Detailed information    

insolico Bioinformatically predicted

Overview

Name   comYF   Type   Machinery gene
Locus tag   LOD77_RS09245 Genome accession   NZ_CP086728
Coordinates   1824286..1824720 (-) Length   144 a.a.
NCBI ID   WP_216806339.1    Uniprot ID   -
Organism   Streptococcus parasuis strain SS20     
Function   dsDNA binding to the cell surface; assembly of the pseudopilus (predicted from homology)   
DNA binding and uptake

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 1823808..1852545 1824286..1824720 within 0


Gene organization within MGE regions


Location: 1823808..1852545
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LOD77_RS09240 (LOD77_09220) comGG 1823808..1824308 (-) 501 WP_171989710.1 competence type IV pilus minor pilin ComGG -
  LOD77_RS09245 (LOD77_09225) comYF 1824286..1824720 (-) 435 WP_216806339.1 competence type IV pilus minor pilin ComGF Machinery gene
  LOD77_RS09250 (LOD77_09230) comGE 1824707..1825000 (-) 294 WP_105126461.1 competence type IV pilus minor pilin ComGE -
  LOD77_RS09255 (LOD77_09235) comGD 1824972..1825376 (-) 405 WP_171989707.1 competence type IV pilus minor pilin ComGD -
  LOD77_RS09260 (LOD77_09240) comYC 1825360..1825677 (-) 318 WP_274505424.1 competence type IV pilus major pilin ComGC Machinery gene
  LOD77_RS09265 (LOD77_09245) comYB 1825679..1826716 (-) 1038 WP_216806336.1 competence type IV pilus assembly protein ComGB Machinery gene
  LOD77_RS09270 (LOD77_09250) comYA 1826628..1827578 (-) 951 WP_171989704.1 competence type IV pilus ATPase ComGA Machinery gene
  LOD77_RS09275 (LOD77_09255) - 1827666..1828616 (+) 951 WP_274505425.1 S66 peptidase family protein -
  LOD77_RS09280 (LOD77_09260) - 1828649..1829017 (-) 369 WP_171989702.1 DUF1033 family protein -
  LOD77_RS09285 (LOD77_09265) rpoC 1829142..1832786 (-) 3645 WP_274505426.1 DNA-directed RNA polymerase subunit beta' -
  LOD77_RS09290 (LOD77_09270) rpoB 1832965..1836537 (-) 3573 WP_174846402.1 DNA-directed RNA polymerase subunit beta -
  LOD77_RS09295 (LOD77_09275) pbp1b 1837200..1839605 (-) 2406 WP_274505427.1 penicillin-binding protein PBP1B -
  LOD77_RS09300 (LOD77_09280) tyrS 1839752..1841008 (+) 1257 WP_274505428.1 tyrosine--tRNA ligase -
  LOD77_RS09305 (LOD77_09285) - 1841065..1841442 (+) 378 WP_171989697.1 HIT family protein -
  LOD77_RS09310 (LOD77_09290) - 1841554..1841838 (+) 285 WP_171989696.1 PASTA domain-containing protein -
  LOD77_RS09315 (LOD77_09295) - 1841849..1842265 (+) 417 WP_274505429.1 PASTA domain-containing protein -
  LOD77_RS09320 (LOD77_09300) - 1842314..1842523 (-) 210 WP_130554922.1 heavy metal-associated domain-containing protein -
  LOD77_RS09325 (LOD77_09305) - 1842691..1843140 (-) 450 WP_216806329.1 CopY/TcrY family copper transport repressor -
  LOD77_RS09330 (LOD77_09310) - 1843241..1844749 (-) 1509 WP_216806328.1 zinc ABC transporter substrate-binding protein AdcA -
  LOD77_RS09335 (LOD77_09315) - 1844759..1845571 (-) 813 WP_130554925.1 metal ABC transporter permease -
  LOD77_RS09340 (LOD77_09320) - 1845564..1846268 (-) 705 WP_216806327.1 metal ABC transporter ATP-binding protein -
  LOD77_RS09345 (LOD77_09325) - 1846269..1846712 (-) 444 WP_171989690.1 zinc-dependent MarR family transcriptional regulator -
  LOD77_RS09350 (LOD77_09330) - 1847362..1848135 (-) 774 WP_087063181.1 nucleoside phosphorylase -
  LOD77_RS09355 (LOD77_09335) - 1848281..1848733 (-) 453 WP_274505430.1 helix-turn-helix transcriptional regulator -
  LOD77_RS09360 (LOD77_09340) - 1849055..1849528 (+) 474 WP_174846396.1 hypothetical protein -
  LOD77_RS09365 (LOD77_09345) - 1849662..1850765 (+) 1104 WP_337999565.1 replication initiation factor domain-containing protein -
  LOD77_RS09370 (LOD77_09350) - 1850768..1851154 (+) 387 WP_121795882.1 hypothetical protein -
  LOD77_RS09375 (LOD77_09355) - 1851214..1851408 (+) 195 WP_021144813.1 DUF3173 domain-containing protein -
  LOD77_RS09380 (LOD77_09360) - 1851412..1852545 (+) 1134 WP_274505432.1 site-specific integrase -

Sequence

Protein


Download         Length: 144 a.a.        Molecular weight: 16450.86 Da        Isoelectric Point: 7.1334

>NTDB_id=626216 LOD77_RS09245 WP_216806339.1 1824286..1824720(-) (comYF) [Streptococcus parasuis strain SS20]
MRKTKLAAFTLLECLIALLIISGSLLVIEGLSKLIAHEVRYQERHVEKQWLLFCDQLRAEWEGASLDRVDSGKLYLTKGE
KSLAFGKSVADDFRKTNANGQGYQPMLYKVYSATYAQQGEVIQLDVTFESGEERSFRYVFEKTN

Nucleotide


Download         Length: 435 bp        

>NTDB_id=626216 LOD77_RS09245 WP_216806339.1 1824286..1824720(-) (comYF) [Streptococcus parasuis strain SS20]
TTGAGAAAAACTAAGTTAGCCGCGTTCACCCTCTTGGAATGTTTAATTGCCTTACTCATTATTTCTGGCAGCTTGCTAGT
GATTGAAGGTTTATCAAAATTGATAGCGCATGAGGTTCGCTATCAAGAGCGTCATGTGGAAAAACAGTGGTTACTATTTT
GTGATCAATTGCGGGCTGAATGGGAAGGAGCAAGTCTTGATCGGGTTGATTCTGGAAAGTTGTACCTAACCAAAGGGGAA
AAATCATTGGCATTTGGCAAGTCTGTGGCAGATGATTTTCGCAAGACAAATGCAAATGGTCAGGGCTATCAGCCCATGTT
GTACAAAGTTTATTCAGCTACTTACGCCCAACAAGGCGAGGTTATACAGCTGGATGTAACATTTGAAAGTGGGGAGGAAA
GGAGTTTTAGGTATGTTTTTGAAAAGACGAATTAA

Domains

Predicted by InterproScan.

Putative Competence protein ComGF (ComGF)

(39-134)


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
  comYF Streptococcus mutans UA159

54.167

100

0.542
  comYF Streptococcus mutans UA140

54.167

100

0.542
  comGF Lactococcus lactis subsp. cremoris KW2

48.227

97.917

0.472
  comGF/cglF Streptococcus mitis NCTC 12261

47.143

97.222

0.458
  comGF/cglF Streptococcus pneumoniae Rx1

45.652

95.833

0.437
  comGF/cglF Streptococcus pneumoniae D39

45.652

95.833

0.437
  comGF/cglF Streptococcus pneumoniae R6

45.652

95.833

0.437
  comGF/cglF Streptococcus pneumoniae TIGR4

45.652

95.833

0.437
  comGF/cglF Streptococcus mitis SK321

44.604

96.528

0.431