Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   RVY74_RS18265 Genome accession   NZ_CP136372
Coordinates   3595551..3596330 (-) Length   259 a.a.
NCBI ID   WP_002014541.1    Uniprot ID   -
Organism   Bacillus mycoides strain PAMC 29434     
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 3569240..3627803 3595551..3596330 within 0


Gene organization within MGE regions


Location: 3569240..3627803
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RVY74_RS18150 (RVY74_18150) - 3569466..3570707 (-) 1242 WP_002088150.1 pitrilysin family protein -
  RVY74_RS18155 (RVY74_18155) - 3570794..3571693 (-) 900 WP_002033683.1 polysaccharide deacetylase family protein -
  RVY74_RS18160 (RVY74_18160) pnp 3571848..3574001 (-) 2154 WP_316281630.1 polyribonucleotide nucleotidyltransferase -
  RVY74_RS18165 (RVY74_18165) rpsO 3574163..3574432 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  RVY74_RS18170 (RVY74_18170) ribF 3574533..3575504 (-) 972 WP_002128800.1 bifunctional riboflavin kinase/FAD synthetase -
  RVY74_RS18175 (RVY74_18175) truB 3575548..3576471 (-) 924 WP_201064577.1 tRNA pseudouridine(55) synthase TruB -
  RVY74_RS18180 (RVY74_18180) rbfA 3576562..3576918 (-) 357 WP_002146104.1 30S ribosome-binding factor RbfA -
  RVY74_RS18185 (RVY74_18185) - 3576934..3577215 (-) 282 WP_002088157.1 DUF503 domain-containing protein -
  RVY74_RS18190 (RVY74_18190) infB 3577212..3579278 (-) 2067 WP_002014558.1 translation initiation factor IF-2 -
  RVY74_RS18195 (RVY74_18195) - 3579283..3579594 (-) 312 WP_002033679.1 YlxQ family RNA-binding protein -
  RVY74_RS18200 (RVY74_18200) rnpM 3579595..3579867 (-) 273 WP_002088161.1 RNase P modulator RnpM -
  RVY74_RS18205 (RVY74_18205) nusA 3579879..3580985 (-) 1107 WP_002014554.1 transcription termination factor NusA -
  RVY74_RS18210 (RVY74_18210) rimP 3581003..3581473 (-) 471 WP_002088165.1 ribosome maturation factor RimP -
  RVY74_RS18215 (RVY74_18215) - 3581807..3586108 (-) 4302 WP_002033677.1 PolC-type DNA polymerase III -
  RVY74_RS18220 (RVY74_18220) - 3586233..3587933 (-) 1701 WP_201064574.1 proline--tRNA ligase -
  RVY74_RS18225 (RVY74_18225) rseP 3588043..3589299 (-) 1257 WP_201064571.1 RIP metalloprotease RseP -
  RVY74_RS18230 (RVY74_18230) dxr 3589317..3590459 (-) 1143 WP_002014547.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  RVY74_RS18235 (RVY74_18235) cdsA 3590483..3591274 (-) 792 WP_002088171.1 phosphatidate cytidylyltransferase -
  RVY74_RS18240 (RVY74_18240) - 3591292..3592068 (-) 777 WP_002014545.1 isoprenyl transferase -
  RVY74_RS18245 (RVY74_18245) frr 3592154..3592711 (-) 558 WP_000531506.1 ribosome recycling factor -
  RVY74_RS18250 (RVY74_18250) pyrH 3592715..3593437 (-) 723 WP_002014544.1 UMP kinase -
  RVY74_RS18255 (RVY74_18255) tsf 3593504..3594391 (-) 888 WP_002088177.1 translation elongation factor Ts -
  RVY74_RS18260 (RVY74_18260) rpsB 3594495..3595196 (-) 702 WP_002088178.1 30S ribosomal protein S2 -
  RVY74_RS18265 (RVY74_18265) codY 3595551..3596330 (-) 780 WP_002014541.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  RVY74_RS18270 (RVY74_18270) hslU 3596408..3597799 (-) 1392 WP_002014539.1 ATP-dependent protease ATPase subunit HslU -
  RVY74_RS18275 (RVY74_18275) hslV 3597822..3598364 (-) 543 WP_002014538.1 ATP-dependent protease proteolytic subunit HslV -
  RVY74_RS18280 (RVY74_18280) xerC 3598407..3599306 (-) 900 WP_201065582.1 tyrosine recombinase XerC -
  RVY74_RS18285 (RVY74_18285) trmFO 3599378..3600682 (-) 1305 WP_002014534.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  RVY74_RS18290 (RVY74_18290) topA 3600731..3602809 (-) 2079 WP_002088184.1 type I DNA topoisomerase -
  RVY74_RS18295 (RVY74_18295) dprA 3602954..3603823 (-) 870 WP_201064568.1 DNA-processing protein DprA -
  RVY74_RS18300 (RVY74_18300) sucD 3603912..3604814 (-) 903 WP_002033796.1 succinate--CoA ligase subunit alpha -
  RVY74_RS18305 (RVY74_18305) sucC 3604834..3605994 (-) 1161 WP_002014529.1 ADP-forming succinate--CoA ligase subunit beta -
  RVY74_RS18310 (RVY74_18310) - 3606188..3606961 (-) 774 WP_002014527.1 ribonuclease HII -
  RVY74_RS18315 (RVY74_18315) ylqF 3607017..3607907 (-) 891 WP_002014526.1 ribosome biogenesis GTPase YlqF -
  RVY74_RS18320 (RVY74_18320) lepB 3607928..3608479 (-) 552 WP_002066791.1 signal peptidase I -
  RVY74_RS18325 (RVY74_18325) rplS 3608580..3608924 (-) 345 WP_002014524.1 50S ribosomal protein L19 -
  RVY74_RS18330 (RVY74_18330) trmD 3609071..3609805 (-) 735 WP_002014522.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  RVY74_RS18335 (RVY74_18335) rimM 3609805..3610320 (-) 516 WP_002014521.1 ribosome maturation factor RimM -
  RVY74_RS18340 (RVY74_18340) - 3610442..3610669 (-) 228 WP_002088196.1 KH domain-containing protein -
  RVY74_RS18345 (RVY74_18345) rpsP 3610684..3610956 (-) 273 WP_000268750.1 30S ribosomal protein S16 -
  RVY74_RS18350 (RVY74_18350) ffh 3611057..3612406 (-) 1350 WP_002014519.1 signal recognition particle protein -
  RVY74_RS18355 (RVY74_18355) - 3612419..3612751 (-) 333 WP_002033794.1 putative DNA-binding protein -
  RVY74_RS18360 (RVY74_18360) ftsY 3612884..3613873 (-) 990 WP_002088200.1 signal recognition particle-docking protein FtsY -
  RVY74_RS18365 (RVY74_18365) smc 3613888..3617457 (-) 3570 WP_201064555.1 chromosome segregation protein SMC -
  RVY74_RS18370 (RVY74_18370) rncS 3617606..3618343 (-) 738 WP_002033792.1 ribonuclease III -
  RVY74_RS18375 (RVY74_18375) acpP 3618402..3618635 (-) 234 WP_002014515.1 acyl carrier protein -
  RVY74_RS18380 (RVY74_18380) fabG 3618705..3619445 (-) 741 WP_002014514.1 3-oxoacyl-[acyl-carrier-protein] reductase -
  RVY74_RS18385 (RVY74_18385) fabD 3619445..3620389 (-) 945 WP_088040046.1 ACP S-malonyltransferase -
  RVY74_RS18390 (RVY74_18390) plsX 3620404..3621396 (-) 993 WP_002128828.1 phosphate acyltransferase PlsX -
  RVY74_RS18395 (RVY74_18395) fapR 3621393..3621986 (-) 594 WP_000747354.1 transcription factor FapR -
  RVY74_RS18400 (RVY74_18400) recG 3622075..3624123 (-) 2049 WP_002014510.1 ATP-dependent DNA helicase RecG -
  RVY74_RS18405 (RVY74_18405) - 3624548..3626224 (-) 1677 WP_002033789.1 DAK2 domain-containing protein -
  RVY74_RS18410 (RVY74_18410) - 3626247..3626609 (-) 363 WP_002014507.1 Asp23/Gls24 family envelope stress response protein -
  RVY74_RS18415 (RVY74_18415) rpmB 3626988..3627176 (+) 189 WP_000124776.1 50S ribosomal protein L28 -
  RVY74_RS18420 (RVY74_18420) spoVM 3627250..3627330 (-) 81 WP_001213599.1 stage V sporulation protein SpoVM -

Sequence

Protein


Download         Length: 259 a.a.        Molecular weight: 28774.99 Da        Isoelectric Point: 4.7251

>NTDB_id=890405 RVY74_RS18265 WP_002014541.1 3595551..3596330(-) (codY) [Bacillus mycoides strain PAMC 29434]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKHMLAERQFPEEYTQSLF
NVTETSSNLGVDSDYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLQELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=890405 RVY74_RS18265 WP_002014541.1 3595551..3596330(-) (codY) [Bacillus mycoides strain PAMC 29434]
ATGGAATTATTAGCAAAAACGAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGAAAGCCTGTAAACTTTAGAGAGAT
GTCTGACACAATGTGTGAAGTAATTGAAGCGAACGTGTTCGTTGTAAGTCGTCGCGGTAAATTATTAGGATATGCGATTC
ACCAACAAATCGAAAACGAACGTATGAAGCACATGCTTGCAGAGCGTCAATTCCCAGAAGAGTATACGCAAAGTTTATTC
AATGTTACAGAAACATCTTCAAATTTAGGTGTAGATAGTGACTACACAGCATTCCCAGTAGAAAATAGAGAATTATTCGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGCGGTGAGCGTCTAGGTACACTAGTATTAGCTCGTCTTGGTCAAG
AGTTCTTAGACGATGATTTAATTCTTGCTGAATACAGCTCAACTGTTGTAGGTATGGAAATCTTACGTGAAAAAGCAGAA
GAAATCGAAGAGGAAGCACGTAGTAAAGCTGTTGTTCAAATGGCGATTAGCTCATTATCTTACAGTGAGTTAGAAGCAAT
CGAGCATATCTTCGAAGAATTAAATGGAACAGAAGGTTTACTTGTTGCAAGTAAAATTGCTGATCGCGTAGGAATTACTC
GTTCGGTAATCGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTTATTGAGTCTCGCTCTTTAGGTATGAAAGGAACA
TACATTAAAGTGCTAAACGACAAGTTTCTACAGGAACTTGCTAAATTAAAAACAAACTAA

Domains

Predicted by InterproScan.

CodY helix-turn-helix domain (HTH_CodY)

(198-255)

CodY GAF-like domain (CodY)

(2-178)


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

81.081

100

0.811
  codY Lactococcus lactis subsp. lactis strain DGCC12653

46.275

98.456

0.456