Detailed information    

insolico Bioinformatically predicted

Overview

Name   comYD   Type   Machinery gene
Locus tag   DK181_RS00925 Genome accession   NZ_CP029490
Coordinates   155920..156354 (+) Length   144 a.a.
NCBI ID   WP_254051091.1    Uniprot ID   -
Organism   Streptococcus sobrinus strain SL1     
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 124667..171478 155920..156354 within 0


Gene organization within MGE regions


Location: 124667..171478
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DK181_RS00795 (DK182_00795) rpoC 127924..131562 (+) 3639 WP_019773487.1 DNA-directed RNA polymerase subunit beta' -
  DK181_RS00800 (DK182_00800) - 131856..133520 (+) 1665 WP_028798551.1 peptide ABC transporter substrate-binding protein -
  DK181_RS00805 (DK182_00805) - 133626..134540 (+) 915 WP_002960866.1 ABC transporter permease -
  DK181_RS00810 (DK182_00810) - 134552..135583 (+) 1032 WP_002960868.1 ABC transporter permease -
  DK181_RS00815 (DK182_00815) oppD 135594..136643 (+) 1050 WP_002960869.1 ABC transporter ATP-binding protein Regulator
  DK181_RS00820 (DK182_00820) amiF 136640..137563 (+) 924 WP_002999065.1 ABC transporter ATP-binding protein Regulator
  DK181_RS00825 (DK182_00825) - 137800..139485 (-) 1686 WP_002960871.1 MFS transporter -
  DK181_RS00830 (DK182_00830) - 139617..140138 (+) 522 WP_002960873.1 PadR family transcriptional regulator -
  DK181_RS00835 (DK182_00835) - 140148..140456 (+) 309 WP_002960875.1 LlsX family protein -
  DK181_RS00845 (DK182_00845) - 140816..141352 (+) 537 Protein_126 TMEM175 family protein -
  DK181_RS00850 (DK182_00850) - 141413..142939 (-) 1527 Protein_127 IS1182 family transposase -
  DK181_RS10775 - 143434..143577 (-) 144 WP_002959475.1 hypothetical protein -
  DK181_RS00855 (DK182_00855) - 143567..143857 (-) 291 WP_002959477.1 hypothetical protein -
  DK181_RS00860 (DK182_00860) - 144079..144801 (+) 723 WP_002959479.1 ABC transporter ATP-binding protein -
  DK181_RS00865 (DK182_00865) - 144806..145945 (+) 1140 WP_002959481.1 ABC transporter permease -
  DK181_RS00870 (DK182_00870) - 146169..146789 (+) 621 WP_002959483.1 TetR/AcrR family transcriptional regulator -
  DK181_RS00875 (DK182_00875) - 146967..147229 (-) 263 Protein_133 type II toxin-antitoxin system YafQ family toxin -
  DK181_RS00880 (DK182_00880) - 147233..147514 (-) 282 WP_002959487.1 type II toxin-antitoxin system RelB/DinJ family antitoxin -
  DK181_RS00885 (DK182_00885) - 147671..148537 (-) 867 WP_002959489.1 LysR family transcriptional regulator -
  DK181_RS00890 (DK182_00890) - 148648..149508 (+) 861 WP_002959490.1 aldo/keto reductase -
  DK181_RS00895 (DK182_00895) - 149608..149970 (-) 363 WP_002959493.1 class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI -
  DK181_RS00900 (DK182_00900) - 150331..152715 (-) 2385 WP_019771344.1 HAD-IC family P-type ATPase -
  DK181_RS00905 (DK182_00905) - 152935..153303 (+) 369 WP_019781971.1 DUF1033 family protein -
  DK181_RS00910 (DK182_00910) comGA/cglA 153729..154676 (+) 948 WP_002959503.1 competence type IV pilus ATPase ComGA Machinery gene
  DK181_RS00915 (DK182_00915) comYB 154600..155643 (+) 1044 WP_002959504.1 competence type IV pilus assembly protein ComGB Machinery gene
  DK181_RS00920 (DK182_00920) comYC 155640..155966 (+) 327 WP_019770073.1 competence type IV pilus major pilin ComGC Machinery gene
  DK181_RS00925 (DK182_00925) comYD 155920..156354 (+) 435 WP_254051091.1 competence type IV pilus minor pilin ComGD Machinery gene
  DK181_RS00930 (DK182_00930) comYE 156326..156619 (+) 294 WP_002959510.1 competence type IV pilus minor pilin ComGE Machinery gene
  DK181_RS00935 (DK182_00935) comYF 156603..157040 (+) 438 WP_002959513.1 competence type IV pilus minor pilin ComGF Machinery gene
  DK181_RS00940 (DK182_00940) comGG 157018..157479 (+) 462 WP_002959515.1 competence type IV pilus minor pilin ComGG -
  DK181_RS00950 (DK182_00950) - 157681..157947 (+) 267 WP_002959516.1 type II toxin-antitoxin system RelE/ParE family toxin -
  DK181_RS00955 (DK182_00955) - 157934..158209 (+) 276 WP_002959518.1 helix-turn-helix domain-containing protein -
  DK181_RS00960 (DK182_00960) comYH 158308..159261 (+) 954 WP_019771347.1 class I SAM-dependent methyltransferase Machinery gene
  DK181_RS00965 (DK182_00965) - 159324..160520 (+) 1197 WP_002959522.1 acetate kinase -
  DK181_RS00970 (DK182_00970) - 160998..161903 (+) 906 WP_002959524.1 LysR family transcriptional regulator -
  DK181_RS00975 (DK182_00975) - 162010..162276 (+) 267 WP_002959526.1 ACT domain-containing protein -
  DK181_RS00980 (DK182_00980) - 162288..163625 (+) 1338 WP_002959528.1 PFL family protein -
  DK181_RS00985 (DK182_00985) - 163864..164166 (-) 303 Protein_154 hypothetical protein -
  DK181_RS00990 (DK182_00990) - 164193..165128 (-) 936 WP_019773382.1 IS30 family transposase -
  DK181_RS00995 (DK182_00995) - 165319..165750 (-) 432 WP_002961167.1 MarR family winged helix-turn-helix transcriptional regulator -
  DK181_RS01000 (DK182_01000) - 165889..166590 (+) 702 WP_002961168.1 histidine phosphatase family protein -
  DK181_RS01005 (DK182_01005) - 166577..167344 (+) 768 WP_002961169.1 M15 family metallopeptidase -
  DK181_RS01010 (DK182_01010) - 167509..168093 (+) 585 WP_002961170.1 glycoside hydrolase family 73 protein -
  DK181_RS01015 (DK182_01015) hrcA 168260..169294 (+) 1035 WP_002961171.1 heat-inducible transcriptional repressor HrcA -
  DK181_RS01020 (DK182_01020) grpE 169314..169865 (+) 552 WP_002961172.1 nucleotide exchange factor GrpE -

Sequence

Protein


Download         Length: 144 a.a.        Molecular weight: 16126.34 Da        Isoelectric Point: 9.6954

>NTDB_id=293147 DK181_RS00925 WP_254051091.1 155920..156354(+) (comYD) [Streptococcus sobrinus strain SL1]
MIITRNIRKVATFRTRAFTLIESLLVLAITSFLLLSFTGGVQQIFTGVQEKLFFLSFEHLYQDSQKLSNAQQKELTLRIA
DGQVTNGQESLSIPDSVRPNQTYSIEFSPAGGNSSLEKLTFTTKDGSVSYQLYIGSGRYKKTEN

Nucleotide


Download         Length: 435 bp        

>NTDB_id=293147 DK181_RS00925 WP_254051091.1 155920..156354(+) (comYD) [Streptococcus sobrinus strain SL1]
ATGATTATTACAAGAAACATAAGGAAAGTCGCAACGTTCCGAACTAGAGCCTTTACTCTGATTGAAAGTCTCTTGGTCTT
GGCCATCACTAGCTTTTTACTCCTAAGCTTCACAGGCGGGGTCCAGCAAATTTTTACGGGCGTGCAGGAGAAACTCTTCT
TTCTCTCTTTTGAACACCTCTATCAGGACAGCCAGAAACTCAGTAATGCCCAGCAAAAGGAACTGACCTTGAGGATTGCT
GACGGCCAGGTGACCAATGGTCAGGAAAGTCTGAGTATCCCTGATTCTGTCAGGCCCAATCAGACCTACAGCATCGAATT
TTCACCAGCCGGTGGCAATTCTTCGCTGGAAAAATTGACCTTCACAACTAAGGATGGCTCTGTCTCTTATCAACTTTATA
TAGGAAGTGGTCGCTATAAAAAAACGGAAAATTAA

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 mutans UA140

58.333

91.667

0.535
  comYD Streptococcus mutans UA159

58.333

91.667

0.535
  comYD Streptococcus gordonii str. Challis substr. CH1

48.592

98.611

0.479
  comGD/cglD Streptococcus pneumoniae Rx1

45.669

88.194

0.403
  comGD/cglD Streptococcus pneumoniae R6

45.669

88.194

0.403
  comGD/cglD Streptococcus pneumoniae TIGR4

45.669

88.194

0.403
  comGD/cglD Streptococcus pneumoniae D39

45.669

88.194

0.403
  comGD/cglD Streptococcus mitis SK321

44.882

88.194

0.396
  comGD/cglD Streptococcus mitis NCTC 12261

42.424

91.667

0.389

Multiple sequence alignment