Detailed information    

insolico Bioinformatically predicted

Overview

Name   codY   Type   Regulator
Locus tag   IQ680_RS25565 Genome accession   NZ_CP064266
Coordinates   4965017..4965796 (-) Length   259 a.a.
NCBI ID   WP_000421292.1    Uniprot ID   -
Organism   Bacillus pseudomycoides strain N451-2     
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 4927573..4994807 4965017..4965796 within 0


Gene organization within MGE regions


Location: 4927573..4994807
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  IQ680_RS25405 - 4929876..4930079 (-) 204 WP_098335909.1 YlzJ-like family protein -
  IQ680_RS25410 - 4930076..4930825 (-) 750 WP_098335910.1 ClpP family protease -
  IQ680_RS25415 - 4930927..4932597 (-) 1671 WP_098335911.1 ribonuclease J -
  IQ680_RS25420 dapA 4933005..4933883 (-) 879 WP_243523837.1 4-hydroxy-tetrahydrodipicolinate synthase -
  IQ680_RS25425 dapG 4933895..4935127 (-) 1233 WP_243523838.1 aspartate kinase -
  IQ680_RS25430 asd 4935151..4936197 (-) 1047 WP_098335914.1 aspartate-semialdehyde dehydrogenase -
  IQ680_RS25435 - 4936347..4936946 (-) 600 WP_243523840.1 dipicolinate synthase subunit B -
  IQ680_RS25440 dpaA 4936943..4937845 (-) 903 WP_243523842.1 dipicolinic acid synthetase subunit A -
  IQ680_RS25445 - 4938176..4938424 (-) 249 WP_098335917.1 YlmC/YmxH family sporulation protein -
  IQ680_RS25450 - 4938654..4939892 (-) 1239 WP_243523844.1 pitrilysin family protein -
  IQ680_RS25455 - 4939979..4940878 (-) 900 WP_243523846.1 polysaccharide deacetylase family protein -
  IQ680_RS25460 pnp 4941042..4943195 (-) 2154 WP_098335920.1 polyribonucleotide nucleotidyltransferase -
  IQ680_RS25465 rpsO 4943357..4943626 (-) 270 WP_001229392.1 30S ribosomal protein S15 -
  IQ680_RS25470 ribF 4943727..4944698 (-) 972 WP_243523848.1 bifunctional riboflavin kinase/FAD synthetase -
  IQ680_RS25475 truB 4944742..4945665 (-) 924 WP_243523849.1 tRNA pseudouridine(55) synthase TruB -
  IQ680_RS25480 rbfA 4945815..4946171 (-) 357 WP_017151269.1 30S ribosome-binding factor RbfA -
  IQ680_RS25485 - 4946187..4946468 (-) 282 WP_243523852.1 DUF503 domain-containing protein -
  IQ680_RS25490 infB 4946465..4948531 (-) 2067 WP_098335924.1 translation initiation factor IF-2 -
  IQ680_RS25495 - 4948536..4948847 (-) 312 WP_243523855.1 YlxQ family RNA-binding protein -
  IQ680_RS25500 rnpM 4948848..4949120 (-) 273 WP_033796365.1 RNase P modulator RnpM -
  IQ680_RS25505 nusA 4949132..4950232 (-) 1101 WP_098335927.1 transcription termination factor NusA -
  IQ680_RS25510 rimP 4950250..4950720 (-) 471 WP_026590331.1 ribosome maturation factor RimP -
  IQ680_RS25515 - 4951056..4955357 (-) 4302 WP_243523858.1 PolC-type DNA polymerase III -
  IQ680_RS25520 - 4955483..4957183 (-) 1701 WP_243523861.1 proline--tRNA ligase -
  IQ680_RS25525 rseP 4957332..4958588 (-) 1257 WP_243523865.1 RIP metalloprotease RseP -
  IQ680_RS25530 dxr 4958606..4959748 (-) 1143 WP_243523867.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  IQ680_RS25535 - 4959769..4960560 (-) 792 WP_243523870.1 phosphatidate cytidylyltransferase -
  IQ680_RS25540 - 4960578..4961354 (-) 777 WP_098335933.1 isoprenyl transferase -
  IQ680_RS25545 frr 4961440..4961997 (-) 558 WP_098335934.1 ribosome recycling factor -
  IQ680_RS25550 pyrH 4962000..4962722 (-) 723 WP_098335935.1 UMP kinase -
  IQ680_RS25555 tsf 4962789..4963676 (-) 888 WP_098335936.1 translation elongation factor Ts -
  IQ680_RS25560 rpsB 4963759..4964460 (-) 702 WP_018764712.1 30S ribosomal protein S2 -
  IQ680_RS25565 codY 4965017..4965796 (-) 780 WP_000421292.1 GTP-sensing pleiotropic transcriptional regulator CodY Regulator
  IQ680_RS25570 hslU 4965874..4967265 (-) 1392 WP_243523873.1 ATP-dependent protease ATPase subunit HslU -
  IQ680_RS25575 hslV 4967288..4967830 (-) 543 WP_098335938.1 ATP-dependent protease proteolytic subunit HslV -
  IQ680_RS25580 xerC 4967873..4968772 (-) 900 WP_243523875.1 tyrosine recombinase XerC -
  IQ680_RS25585 trmFO 4968838..4970142 (-) 1305 WP_098335940.1 FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))- methyltransferase TrmFO -
  IQ680_RS25590 topA 4970194..4972272 (-) 2079 WP_243523877.1 type I DNA topoisomerase -
  IQ680_RS25595 dprA 4972417..4973286 (-) 870 WP_243523880.1 DNA-processing protein DprA -
  IQ680_RS25600 sucD 4973376..4974278 (-) 903 WP_098335943.1 succinate--CoA ligase subunit alpha -
  IQ680_RS25605 sucC 4974298..4975458 (-) 1161 WP_016115965.1 ADP-forming succinate--CoA ligase subunit beta -
  IQ680_RS25610 - 4975653..4976426 (-) 774 WP_243523882.1 ribonuclease HII -
  IQ680_RS25615 ylqF 4976484..4977347 (-) 864 WP_243523884.1 ribosome biogenesis GTPase YlqF -
  IQ680_RS25620 lepB 4977370..4977921 (-) 552 WP_243523886.1 signal peptidase I -
  IQ680_RS25625 rplS 4978023..4978367 (-) 345 WP_033672113.1 50S ribosomal protein L19 -
  IQ680_RS25630 trmD 4978518..4979249 (-) 732 WP_243523887.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  IQ680_RS25635 rimM 4979249..4979764 (-) 516 WP_033671426.1 ribosome maturation factor RimM -
  IQ680_RS25640 - 4979884..4980111 (-) 228 WP_243523888.1 KH domain-containing protein -
  IQ680_RS25645 rpsP 4980126..4980398 (-) 273 WP_000268750.1 30S ribosomal protein S16 -
  IQ680_RS25650 ffh 4980500..4981849 (-) 1350 WP_243523889.1 signal recognition particle protein -
  IQ680_RS25655 - 4981862..4982194 (-) 333 WP_098335950.1 putative DNA-binding protein -
  IQ680_RS25660 ftsY 4982328..4983317 (-) 990 WP_243523890.1 signal recognition particle-docking protein FtsY -
  IQ680_RS25665 smc 4983332..4986904 (-) 3573 WP_243523891.1 chromosome segregation protein SMC -
  IQ680_RS25670 rncS 4987054..4987791 (-) 738 WP_098335953.1 ribonuclease III -
  IQ680_RS25675 acpP 4987851..4988084 (-) 234 WP_098335954.1 acyl carrier protein -
  IQ680_RS25680 fabG 4988156..4988896 (-) 741 WP_098335955.1 3-oxoacyl-[acyl-carrier-protein] reductase -
  IQ680_RS25685 fabD 4988890..4989840 (-) 951 WP_243523892.1 ACP S-malonyltransferase -
  IQ680_RS25690 plsX 4989855..4990847 (-) 993 WP_243523895.1 phosphate acyltransferase PlsX -
  IQ680_RS25695 fapR 4990844..4991437 (-) 594 WP_098335958.1 transcription factor FapR -
  IQ680_RS25700 recG 4991528..4993576 (-) 2049 WP_243523897.1 ATP-dependent DNA helicase RecG -

Sequence

Protein


Download         Length: 259 a.a.        Molecular weight: 28801.07 Da        Isoelectric Point: 4.7947

>NTDB_id=500429 IQ680_RS25565 WP_000421292.1 4965017..4965796(-) (codY) [Bacillus pseudomycoides strain N451-2]
MELLAKTRKLNALLQSAAGKPVNFREMSDTMCEVIEANVFVVSRRGKLLGYAIHQQIENERMKQMLAERQFPEEYTQSLF
NVTETSSNLDVNSQFTAFPVENKELFGQGLTTIVPIVGGGERLGTLVLARLGQEFLDDDLILAEYSSTVVGMEILREKAE
EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELNGTEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGT
YIKVLNDKFLHELAKLKTN

Nucleotide


Download         Length: 780 bp        

>NTDB_id=500429 IQ680_RS25565 WP_000421292.1 4965017..4965796(-) (codY) [Bacillus pseudomycoides strain N451-2]
ATGGAATTATTAGCAAAAACGAGAAAATTAAATGCGTTATTACAGAGCGCAGCAGGAAAACCGGTAAACTTTAGAGAAAT
GTCAGATACAATGTGTGAAGTAATTGAAGCGAACGTATTCGTTGTAAGTCGTCGCGGTAAATTATTAGGATATGCAATTC
ACCAACAAATCGAGAATGAGCGTATGAAACAAATGCTTGCAGAGCGTCAATTCCCAGAAGAATATACACAAAGCCTATTC
AACGTTACAGAAACATCTTCAAACTTAGATGTAAATAGTCAATTTACAGCATTCCCTGTAGAAAACAAAGAGCTATTTGG
TCAAGGTTTAACTACAATCGTACCAATCGTTGGTGGTGGTGAGCGTCTAGGTACACTAGTGTTAGCTCGTCTTGGTCAAG
AATTCTTAGATGATGATTTAATTCTTGCTGAATACAGCTCAACTGTAGTAGGTATGGAAATCTTACGTGAAAAAGCAGAA
GAAATCGAAGAGGAAGCGCGTAGTAAAGCTGTTGTTCAAATGGCGATTAGCTCGTTATCATACAGTGAGTTAGAAGCAAT
CGAGCACATCTTCGAAGAATTAAACGGAACAGAAGGTTTACTTGTTGCAAGTAAAATTGCTGATCGTGTTGGAATTACTC
GTTCTGTAATCGTAAACGCACTTCGTAAATTAGAAAGTGCAGGCGTTATCGAGTCTCGTTCTTTAGGTATGAAAGGAACG
TACATTAAAGTATTAAACGACAAGTTTTTACATGAACTTGCTAAATTAAAAACAAACTAA

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

81.081

100

0.811
  codY Lactococcus lactis subsp. lactis strain DGCC12653

46.275

98.456

0.456