Detailed information    

insolico Bioinformatically predicted

Overview

Name   comYD   Type   Machinery gene
Locus tag   SCIM_RS08230 Genome accession   NC_018073
Coordinates   1700111..1700539 (-) Length   142 a.a.
NCBI ID   WP_014829819.1    Uniprot ID   -
Organism   Streptococcus intermedius JTH08     
Function   dsDNA binding to the cell surface; assembly of the pseudopilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1695111..1705539
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SCIM_RS08205 (SCIM_1488) - 1696828..1698027 (-) 1200 WP_003076127.1 acetate kinase -
  SCIM_RS08210 (SCIM_1489) comYH 1698074..1699027 (-) 954 WP_003075742.1 class I SAM-dependent methyltransferase Machinery gene
  SCIM_RS08215 (SCIM_1490) comGG 1699118..1699444 (-) 327 WP_014829817.1 competence type IV pilus minor pilin ComGG -
  SCIM_RS08220 (SCIM_1491) comGF/cglF 1699425..1699862 (-) 438 WP_003073990.1 competence type IV pilus minor pilin ComGF Machinery gene
  SCIM_RS08225 (SCIM_1492) comGE/cglE 1699846..1700139 (-) 294 WP_003073987.1 competence type IV pilus minor pilin ComGE Machinery gene
  SCIM_RS08230 (SCIM_1493) comYD 1700111..1700539 (-) 429 WP_014829819.1 competence type IV pilus minor pilin ComGD Machinery gene
  SCIM_RS08235 (SCIM_1494) comYC 1700499..1700816 (-) 318 WP_003075998.1 competence type IV pilus major pilin ComGC Machinery gene
  SCIM_RS08240 (SCIM_1495) comYB 1700813..1701835 (-) 1023 WP_172634362.1 competence type IV pilus assembly protein ComGB Machinery gene
  SCIM_RS08245 (SCIM_1497) comYA 1701777..1702718 (-) 942 WP_003073980.1 competence type IV pilus ATPase ComGA Machinery gene
  SCIM_RS08250 (SCIM_1498) - 1702787..1703152 (-) 366 WP_003075933.1 DUF1033 family protein -
  SCIM_RS08255 (SCIM_1499) glnA 1703374..1704720 (-) 1347 WP_003076201.1 type I glutamate--ammonia ligase -
  SCIM_RS08260 (SCIM_1500) - 1704759..1705118 (-) 360 WP_003073972.1 MerR family transcriptional regulator -

Sequence

Protein


Download         Length: 142 a.a.        Molecular weight: 16276.88 Da        Isoelectric Point: 10.4613

>NTDB_id=51898 SCIM_RS08230 WP_014829819.1 1700111..1700539(-) (comYD) [Streptococcus intermedius JTH08]
MRNIQKKLVLLQIKGFTILESLLTLFVASFLLLAVSGAVRSSFEQVEEQIFFLEFEHFYRESQKLSNATQRQLDMNFSRA
RISNGYNSLSIPRSVHAPDDLTLRFDKAGGNSSLGKIVFQTKRQTIMYQLYLGNGKFKKTIC

Nucleotide


Download         Length: 429 bp        

>NTDB_id=51898 SCIM_RS08230 WP_014829819.1 1700111..1700539(-) (comYD) [Streptococcus intermedius JTH08]
ATGCGAAACATACAAAAGAAACTCGTTCTGTTGCAGATTAAGGGATTTACAATTTTGGAAAGTTTGCTGACTTTGTTTGT
AGCGAGTTTTTTATTACTTGCTGTGTCAGGGGCTGTCCGTTCCTCTTTTGAACAAGTGGAAGAGCAGATTTTCTTTCTTG
AGTTTGAGCATTTTTACCGAGAAAGTCAGAAGTTGAGTAATGCTACTCAAAGGCAATTGGACATGAATTTTTCTCGTGCG
CGAATTTCTAATGGGTACAATTCTTTATCAATTCCTCGCTCGGTTCACGCTCCAGATGATTTAACACTTCGTTTTGATAA
GGCAGGTGGTAATTCCTCGCTTGGTAAGATTGTATTTCAGACGAAAAGACAGACAATTATGTATCAATTATATCTAGGAA
ATGGAAAATTTAAGAAAACAATATGTTAG

Domains


No domain identified.



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
  comYD Streptococcus gordonii str. Challis substr. CH1

60

91.549

0.549
  comGD/cglD Streptococcus mitis NCTC 12261

55.039

90.845

0.5
  comGD/cglD Streptococcus mitis SK321

54.331

89.437

0.486
  comGD/cglD Streptococcus pneumoniae Rx1

54.331

89.437

0.486
  comGD/cglD Streptococcus pneumoniae D39

54.331

89.437

0.486
  comGD/cglD Streptococcus pneumoniae R6

54.331

89.437

0.486
  comGD/cglD Streptococcus pneumoniae TIGR4

53.543

89.437

0.479
  comYD Streptococcus mutans UA140

49.231

91.549

0.451
  comYD Streptococcus mutans UA159

49.231

91.549

0.451

Multiple sequence alignment