Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   HCM98_RS20115 Genome accession   NZ_CP051013
Coordinates   3887411..3888190 (-) Length   259 a.a.
NCBI ID   WP_000421290.1    Uniprot ID   A0A9W5VKA1
Organism   Bacillus tropicus strain LM1212-DB     
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 3851534..3905447 3887411..3888190 within 0


Gene organization within MGE regions


Location: 3851534..3905447
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HCM98_RS19955 (HCM98_19985) - 3852422..3852625 (-) 204 WP_029439580.1 YlzJ-like family protein -
  HCM98_RS19960 (HCM98_19990) tepA 3852622..3853371 (-) 750 WP_029439581.1 translocation-enhancing protein TepA -
  HCM98_RS19965 (HCM98_19995) - 3853474..3855144 (-) 1671 WP_000823084.1 ribonuclease J -
  HCM98_RS19970 (HCM98_20000) dapA 3855902..3856780 (-) 879 WP_029439583.1 4-hydroxy-tetrahydrodipicolinate synthase -
  HCM98_RS19975 (HCM98_20005) dapG 3856792..3858024 (-) 1233 WP_001978141.1 aspartate kinase -
  HCM98_RS19980 (HCM98_20010) asd 3858048..3859094 (-) 1047 WP_000414855.1 aspartate-semialdehyde dehydrogenase -
  HCM98_RS19985 (HCM98_20015) dpaB 3859245..3859844 (-) 600 WP_001049480.1 dipicolinate synthase subunit B -
  HCM98_RS19990 (HCM98_20020) dpaA 3859841..3860743 (-) 903 WP_000954726.1 dipicolinic acid synthetase subunit A -
  HCM98_RS19995 (HCM98_20025) - 3860983..3861234 (-) 252 WP_029439584.1 YlmC/YmxH family sporulation protein -
  HCM98_RS20000 (HCM98_20030) - 3861365..3862606 (-) 1242 WP_000592994.1 pitrilysin family protein -
  HCM98_RS20005 (HCM98_20035) - 3862693..3863592 (-) 900 WP_000647529.1 polysaccharide deacetylase family protein -
  HCM98_RS20010 (HCM98_20040) pnp 3863743..3865881 (-) 2139 WP_029439585.1 polyribonucleotide nucleotidyltransferase -
  HCM98_RS20015 (HCM98_20045) rpsO 3866042..3866311 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  HCM98_RS20020 (HCM98_20050) ribF 3866412..3867383 (-) 972 WP_000766719.1 bifunctional riboflavin kinase/FAD synthetase -
  HCM98_RS20025 (HCM98_20055) truB 3867427..3868350 (-) 924 WP_000399340.1 tRNA pseudouridine(55) synthase TruB -
  HCM98_RS20030 (HCM98_20060) rbfA 3868437..3868793 (-) 357 WP_000776442.1 30S ribosome-binding factor RbfA -
  HCM98_RS20035 (HCM98_20065) - 3868809..3869090 (-) 282 WP_000582364.1 DUF503 family protein -
  HCM98_RS20040 (HCM98_20070) infB 3869087..3871147 (-) 2061 WP_000036341.1 translation initiation factor IF-2 -
  HCM98_RS20045 (HCM98_20075) - 3871152..3871463 (-) 312 WP_001286518.1 YlxQ family RNA-binding protein -
  HCM98_RS20050 (HCM98_20080) - 3871464..3871736 (-) 273 WP_000071128.1 YlxR family protein -
  HCM98_RS20055 (HCM98_20085) nusA 3871748..3872854 (-) 1107 WP_000102609.1 transcription termination factor NusA -
  HCM98_RS20060 (HCM98_20090) rimP 3872872..3873342 (-) 471 WP_000359097.1 ribosome maturation factor RimP -
  HCM98_RS20065 (HCM98_20095) - 3873675..3877976 (-) 4302 WP_029439586.1 PolC-type DNA polymerase III -
  HCM98_RS20070 (HCM98_20100) - 3878101..3879801 (-) 1701 WP_029439587.1 proline--tRNA ligase -
  HCM98_RS20075 (HCM98_20105) rseP 3879911..3881167 (-) 1257 WP_001090234.1 RIP metalloprotease RseP -
  HCM98_RS20080 (HCM98_20110) dxr 3881184..3882326 (-) 1143 WP_029439588.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  HCM98_RS20085 (HCM98_20115) cdsA 3882350..3883141 (-) 792 WP_000813584.1 phosphatidate cytidylyltransferase -
  HCM98_RS20090 (HCM98_20120) uppS 3883159..3883935 (-) 777 WP_029439589.1 isoprenyl transferase -
  HCM98_RS20095 (HCM98_20125) frr 3884021..3884578 (-) 558 WP_000531501.1 ribosome recycling factor -
  HCM98_RS20100 (HCM98_20130) pyrH 3884581..3885303 (-) 723 WP_000042663.1 UMP kinase -
  HCM98_RS20105 (HCM98_20135) tsf 3885370..3886257 (-) 888 WP_029439590.1 translation elongation factor Ts -
  HCM98_RS20110 (HCM98_20140) rpsB 3886361..3887062 (-) 702 WP_000111485.1 30S ribosomal protein S2 -
  HCM98_RS20115 (HCM98_20145) codY 3887411..3888190 (-) 780 WP_000421290.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  HCM98_RS20120 (HCM98_20150) hslU 3888268..3889659 (-) 1392 WP_000550082.1 ATP-dependent protease ATPase subunit HslU -
  HCM98_RS20125 (HCM98_20155) hslV 3889682..3890224 (-) 543 WP_000526274.1 ATP-dependent protease proteolytic subunit HslV -
  HCM98_RS20130 (HCM98_20160) xerC 3890267..3891166 (-) 900 WP_029439591.1 tyrosine recombinase XerC -
  HCM98_RS20135 (HCM98_20165) trmFO 3891232..3892536 (-) 1305 WP_029439592.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  HCM98_RS20140 (HCM98_20170) topA 3892587..3894665 (-) 2079 WP_029439593.1 type I DNA topoisomerase -
  HCM98_RS20145 (HCM98_20175) - 3894810..3895196 (-) 387 Protein_3955 DNA-processing protein DprA -
  HCM98_RS20155 (HCM98_20185) - 3896042..3896530 (-) 489 Protein_3957 DNA-processing protein DprA -
  HCM98_RS20160 (HCM98_20190) sucD 3896618..3897520 (-) 903 WP_000115178.1 succinate--CoA ligase subunit alpha -
  HCM98_RS20165 (HCM98_20195) sucC 3897540..3898700 (-) 1161 WP_001020785.1 ADP-forming succinate--CoA ligase subunit beta -
  HCM98_RS20170 (HCM98_20200) rnhB 3898894..3899667 (-) 774 WP_029439595.1 ribonuclease HII -
  HCM98_RS20175 (HCM98_20205) ylqF 3899719..3900609 (-) 891 WP_000236700.1 ribosome biogenesis GTPase YlqF -
  HCM98_RS20180 (HCM98_20210) lepB 3900630..3901181 (-) 552 WP_029439596.1 signal peptidase I -
  HCM98_RS20185 (HCM98_20215) rplS 3901283..3901627 (-) 345 WP_001186516.1 50S ribosomal protein L19 -
  HCM98_RS20190 (HCM98_20220) trmD 3901774..3902508 (-) 735 WP_029439597.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  HCM98_RS20195 (HCM98_20225) rimM 3902508..3903023 (-) 516 WP_000170268.1 ribosome maturation factor RimM -
  HCM98_RS20200 (HCM98_20230) - 3903145..3903372 (-) 228 WP_000737398.1 KH domain-containing protein -
  HCM98_RS20205 (HCM98_20235) rpsP 3903387..3903659 (-) 273 WP_000268750.1 30S ribosomal protein S16 -
  HCM98_RS20210 (HCM98_20240) ffh 3903760..3905109 (-) 1350 WP_000863460.1 signal recognition particle protein -

Sequence

Protein


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

>NTDB_id=436072 HCM98_RS20115 WP_000421290.1 3887411..3888190(-) (codY) [Bacillus tropicus strain LM1212-DB]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKQMLAERQFPEEYTQSLF
NITETSSNLDVNSAYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLQELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=436072 HCM98_RS20115 WP_000421290.1 3887411..3888190(-) (codY) [Bacillus tropicus strain LM1212-DB]
ATGGAATTATTAGCAAAAACAAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGAAAACCTGTAAACTTTAGAGAAAT
GTCTGACACAATGTGTGAAGTAATCGAAGCGAATGTGTTCGTAGTAAGCCGTCGTGGTAAATTACTAGGTTATGCAATTC
ACCAACAAATTGAGAATGAGCGTATGAAACAAATGCTTGCAGAGCGTCAATTCCCAGAAGAGTATACACAAAGCTTATTC
AACATTACAGAAACATCTTCAAACTTAGATGTAAACAGTGCTTACACAGCATTCCCAGTAGAAAATAGAGAATTATTCGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGCGGTGAGCGTCTAGGCACATTAGTGTTAGCTCGTCTTGGTCAAG
AGTTCTTAGATGATGATTTAATCCTTGCTGAATACAGTTCAACTGTAGTAGGTATGGAAATTTTACGTGAAAAAGCAGAA
GAAATCGAAGAGGAAGCACGTAGTAAAGCTGTTGTTCAAATGGCGATTAGCTCATTATCTTACAGTGAGTTAGAAGCAAT
CGAGCATATCTTCGAAGAATTAAATGGAACAGAAGGATTACTTGTTGCAAGTAAAATTGCTGATCGCGTAGGAATTACTC
GTTCTGTAATCGTAAATGCATTACGTAAATTAGAAAGTGCTGGTGTTATTGAGTCTCGCTCTTTAGGTATGAAAGGAACA
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