Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   LIT24_RS18920 Genome accession   NZ_CP085406
Coordinates   3709198..3709977 (-) Length   259 a.a.
NCBI ID   WP_000421290.1    Uniprot ID   A0A9W5VKA1
Organism   Bacillus bombysepticus strain F12     
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 3680417..3730404 3709198..3709977 within 0


Gene organization within MGE regions


Location: 3680417..3730404
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LIT24_RS18790 (LIT24_18790) dpaB 3681088..3681687 (-) 600 WP_000053596.1 dipicolinate synthase subunit B -
  LIT24_RS18795 (LIT24_18795) dpaA 3681684..3682586 (-) 903 WP_000954735.1 dipicolinic acid synthetase subunit A -
  LIT24_RS18800 (LIT24_18800) - 3682757..3683008 (-) 252 WP_001239756.1 YlmC/YmxH family sporulation protein -
  LIT24_RS18805 (LIT24_18805) - 3683143..3684384 (-) 1242 WP_000592989.1 pitrilysin family protein -
  LIT24_RS18810 (LIT24_18810) - 3684471..3685370 (-) 900 WP_000868232.1 polysaccharide deacetylase family protein -
  LIT24_RS18815 (LIT24_18815) pnp 3685525..3687663 (-) 2139 WP_000076754.1 polyribonucleotide nucleotidyltransferase -
  LIT24_RS18820 (LIT24_18820) rpsO 3687824..3688093 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  LIT24_RS18825 (LIT24_18825) ribF 3688194..3689165 (-) 972 WP_119780756.1 bifunctional riboflavin kinase/FAD synthetase -
  LIT24_RS18830 (LIT24_18830) truB 3689209..3690132 (-) 924 WP_000399348.1 tRNA pseudouridine(55) synthase TruB -
  LIT24_RS18835 (LIT24_18835) rbfA 3690219..3690575 (-) 357 WP_000776437.1 30S ribosome-binding factor RbfA -
  LIT24_RS18840 (LIT24_18840) - 3690591..3690872 (-) 282 WP_000582363.1 DUF503 family protein -
  LIT24_RS18845 (LIT24_18845) infB 3690869..3692929 (-) 2061 WP_000036343.1 translation initiation factor IF-2 -
  LIT24_RS18850 (LIT24_18850) - 3692934..3693245 (-) 312 WP_001286524.1 YlxQ family RNA-binding protein -
  LIT24_RS18855 (LIT24_18855) - 3693246..3693518 (-) 273 WP_000071127.1 YlxR family protein -
  LIT24_RS18860 (LIT24_18860) nusA 3693530..3694636 (-) 1107 WP_000102604.1 transcription termination factor NusA -
  LIT24_RS18865 (LIT24_18865) rimP 3694654..3695124 (-) 471 WP_000359096.1 ribosome maturation factor RimP -
  LIT24_RS18870 (LIT24_18870) - 3695461..3699762 (-) 4302 WP_000060005.1 PolC-type DNA polymerase III -
  LIT24_RS18875 (LIT24_18875) - 3699887..3701587 (-) 1701 WP_100619338.1 proline--tRNA ligase -
  LIT24_RS18880 (LIT24_18880) rseP 3701697..3702953 (-) 1257 WP_001090243.1 RIP metalloprotease RseP -
  LIT24_RS18885 (LIT24_18885) dxr 3702971..3704113 (-) 1143 WP_000790375.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  LIT24_RS18890 (LIT24_18890) cdsA 3704137..3704928 (-) 792 WP_100619336.1 phosphatidate cytidylyltransferase -
  LIT24_RS18895 (LIT24_18895) uppS 3704946..3705722 (-) 777 WP_000971296.1 isoprenyl transferase -
  LIT24_RS18900 (LIT24_18900) frr 3705808..3706365 (-) 558 WP_000531501.1 ribosome recycling factor -
  LIT24_RS18905 (LIT24_18905) pyrH 3706368..3707090 (-) 723 WP_000042668.1 UMP kinase -
  LIT24_RS18910 (LIT24_18910) tsf 3707157..3708044 (-) 888 WP_001018578.1 translation elongation factor Ts -
  LIT24_RS18915 (LIT24_18915) rpsB 3708148..3708849 (-) 702 WP_000111485.1 30S ribosomal protein S2 -
  LIT24_RS18920 (LIT24_18920) codY 3709198..3709977 (-) 780 WP_000421290.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  LIT24_RS18925 (LIT24_18925) hslU 3710055..3711446 (-) 1392 WP_000550087.1 ATP-dependent protease ATPase subunit HslU -
  LIT24_RS18930 (LIT24_18930) hslV 3711469..3712011 (-) 543 WP_000526272.1 ATP-dependent protease proteolytic subunit HslV -
  LIT24_RS18935 (LIT24_18935) xerC 3712054..3712953 (-) 900 WP_044584806.1 tyrosine recombinase XerC -
  LIT24_RS18940 (LIT24_18940) trmFO 3713019..3714323 (-) 1305 WP_000213002.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  LIT24_RS18945 (LIT24_18945) topA 3714372..3716450 (-) 2079 WP_001286960.1 type I DNA topoisomerase -
  LIT24_RS18950 (LIT24_18950) dprA 3716595..3717464 (-) 870 WP_000818058.1 DNA-processing protein DprA -
  LIT24_RS18955 (LIT24_18955) sucD 3717553..3718455 (-) 903 WP_000115178.1 succinate--CoA ligase subunit alpha -
  LIT24_RS18960 (LIT24_18960) sucC 3718475..3719635 (-) 1161 WP_001020791.1 ADP-forming succinate--CoA ligase subunit beta -
  LIT24_RS18965 (LIT24_18965) - 3719830..3720603 (-) 774 WP_001194266.1 ribonuclease HII -
  LIT24_RS18970 (LIT24_18970) ylqF 3720660..3721550 (-) 891 WP_000236702.1 ribosome biogenesis GTPase YlqF -
  LIT24_RS18975 (LIT24_18975) lepB 3721571..3722122 (-) 552 WP_000711853.1 signal peptidase I -
  LIT24_RS18980 (LIT24_18980) rplS 3722224..3722568 (-) 345 WP_001186516.1 50S ribosomal protein L19 -
  LIT24_RS18985 (LIT24_18985) trmD 3722715..3723449 (-) 735 WP_000686903.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  LIT24_RS18990 (LIT24_18990) rimM 3723449..3723964 (-) 516 WP_000170278.1 ribosome maturation factor RimM -
  LIT24_RS18995 (LIT24_18995) - 3724085..3724312 (-) 228 WP_100619332.1 KH domain-containing protein -
  LIT24_RS19000 (LIT24_19000) rpsP 3724327..3724599 (-) 273 WP_000268750.1 30S ribosomal protein S16 -
  LIT24_RS19005 (LIT24_19005) ffh 3724701..3726050 (-) 1350 WP_000863460.1 signal recognition particle protein -
  LIT24_RS19010 (LIT24_19010) - 3726063..3726395 (-) 333 WP_000891062.1 putative DNA-binding protein -
  LIT24_RS19015 (LIT24_19015) ftsY 3726529..3727518 (-) 990 WP_000007655.1 signal recognition particle-docking protein FtsY -

Sequence

Protein


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

>NTDB_id=617826 LIT24_RS18920 WP_000421290.1 3709198..3709977(-) (codY) [Bacillus bombysepticus strain F12]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKQMLAERQFPEEYTQSLF
NITETSSNLDVNSAYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLQELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=617826 LIT24_RS18920 WP_000421290.1 3709198..3709977(-) (codY) [Bacillus bombysepticus strain F12]
ATGGAATTATTAGCAAAAACGAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGGAAGCCTGTAAACTTTAGAGAAAT
GTCTGACACAATGTGTGAAGTAATCGAAGCAAACGTATTCGTAGTTAGCCGTCGTGGTAAATTACTAGGTTATGCAATTC
ACCAACAAATCGAAAACGAACGCATGAAGCAAATGCTTGCAGAACGTCAATTCCCAGAAGAATATACACAAAGCTTATTC
AACATTACAGAAACATCTTCAAACTTAGATGTGAACAGTGCTTACACAGCATTCCCAGTAGAAAACAGAGAATTATTTGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGCGGTGAGCGTCTAGGTACATTAGTATTAGCTCGTCTTGGTCAAG
AGTTCTTAGATGATGATTTAATCCTTGCTGAGTACAGCTCAACTGTTGTAGGTATGGAAATCTTACGTGAAAAAGCAGAA
GAAATCGAAGAGGAAGCACGTAGTAAAGCTGTTGTTCAAATGGCAATCAGCTCATTATCTTACAGTGAGTTAGAAGCGAT
TGAGCACATCTTCGAAGAATTAAATGGAACAGAAGGTTTACTTGTTGCAAGTAAAATTGCTGATCGCGTAGGAATTACTC
GTTCTGTAATCGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTTATTGAGTCTCGTTCTTTAGGTATGAAAGGAACA
TACATTAAAGTGCTAAACGACAAGTTTCTACAGGAACTTGCTAAATTAAAAACAAACTAA

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