399_RS18825 (DN399_18825) rpsP 3672421..3672693 (-) 273 WP_000268750.1 30S ribosomal protein S16 -
  DN399_RS18830 (DN399_18830) ffh 3672795..3674144 (-) 1350 WP_000863460.1 signal recognition particle protein -
  DN399_RS18835 (DN399_18835) - 3674157..3674489 (-) 333 WP_000891062.1 putative DNA-binding protein -
  DN399_RS18840 (DN399_18840) ftsY 3674623..3675612 (-) 990 WP_000007655.1 signal recognition particle-docking protein FtsY -
  DN399_RS18845 (DN399_18845) smc 3675628..3679197 (-) 3570 WP_000478974.1 chromosome segregation protein SMC -
  DN399_RS18850 (DN399_18850) rncS 3679344..3680081 (-) 738 WP_001146875.1 ribonuclease III -
  DN399_RS18855 (DN399_18855) acpP 3680140..3680373 (-) 234 WP_000786062.1 acyl carrier protein -
  DN399_RS18860 (DN399_18860) fabG 3680443..3681183 (-) 741 WP_000911773.1 3-oxoacyl-[acyl-carrier-protein] reductase -
  DN399_RS18865 (DN399_18865) fabD 3681183..3682127 (-) 945 WP_000515899.1 ACP S-malonyltransferase -
  DN399_RS18870 (DN399_18870) plsX 3682142..3683134 (-) 993 WP_000684100.1 phosphate acyltransferase PlsX -
  DN399_RS18875 (DN399_18875) fapR 3683131..3683724 (-) 594 WP_000747348.1 transcription factor FapR -
  DN399_RS18880 (DN399_18880) recG 3683813..3685861 (-) 2049 WP_006928337.1 ATP-dependent DNA helicase RecG -
  DN399_RS18885 (DN399_18885) - 3686152..3687828 (-) 1677 WP_000027129.1 DAK2 domain-containing protein -
  DN399_RS18890 (DN399_18890) - 3687851..3688213 (-) 363 WP_000021109.1 Asp23/Gls24 family envelope stress response protein -
  DN399_RS18895 (DN399_18895) rpmB 3688590..3688778 (+) 189 WP_000124776.1 50S ribosomal protein L28 -
  DN399_RS18900 (DN399_18900) spoVM 3688852..3688932 (-) 81 WP_001213599.1 stage V sporulation protein SpoVM -
  DN399_RS18905 (DN399_18905) - 3688999..3689679 (-) 681 WP_033692901.1 thiamine diphosphokinase -
  DN399_RS18910 (DN399_18910) rpe 3689749..3690393 (-) 645 WP_006928335.1 ribulose-phosphate 3-epimerase -
  DN399_RS18915 (DN399_18915) rsgA 3690396..3691277 (-) 882 WP_001113932.1 ribosome small subunit-dependent GTPase A -
  DN399_RS18920 (DN399_18920) pknB 3691524..3693497 (-) 1974 WP_000904747.1 Stk1 family PASTA domain-containing Ser/Thr kinase -

Sequence

Protein


Download         Length: 259 a.a.        Molecular weight: 28793.05 Da        Isoelectric Point: 4.7165

>NTDB_id=303067 DN399_RS18745 WP_000421290.1 3657291..3658070(-) (codY) [Bacillus sp. AR4-2]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKQMLAERQFPEEYTQSLF
NITETSSNLDVNSAYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLQELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=303067 DN399_RS18745 WP_000421290.1 3657291..3658070(-) (codY) [Bacillus sp. AR4-2]
ATGGAATTATTAGCAAAAACGAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGGAAGCCTGTAAACTTTAGAGAAAT
GTCTGACACAATGTGTGAAGTAATCGAAGCAAACGTATTCGTAGTTAGCCGTCGTGGTAAATTACTAGGTTATGCAATTC
ACCAACAAATCGAAAACGAACGCATGAAGCAAATGCTTGCAGAACGTCAATTCCCAGAAGAATATACACAAAGCTTATTC
AACATTACAGAAACATCTTCAAACTTAGATGTGAACAGTGCTTACACAGCATTCCCAGTAGAAAACAGAGAATTATTCGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGCGGTGAGCGTCTAGGTACATTAGTATTAGCTCGTCTTGGTCAAG
AGTTCTTAGATGATGATTTAATCCTTGCTGAGTACAGCTCAACTGTTGTAGGTATGGAAATCTTACGTGAAAAAGCAGAA
GAAATCGAAGAGGAAGCGCGTAGTAAAGCTGTTGTTCAAATGGCAATCAGCTCATTATCTTACAGTGAGTTAGAAGCAAT
TGAGCATATCTTCGAAGAATTAAATGGAACAGAAGGTTTACTTGTTGCAAGTAAAATTGCTGATCGCGTAGGAATTACTC
GCTCTGTAATCGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTTATTGAGTCTCGCTCTTTAGGTATGAAAGGAACA
TACATTAAAGTGCTAAACGACAAGTTTCTACAAGAACTTGCTAAATTAAAAACAAACTAA

Domains

Predicted by InterproScan.

CodY GAF-like domain (CodY)

(2-178)

CodY helix-turn-helix domain (HTH_CodY)

(198-255)


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
  codY Bacillus subtilis subsp. subtilis str. 168

81.467

100

0.815
  codY Lactococcus lactis subsp. lactis strain DGCC12653

46.667

98.456

0.459

Multiple sequence alignment