Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   PYW38_RS18855 Genome accession   NZ_CP118958
Coordinates   3665319..3666098 (-) Length   259 a.a.
NCBI ID   WP_002014541.1    Uniprot ID   -
Organism   Bacillus mycoides strain DSM 2048     
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 3633795..3700790 3665319..3666098 within 0


Gene organization within MGE regions


Location: 3633795..3700790
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PYW38_RS18710 dapA 3633859..3634737 (-) 879 WP_002014579.1 4-hydroxy-tetrahydrodipicolinate synthase -
  PYW38_RS18715 dapG 3634749..3635981 (-) 1233 WP_002088068.1 aspartate kinase -
  PYW38_RS18720 asd 3636005..3637051 (-) 1047 WP_002014577.1 aspartate-semialdehyde dehydrogenase -
  PYW38_RS18725 dpaB 3637201..3637800 (-) 600 WP_002111357.1 dipicolinate synthase subunit B -
  PYW38_RS18730 dpaA 3637797..3638699 (-) 903 WP_002128797.1 dipicolinic acid synthetase subunit A -
  PYW38_RS18735 - 3638872..3639120 (-) 249 WP_002014571.1 YlmC/YmxH family sporulation protein -
  PYW38_RS18740 - 3639256..3640497 (-) 1242 WP_033734213.1 M16 family metallopeptidase -
  PYW38_RS18745 - 3640584..3641483 (-) 900 WP_002128798.1 polysaccharide deacetylase family protein -
  PYW38_RS18750 pnp 3641638..3643791 (-) 2154 WP_002128799.1 polyribonucleotide nucleotidyltransferase -
  PYW38_RS18755 rpsO 3643953..3644222 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  PYW38_RS18760 ribF 3644323..3645294 (-) 972 WP_002128800.1 bifunctional riboflavin kinase/FAD synthetase -
  PYW38_RS18765 truB 3645338..3646261 (-) 924 WP_002014562.1 tRNA pseudouridine(55) synthase TruB -
  PYW38_RS18770 rbfA 3646352..3646708 (-) 357 WP_000776437.1 30S ribosome-binding factor RbfA -
  PYW38_RS18775 - 3646724..3647005 (-) 282 WP_002088157.1 DUF503 domain-containing protein -
  PYW38_RS18780 infB 3647002..3649068 (-) 2067 WP_002014558.1 translation initiation factor IF-2 -
  PYW38_RS18785 - 3649073..3649384 (-) 312 WP_001286519.1 YlxQ family RNA-binding protein -
  PYW38_RS18790 rnpM 3649385..3649657 (-) 273 WP_002088161.1 RNase P modulator RnpM -
  PYW38_RS18795 nusA 3649669..3650775 (-) 1107 WP_002014554.1 transcription termination factor NusA -
  PYW38_RS18800 rimP 3650793..3651263 (-) 471 WP_002088165.1 ribosome maturation factor RimP -
  PYW38_RS18805 - 3651597..3655898 (-) 4302 WP_002185075.1 PolC-type DNA polymerase III -
  PYW38_RS18810 - 3656023..3657723 (-) 1701 WP_002128803.1 proline--tRNA ligase -
  PYW38_RS18815 rseP 3657833..3659089 (-) 1257 WP_002185073.1 RIP metalloprotease RseP -
  PYW38_RS18820 dxr 3659107..3660249 (-) 1143 WP_002014547.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  PYW38_RS18825 cdsA 3660273..3661064 (-) 792 WP_002088171.1 phosphatidate cytidylyltransferase -
  PYW38_RS18830 - 3661082..3661858 (-) 777 WP_002185072.1 isoprenyl transferase -
  PYW38_RS18835 frr 3661944..3662501 (-) 558 WP_000531506.1 ribosome recycling factor -
  PYW38_RS18840 pyrH 3662505..3663227 (-) 723 WP_002014544.1 UMP kinase -
  PYW38_RS18845 tsf 3663294..3664181 (-) 888 WP_002185071.1 translation elongation factor Ts -
  PYW38_RS18850 rpsB 3664264..3664965 (-) 702 WP_002185070.1 30S ribosomal protein S2 -
  PYW38_RS18855 codY 3665319..3666098 (-) 780 WP_002014541.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  PYW38_RS18860 hslU 3666176..3667567 (-) 1392 WP_002014539.1 ATP-dependent protease ATPase subunit HslU -
  PYW38_RS18865 hslV 3667590..3668132 (-) 543 WP_002014538.1 ATP-dependent protease proteolytic subunit HslV -
  PYW38_RS18870 xerC 3668175..3669074 (-) 900 WP_078175468.1 tyrosine recombinase XerC -
  PYW38_RS18875 trmFO 3669146..3670450 (-) 1305 WP_002066796.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  PYW38_RS18880 topA 3670499..3672577 (-) 2079 WP_002088184.1 type I DNA topoisomerase -
  PYW38_RS18885 dprA 3672779..3673573 (-) 795 WP_003190974.1 DNA-processing protein DprA -
  PYW38_RS18890 sucD 3673662..3674564 (-) 903 WP_002033796.1 succinate--CoA ligase subunit alpha -
  PYW38_RS18895 sucC 3674584..3675744 (-) 1161 WP_002014529.1 ADP-forming succinate--CoA ligase subunit beta -
  PYW38_RS18900 - 3675938..3676711 (-) 774 WP_002014527.1 ribonuclease HII -
  PYW38_RS18905 ylqF 3676767..3677657 (-) 891 WP_002128821.1 ribosome biogenesis GTPase YlqF -
  PYW38_RS18910 lepB 3677678..3678229 (-) 552 WP_002066791.1 signal peptidase I -
  PYW38_RS18915 rplS 3678330..3678674 (-) 345 WP_002185067.1 50S ribosomal protein L19 -
  PYW38_RS18920 trmD 3678821..3679555 (-) 735 WP_002014522.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  PYW38_RS18925 rimM 3679555..3680070 (-) 516 WP_002014521.1 ribosome maturation factor RimM -
  PYW38_RS18930 - 3680192..3680419 (-) 228 WP_002088196.1 KH domain-containing protein -
  PYW38_RS18935 rpsP 3680434..3680706 (-) 273 WP_002185065.1 30S ribosomal protein S16 -
  PYW38_RS18940 ffh 3680807..3682156 (-) 1350 WP_002014519.1 signal recognition particle protein -
  PYW38_RS18945 - 3682169..3682501 (-) 333 WP_000891061.1 putative DNA-binding protein -
  PYW38_RS18950 ftsY 3682634..3683623 (-) 990 WP_002185064.1 signal recognition particle-docking protein FtsY -
  PYW38_RS18955 smc 3683638..3687207 (-) 3570 WP_002014517.1 chromosome segregation protein SMC -
  PYW38_RS18960 rncS 3687356..3688093 (-) 738 WP_002033792.1 ribonuclease III -
  PYW38_RS18965 acpP 3688152..3688385 (-) 234 WP_002014515.1 acyl carrier protein -
  PYW38_RS18970 fabG 3688455..3689195 (-) 741 WP_002014514.1 3-oxoacyl-[acyl-carrier-protein] reductase -
  PYW38_RS18975 fabD 3689195..3690139 (-) 945 WP_002128825.1 ACP S-malonyltransferase -
  PYW38_RS18980 plsX 3690154..3691146 (-) 993 WP_002128828.1 phosphate acyltransferase PlsX -
  PYW38_RS18985 fapR 3691143..3691736 (-) 594 WP_002185063.1 transcription factor FapR -
  PYW38_RS18990 recG 3691825..3693873 (-) 2049 WP_003190964.1 ATP-dependent DNA helicase RecG -
  PYW38_RS18995 - 3694298..3695974 (-) 1677 WP_002185060.1 DAK2 domain-containing protein -
  PYW38_RS19000 - 3695997..3696359 (-) 363 WP_002014507.1 Asp23/Gls24 family envelope stress response protein -
  PYW38_RS19005 rpmB 3696738..3696926 (+) 189 WP_000124776.1 50S ribosomal protein L28 -
  PYW38_RS19010 spoVM 3697000..3697080 (-) 81 WP_001213599.1 stage V sporulation protein SpoVM -
  PYW38_RS19015 - 3697147..3697827 (-) 681 WP_002014506.1 thiamine diphosphokinase -
  PYW38_RS19020 rpe 3697928..3698572 (-) 645 WP_002185059.1 ribulose-phosphate 3-epimerase -
  PYW38_RS19025 rsgA 3698575..3699456 (-) 882 WP_002014503.1 ribosome small subunit-dependent GTPase A -

Sequence

Protein


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

>NTDB_id=796839 PYW38_RS18855 WP_002014541.1 3665319..3666098(-) (codY) [Bacillus mycoides strain DSM 2048]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKHMLAERQFPEEYTQSLF
NVTETSSNLGVDSDYTAFPVENRELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLQELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=796839 PYW38_RS18855 WP_002014541.1 3665319..3666098(-) (codY) [Bacillus mycoides strain DSM 2048]
ATGGAATTATTAGCAAAAACGAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGAAAGCCTGTAAACTTTAGAGAGAT
GTCTGACACAATGTGTGAAGTAATTGAAGCGAACGTGTTCGTTGTAAGTCGTCGCGGTAAATTATTAGGATATGCGATTC
ACCAACAAATCGAAAACGAACGTATGAAGCACATGCTTGCAGAGCGTCAATTCCCAGAAGAGTATACGCAAAGTTTATTC
AATGTTACAGAAACATCTTCAAATTTAGGTGTGGATAGTGACTACACAGCATTCCCGGTAGAAAATAGAGAATTATTCGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGCGGTGAGCGTCTAGGTACACTAGTATTAGCTCGTCTTGGTCAAG
AGTTCTTAGACGATGATTTAATTCTTGCTGAATACAGCTCAACTGTTGTAGGTATGGAAATCTTACGTGAAAAAGCAGAA
GAAATCGAAGAGGAAGCACGTAGTAAAGCTGTTGTTCAAATGGCGATTAGCTCATTATCTTACAGTGAGTTAGAAGCAAT
CGAGCATATCTTCGAAGAATTAAATGGAACAGAAGGTTTACTTGTTGCAAGTAAAATTGCTGATCGCGTGGGAATTACTC
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