Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   LIT28_RS19510 Genome accession   NZ_CP085409
Coordinates   3826570..3827349 (-) Length   259 a.a.
NCBI ID   WP_000421290.1    Uniprot ID   A0A9W5VKA1
Organism   Bacillus thuringiensis strain KF1     
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 3788997..3861479 3826570..3827349 within 0


Gene organization within MGE regions


Location: 3788997..3861479
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LIT28_RS19340 (LIT28_19350) - 3790226..3790429 (-) 204 WP_063221063.1 YlzJ-like family protein -
  LIT28_RS19345 (LIT28_19355) tepA 3790426..3791175 (-) 750 WP_060631960.1 translocation-enhancing protein TepA -
  LIT28_RS19350 (LIT28_19360) - 3791340..3791636 (+) 297 WP_088079863.1 transposase -
  LIT28_RS19355 (LIT28_19365) - 3791645..3792526 (+) 882 WP_252209167.1 IS3 family transposase -
  LIT28_RS19360 (LIT28_19370) - 3792584..3794254 (-) 1671 WP_063221064.1 ribonuclease J -
  LIT28_RS19365 (LIT28_19375) dapA 3795030..3795908 (-) 879 WP_000564761.1 4-hydroxy-tetrahydrodipicolinate synthase -
  LIT28_RS19370 (LIT28_19380) dapG 3795920..3797152 (-) 1233 WP_063221065.1 aspartate kinase -
  LIT28_RS19375 (LIT28_19385) asd 3797176..3798222 (-) 1047 WP_063221066.1 aspartate-semialdehyde dehydrogenase -
  LIT28_RS19380 (LIT28_19390) dpaB 3798373..3798972 (-) 600 WP_098555003.1 dipicolinate synthase subunit B -
  LIT28_RS19385 (LIT28_19395) dpaA 3798969..3799871 (-) 903 WP_063221113.1 dipicolinic acid synthetase subunit A -
  LIT28_RS19390 (LIT28_19400) - 3800146..3800397 (-) 252 WP_063221114.1 YlmC/YmxH family sporulation protein -
  LIT28_RS19395 (LIT28_19405) - 3800524..3801765 (-) 1242 WP_063221115.1 pitrilysin family protein -
  LIT28_RS19400 (LIT28_19410) - 3801852..3802751 (-) 900 WP_063221116.1 polysaccharide deacetylase family protein -
  LIT28_RS19405 (LIT28_19415) pnp 3802902..3805040 (-) 2139 WP_063221117.1 polyribonucleotide nucleotidyltransferase -
  LIT28_RS19410 (LIT28_19420) rpsO 3805201..3805470 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  LIT28_RS19415 (LIT28_19425) ribF 3805571..3806542 (-) 972 WP_242252009.1 bifunctional riboflavin kinase/FAD synthetase -
  LIT28_RS19420 (LIT28_19430) truB 3806586..3807509 (-) 924 WP_242252011.1 tRNA pseudouridine(55) synthase TruB -
  LIT28_RS19425 (LIT28_19435) rbfA 3807596..3807952 (-) 357 WP_000776443.1 30S ribosome-binding factor RbfA -
  LIT28_RS19430 (LIT28_19440) - 3807968..3808249 (-) 282 WP_000582364.1 DUF503 family protein -
  LIT28_RS19435 (LIT28_19445) infB 3808246..3810306 (-) 2061 WP_063221120.1 translation initiation factor IF-2 -
  LIT28_RS19440 (LIT28_19450) - 3810311..3810622 (-) 312 WP_001286522.1 YlxQ family RNA-binding protein -
  LIT28_RS19445 (LIT28_19455) - 3810623..3810895 (-) 273 WP_000071125.1 YlxR family protein -
  LIT28_RS19450 (LIT28_19460) nusA 3810907..3812013 (-) 1107 WP_000102598.1 transcription termination factor NusA -
  LIT28_RS19455 (LIT28_19465) rimP 3812031..3812501 (-) 471 WP_000359096.1 ribosome maturation factor RimP -
  LIT28_RS19460 (LIT28_19470) - 3812835..3817136 (-) 4302 WP_242252012.1 PolC-type DNA polymerase III -
  LIT28_RS19465 (LIT28_19475) - 3817261..3818961 (-) 1701 WP_242252013.1 proline--tRNA ligase -
  LIT28_RS19470 (LIT28_19480) rseP 3819071..3820327 (-) 1257 WP_063221123.1 RIP metalloprotease RseP -
  LIT28_RS19475 (LIT28_19485) dxr 3820345..3821487 (-) 1143 WP_063221124.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  LIT28_RS19480 (LIT28_19490) cdsA 3821511..3822302 (-) 792 WP_060631981.1 phosphatidate cytidylyltransferase -
  LIT28_RS19485 (LIT28_19495) uppS 3822320..3823096 (-) 777 WP_060631982.1 isoprenyl transferase -
  LIT28_RS19490 (LIT28_19500) frr 3823182..3823739 (-) 558 WP_000531504.1 ribosome recycling factor -
  LIT28_RS19495 (LIT28_19505) pyrH 3823742..3824464 (-) 723 WP_000042667.1 UMP kinase -
  LIT28_RS19500 (LIT28_19510) tsf 3824531..3825418 (-) 888 WP_001018584.1 translation elongation factor Ts -
  LIT28_RS19505 (LIT28_19515) rpsB 3825522..3826223 (-) 702 WP_000111485.1 30S ribosomal protein S2 -
  LIT28_RS19510 (LIT28_19520) codY 3826570..3827349 (-) 780 WP_000421290.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  LIT28_RS19515 (LIT28_19525) hslU 3827427..3828818 (-) 1392 WP_242252015.1 ATP-dependent protease ATPase subunit HslU -
  LIT28_RS19520 (LIT28_19530) hslV 3828841..3829383 (-) 543 WP_000526271.1 ATP-dependent protease proteolytic subunit HslV -
  LIT28_RS19525 (LIT28_19535) xerC 3829426..3830325 (-) 900 WP_063221128.1 tyrosine recombinase XerC -
  LIT28_RS19530 (LIT28_19540) trmFO 3830391..3831695 (-) 1305 WP_060631987.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  LIT28_RS19535 (LIT28_19545) topA 3831746..3833830 (-) 2085 WP_060631988.1 type I DNA topoisomerase -
  LIT28_RS19540 (LIT28_19550) dprA 3833975..3834844 (-) 870 WP_063221129.1 DNA-processing protein DprA -
  LIT28_RS19545 (LIT28_19555) sucD 3834932..3835834 (-) 903 WP_000115179.1 succinate--CoA ligase subunit alpha -
  LIT28_RS19550 (LIT28_19560) sucC 3835854..3837014 (-) 1161 WP_001020788.1 ADP-forming succinate--CoA ligase subunit beta -
  LIT28_RS19555 (LIT28_19565) - 3837208..3837981 (-) 774 WP_242252016.1 ribonuclease HII -
  LIT28_RS19560 (LIT28_19570) ylqF 3838033..3838923 (-) 891 WP_063221131.1 ribosome biogenesis GTPase YlqF -
  LIT28_RS19565 (LIT28_19575) lepB 3838944..3839495 (-) 552 WP_060631992.1 signal peptidase I -
  LIT28_RS19570 (LIT28_19580) rplS 3839597..3839941 (-) 345 WP_001186516.1 50S ribosomal protein L19 -
  LIT28_RS19575 (LIT28_19585) trmD 3840088..3840822 (-) 735 WP_242252017.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  LIT28_RS19580 (LIT28_19590) rimM 3840822..3841337 (-) 516 WP_242252018.1 ribosome maturation factor RimM -
  LIT28_RS19585 (LIT28_19595) - 3841459..3841686 (-) 228 WP_060631995.1 KH domain-containing protein -
  LIT28_RS19590 (LIT28_19600) rpsP 3841701..3841973 (-) 273 WP_000268750.1 30S ribosomal protein S16 -
  LIT28_RS19595 (LIT28_19605) ffh 3842075..3843424 (-) 1350 WP_000863460.1 signal recognition particle protein -
  LIT28_RS19600 (LIT28_19610) - 3843437..3843769 (-) 333 WP_000891061.1 putative DNA-binding protein -
  LIT28_RS19605 (LIT28_19615) ftsY 3843903..3844892 (-) 990 WP_063221134.1 signal recognition particle-docking protein FtsY -
  LIT28_RS19610 (LIT28_19620) smc 3844908..3848477 (-) 3570 WP_242252019.1 chromosome segregation protein SMC -
  LIT28_RS19615 (LIT28_19625) rncS 3848625..3849362 (-) 738 WP_060631998.1 ribonuclease III -
  LIT28_RS19620 (LIT28_19630) acpP 3849421..3849654 (-) 234 WP_000786062.1 acyl carrier protein -
  LIT28_RS19625 (LIT28_19635) fabG 3849724..3850464 (-) 741 WP_063221136.1 3-oxoacyl-[acyl-carrier-protein] reductase -
  LIT28_RS19630 (LIT28_19640) fabD 3850464..3851408 (-) 945 WP_242252020.1 ACP S-malonyltransferase -
  LIT28_RS19635 (LIT28_19645) plsX 3851423..3852415 (-) 993 WP_063221138.1 phosphate acyltransferase PlsX -
  LIT28_RS19640 (LIT28_19650) fapR 3852412..3853005 (-) 594 WP_242252297.1 transcription factor FapR -
  LIT28_RS19645 (LIT28_19655) recG 3853094..3855142 (-) 2049 WP_063221139.1 ATP-dependent DNA helicase RecG -
  LIT28_RS19650 (LIT28_19660) - 3855442..3857118 (-) 1677 WP_242252021.1 DAK2 domain-containing protein -
  LIT28_RS19655 (LIT28_19665) - 3857141..3857503 (-) 363 WP_000021109.1 Asp23/Gls24 family envelope stress response protein -
  LIT28_RS19660 (LIT28_19670) rpmB 3857879..3858067 (+) 189 WP_000124776.1 50S ribosomal protein L28 -
  LIT28_RS19665 (LIT28_19675) spoVM 3858141..3858221 (-) 81 WP_001213599.1 stage V sporulation protein SpoVM -
  LIT28_RS19670 (LIT28_19680) - 3858288..3858968 (-) 681 WP_142332664.1 thiamine diphosphokinase -
  LIT28_RS19675 (LIT28_19685) rpe 3859069..3859713 (-) 645 WP_060632004.1 ribulose-phosphate 3-epimerase -
  LIT28_RS19680 (LIT28_19690) rsgA 3859716..3860597 (-) 882 WP_063221142.1 ribosome small subunit-dependent GTPase A -

Sequence

Protein


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

>NTDB_id=617873 LIT28_RS19510 WP_000421290.1 3826570..3827349(-) (codY) [Bacillus thuringiensis strain KF1]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKQMLAERQFPEEYTQSLF
NITETSSNLDVNSAYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLQELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=617873 LIT28_RS19510 WP_000421290.1 3826570..3827349(-) (codY) [Bacillus thuringiensis strain KF1]
ATGGAATTATTAGCAAAAACAAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGAAAGCCTGTAAACTTTAGAGAAAT
GTCTGACACAATGTGTGAAGTAATCGAAGCGAACGTATTCGTAGTAAGCCGTCGTGGTAAATTACTAGGTTATGCAATTC
ACCAACAAATTGAGAATGAGCGTATGAAACAAATGCTTGCAGAGCGTCAATTCCCGGAAGAATACACACAAAGCTTATTC
AACATTACAGAAACATCTTCTAACTTAGATGTAAACAGTGCTTACACAGCATTCCCGGTAGAAAATAGAGAATTATTCGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGCGGTGAGCGTCTAGGCACATTAGTGTTAGCTCGTCTTGGTCAAG
AGTTCTTAGACGATGATTTAATCCTTGCTGAATACAGTTCAACTGTAGTAGGTATGGAAATCTTACGTGAAAAAGCAGAA
GAAATTGAAGAGGAAGCACGTAGTAAAGCTGTTGTTCAAATGGCGATTAGTTCATTGTCTTACAGTGAGTTAGAAGCAAT
CGAGCATATCTTCGAAGAATTAAATGGAACAGAAGGATTACTTGTTGCAAGTAAAATTGCTGATCGCGTAGGAATTACTC
GTTCTGTAATCGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTTATTGAGTCGCGCTCTTTAGGTATGAAAGGAACA
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