Detailed information    

insolico Bioinformatically predicted

Overview

Name   comGD/cglD   Type   Machinery gene
Locus tag   R4703_RS04570 Genome accession   NZ_CP137100
Coordinates   835630..836034 (-) Length   134 a.a.
NCBI ID   WP_000588023.1    Uniprot ID   -
Organism   Streptococcus pneumoniae strain LYP     
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)
Prophage 836784..888642 835630..836034 flank 750


Gene organization within MGE regions


Location: 835630..888642
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  R4703_RS04570 comGD/cglD 835630..836034 (-) 405 WP_000588023.1 competence type IV pilus minor pilin ComGD Machinery gene
  R4703_RS04575 comGC/cglC 836027..836293 (-) 267 WP_050129046.1 competence type IV pilus major pilin ComGC Machinery gene
  R4703_RS04580 - 836295..836552 (-) 258 WP_000698513.1 hypothetical protein -
  R4703_RS04585 - 836784..837740 (-) 957 WP_219576515.1 N-acetylmuramoyl-L-alanine amidase family protein -
  R4703_RS04590 - 837743..838078 (-) 336 WP_050200954.1 phage holin -
  R4703_RS04595 - 838082..838381 (-) 300 WP_001811580.1 hypothetical protein -
  R4703_RS04600 - 838390..838740 (-) 351 WP_000852245.1 hypothetical protein -
  R4703_RS04605 - 838743..838946 (-) 204 WP_001091112.1 hypothetical protein -
  R4703_RS04610 - 838927..839044 (-) 118 Protein_882 dihydrodipicolinate reductase -
  R4703_RS04615 - 839041..845439 (-) 6399 WP_317818026.1 tail fiber domain-containing protein -
  R4703_RS04620 - 845444..845794 (-) 351 WP_000068025.1 DUF6711 family protein -
  R4703_RS04625 - 845803..849456 (-) 3654 WP_317818031.1 hypothetical protein -
  R4703_RS04630 - 849443..849793 (-) 351 WP_050199219.1 hypothetical protein -
  R4703_RS04635 - 849832..850212 (-) 381 WP_023396733.1 DUF6096 family protein -
  R4703_RS04640 - 850217..850630 (-) 414 WP_000880666.1 phage tail tube protein -
  R4703_RS04645 - 850633..851001 (-) 369 WP_050141942.1 hypothetical protein -
  R4703_RS04650 - 850998..851513 (-) 516 WP_050105871.1 HK97-gp10 family putative phage morphogenesis protein -
  R4703_RS04655 - 851488..851826 (-) 339 WP_050118024.1 hypothetical protein -
  R4703_RS04660 - 851807..852118 (-) 312 WP_317818032.1 phage head-tail connector protein -
  R4703_RS04665 - 852120..852308 (-) 189 WP_000669348.1 hypothetical protein -
  R4703_RS04670 - 852318..853343 (-) 1026 WP_317818033.1 carbohydrate-binding protein -
  R4703_RS04675 - 853366..853881 (-) 516 WP_050201111.1 DUF4355 domain-containing protein -
  R4703_RS04680 - 854049..854300 (-) 252 WP_050167231.1 DUF6275 family protein -
  R4703_RS04685 - 854302..854547 (-) 246 WP_000877357.1 hypothetical protein -
  R4703_RS04690 - 854599..854826 (-) 228 WP_050168037.1 hypothetical protein -
  R4703_RS04695 - 854814..856217 (-) 1404 WP_224782169.1 minor capsid protein -
  R4703_RS04700 - 856126..857595 (-) 1470 WP_000285394.1 phage portal protein -
  R4703_RS04705 - 857607..858821 (-) 1215 WP_050140470.1 PBSX family phage terminase large subunit -
  R4703_RS04710 - 858811..859305 (-) 495 WP_000351060.1 terminase small subunit -
  R4703_RS04720 - 860608..861030 (-) 423 WP_317818037.1 DUF1492 domain-containing protein -
  R4703_RS04725 - 861102..861473 (-) 372 WP_317818039.1 hypothetical protein -
  R4703_RS04730 - 861470..861790 (-) 321 WP_055386256.1 hypothetical protein -
  R4703_RS04735 - 862046..862225 (-) 180 WP_001042650.1 hypothetical protein -
  R4703_RS04740 - 862218..862712 (-) 495 WP_233922966.1 YopX family protein -
  R4703_RS04745 - 862709..863227 (-) 519 WP_233922967.1 DUF1642 domain-containing protein -
  R4703_RS04750 - 863229..863546 (-) 318 WP_174222359.1 hypothetical protein -
  R4703_RS04755 - 863571..863753 (-) 183 WP_050245501.1 hypothetical protein -
  R4703_RS04760 - 863769..864200 (-) 432 WP_000779143.1 RusA family crossover junction endodeoxyribonuclease -
  R4703_RS04765 - 864197..864526 (-) 330 WP_050210841.1 hypothetical protein -
  R4703_RS04770 - 864540..864749 (-) 210 WP_000455269.1 hypothetical protein -
  R4703_RS04775 - 864751..865446 (-) 696 WP_050099130.1 site-specific DNA-methyltransferase -
  R4703_RS04780 ssbA 865459..865875 (-) 417 WP_050201984.1 single-stranded DNA-binding protein Machinery gene
  R4703_RS04785 - 865865..866008 (-) 144 WP_153277088.1 hypothetical protein -
  R4703_RS04790 - 866011..867075 (-) 1065 WP_219576743.1 DUF1351 domain-containing protein -
  R4703_RS04795 bet 867085..867837 (-) 753 WP_050263779.1 phage recombination protein Bet -
  R4703_RS04800 - 867855..868040 (-) 186 WP_000746960.1 hypothetical protein -
  R4703_RS04805 - 868294..868554 (-) 261 WP_219576744.1 hypothetical protein -
  R4703_RS04810 - 868567..868821 (-) 255 WP_000275521.1 hypothetical protein -
  R4703_RS04815 - 868822..869043 (-) 222 WP_001864263.1 hypothetical protein -
  R4703_RS04820 - 869043..869204 (-) 162 WP_000823399.1 BOW99_gp33 family protein -
  R4703_RS04825 - 869269..869412 (-) 144 WP_000389589.1 hypothetical protein -
  R4703_RS04830 - 869529..869753 (+) 225 WP_000517704.1 DUF2188 domain-containing protein -
  R4703_RS04835 - 869750..869932 (-) 183 WP_001247797.1 hypothetical protein -
  R4703_RS04840 - 870114..870392 (-) 279 WP_000261154.1 HTH domain-containing protein -
  R4703_RS04845 - 870559..870795 (-) 237 WP_001157069.1 hypothetical protein -
  R4703_RS04850 - 870869..870994 (+) 126 WP_257885839.1 hypothetical protein -
  R4703_RS04855 - 870987..871286 (-) 300 WP_191855094.1 hypothetical protein -
  R4703_RS04860 - 871361..871636 (-) 276 WP_050202804.1 hypothetical protein -
  R4703_RS04865 - 871797..872549 (+) 753 WP_219566337.1 XRE family transcriptional regulator -
  R4703_RS04870 - 872551..873315 (+) 765 WP_219576745.1 hypothetical protein -
  R4703_RS04875 - 873622..875067 (+) 1446 WP_317818056.1 recombinase family protein -
  R4703_RS04885 comGB/cglB 875149..876165 (-) 1017 WP_073177425.1 competence type IV pilus assembly protein ComGB Machinery gene
  R4703_RS04890 comGA/cglA/cilD 876113..877054 (-) 942 WP_000249559.1 competence type IV pilus ATPase ComGA Machinery gene
  R4703_RS04895 - 877130..877495 (-) 366 WP_000286415.1 DUF1033 family protein -
  R4703_RS04900 - 877762..879017 (+) 1256 WP_370657740.1 ISL3 family transposase -
  R4703_RS04905 - 879066..880124 (-) 1059 WP_000649468.1 zinc-dependent alcohol dehydrogenase family protein -
  R4703_RS04910 nagA 880287..881438 (-) 1152 WP_001134457.1 N-acetylglucosamine-6-phosphate deacetylase -
  R4703_RS04915 - 881591..883408 (-) 1818 WP_001220918.1 acyltransferase family protein -
  R4703_RS04920 tgt 883506..884648 (-) 1143 WP_001285241.1 tRNA guanosine(34) transglycosylase Tgt -
  R4703_RS04925 - 884778..885635 (+) 858 WP_001108866.1 DUF975 family protein -
  R4703_RS04930 pcp 885663..886280 (-) 618 Protein_944 pyroglutamyl-peptidase I -
  R4703_RS04935 - 886387..886745 (-) 359 Protein_945 DUF1304 domain-containing protein -
  R4703_RS04940 - 886756..887180 (-) 425 Protein_946 MarR family winged helix-turn-helix transcriptional regulator -
  R4703_RS04945 - 887500..888642 (-) 1143 WP_001842127.1 LysM domain-containing protein -

Sequence

Protein


Download         Length: 134 a.a.        Molecular weight: 14638.82 Da        Isoelectric Point: 10.2164

>NTDB_id=895100 R4703_RS04570 WP_000588023.1 835630..836034(-) (comGD/cglD) [Streptococcus pneumoniae strain LYP]
MIKAFTMLESLLVLGLVSILALGLSGSVQSTFAAVEEQIFFMEFEELYRETQKRSVASQQKTSLNLDGQTLSNGSQKLTV
PKGIQAPSGQSITFDRAGGNSSLAKVEFQTSKGAIRYQLYLGNGKIKRIKETKN

Nucleotide


Download         Length: 405 bp        

>NTDB_id=895100 R4703_RS04570 WP_000588023.1 835630..836034(-) (comGD/cglD) [Streptococcus pneumoniae strain LYP]
ATGATTAAGGCCTTTACCATGCTGGAAAGTCTCTTGGTTTTGGGTCTTGTGAGTATCCTTGCCTTGGGCTTGTCCGGCTC
TGTTCAGTCCACTTTTGCGGCGGTAGAGGAACAGATTTTCTTTATGGAGTTTGAAGAACTCTATCGGGAAACCCAAAAAC
GCAGTGTAGCCAGTCAGCAAAAGACTAGTCTGAACTTAGATGGGCAGACGCTTAGCAATGGCAGTCAAAAGTTGACAGTT
CCTAAAGGAATTCAGGCACCATCAGGCCAAAGTATTACATTTGACCGAGCTGGGGGCAATTCGTCCCTGGCTAAGGTTGA
ATTTCAGACCAGTAAAGGAGCGATTCGCTATCAATTATATCTAGGAAATGGAAAAATTAAACGCATTAAGGAAACAAAAA
ATTAG

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
  comGD/cglD Streptococcus pneumoniae TIGR4

98.507

100

0.985
  comGD/cglD Streptococcus pneumoniae Rx1

97.761

100

0.978
  comGD/cglD Streptococcus pneumoniae D39

97.761

100

0.978
  comGD/cglD Streptococcus pneumoniae R6

97.761

100

0.978
  comGD/cglD Streptococcus mitis SK321

97.015

100

0.97
  comGD/cglD Streptococcus mitis NCTC 12261

97.744

99.254

0.97
  comYD Streptococcus gordonii str. Challis substr. CH1

58.268

94.776

0.552
  comYD Streptococcus mutans UA140

49.219

95.522

0.47
  comYD Streptococcus mutans UA159

49.219

95.522

0.47