Detailed information    

insolico Bioinformatically predicted

Overview

Name   comYB   Type   Machinery gene
Locus tag   K6972_RS01020 Genome accession   NZ_CP082203
Coordinates   159885..160922 (+) Length   345 a.a.
NCBI ID   WP_261984178.1    Uniprot ID   -
Organism   Streptococcus suis strain NJ3     
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 122430..159646 159885..160922 flank 239


Gene organization within MGE regions


Location: 122430..160922
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  K6972_RS00760 (K6972_00760) - 122430..123869 (-) 1440 WP_016056215.1 recombinase family protein -
  K6972_RS00765 (K6972_00765) - 124003..124572 (-) 570 WP_222812621.1 hypothetical protein -
  K6972_RS00770 (K6972_00770) - 124586..125302 (-) 717 WP_222812623.1 S24 family peptidase -
  K6972_RS00775 (K6972_00775) - 125550..125774 (+) 225 WP_105116292.1 DUF739 family protein -
  K6972_RS00780 (K6972_00780) - 125879..126052 (+) 174 WP_016056211.1 hypothetical protein -
  K6972_RS10715 - 126028..126174 (+) 147 WP_202846486.1 BOW99_gp33 family protein -
  K6972_RS00785 (K6972_00785) - 126217..126534 (+) 318 WP_016056209.1 hypothetical protein -
  K6972_RS00790 (K6972_00790) - 126786..127361 (+) 576 WP_016056208.1 hypothetical protein -
  K6972_RS00795 (K6972_00795) - 127365..128063 (+) 699 WP_016056207.1 ERF family protein -
  K6972_RS00800 (K6972_00800) - 128078..128404 (+) 327 WP_016056206.1 hypothetical protein -
  K6972_RS00805 (K6972_00805) - 128415..129476 (+) 1062 WP_016056205.1 DUF1351 domain-containing protein -
  K6972_RS00810 (K6972_00810) - 129466..129987 (+) 522 WP_016056204.1 MazG-like family protein -
  K6972_RS00815 (K6972_00815) - 129998..130198 (+) 201 WP_105135895.1 hypothetical protein -
  K6972_RS00820 (K6972_00820) ssbA 130188..130700 (+) 513 WP_016056202.1 single-stranded DNA-binding protein Machinery gene
  K6972_RS00825 (K6972_00825) - 130716..130994 (+) 279 WP_016056201.1 hypothetical protein -
  K6972_RS00830 (K6972_00830) - 131008..131787 (+) 780 WP_222812625.1 DNA methyltransferase -
  K6972_RS00835 (K6972_00835) - 131984..132418 (+) 435 WP_016056198.1 helix-turn-helix domain-containing protein -
  K6972_RS00840 (K6972_00840) - 132429..132866 (+) 438 WP_016056197.1 hypothetical protein -
  K6972_RS00845 (K6972_00845) - 132868..133605 (+) 738 WP_016056196.1 hypothetical protein -
  K6972_RS00850 (K6972_00850) - 133625..134011 (+) 387 WP_016056195.1 hypothetical protein -
  K6972_RS00855 (K6972_00855) - 134137..134439 (+) 303 WP_016056193.1 DUF1372 family protein -
  K6972_RS00860 (K6972_00860) - 134440..134616 (+) 177 WP_016056192.1 hypothetical protein -
  K6972_RS00865 (K6972_00865) - 134623..134853 (+) 231 WP_016056191.1 hypothetical protein -
  K6972_RS00870 (K6972_00870) - 134850..135269 (+) 420 WP_016056190.1 hypothetical protein -
  K6972_RS00875 (K6972_00875) - 135253..135645 (+) 393 WP_016056189.1 putative yopX protein -
  K6972_RS00880 (K6972_00880) - 135642..136022 (+) 381 WP_016056188.1 hypothetical protein -
  K6972_RS00885 (K6972_00885) - 136090..136761 (+) 672 WP_016056187.1 DUF4417 domain-containing protein -
  K6972_RS00890 (K6972_00890) - 136758..137141 (+) 384 WP_016056186.1 hypothetical protein -
  K6972_RS00895 (K6972_00895) - 137333..137812 (+) 480 WP_016056185.1 terminase small subunit -
  K6972_RS00900 (K6972_00900) - 137799..139112 (+) 1314 WP_016056184.1 PBSX family phage terminase large subunit -
  K6972_RS00905 (K6972_00905) - 139125..140708 (+) 1584 WP_016056183.1 phage portal protein -
  K6972_RS00910 (K6972_00910) - 140711..141862 (+) 1152 WP_016056182.1 phage minor capsid protein -
  K6972_RS00915 (K6972_00915) - 142009..142626 (+) 618 WP_016056181.1 phage scaffolding protein -
  K6972_RS00920 (K6972_00920) - 142630..143469 (+) 840 WP_016056180.1 N4-gp56 family major capsid protein -
  K6972_RS00925 (K6972_00925) - 143469..143654 (+) 186 WP_016056179.1 Rho termination factor N-terminal domain-containing protein -
  K6972_RS00930 (K6972_00930) - 143632..143859 (+) 228 WP_016056178.1 hypothetical protein -
  K6972_RS00935 (K6972_00935) - 143901..144296 (+) 396 WP_016056177.1 hypothetical protein -
  K6972_RS00940 (K6972_00940) - 144286..144612 (+) 327 WP_016056176.1 putative minor capsid protein -
  K6972_RS00945 (K6972_00945) - 144612..144962 (+) 351 WP_016056175.1 minor capsid protein -
  K6972_RS00950 (K6972_00950) - 144964..145371 (+) 408 WP_016056174.1 minor capsid protein -
  K6972_RS00955 (K6972_00955) - 145375..145833 (+) 459 WP_016056173.1 phage tail tube protein -
  K6972_RS00960 (K6972_00960) - 145855..146223 (+) 369 WP_016056172.1 hypothetical protein -
  K6972_RS00965 (K6972_00965) - 146223..146810 (+) 588 WP_105116263.1 Gp15 family bacteriophage protein -
  K6972_RS00970 (K6972_00970) - 146830..150117 (+) 3288 WP_222812626.1 hypothetical protein -
  K6972_RS00975 (K6972_00975) - 150114..151616 (+) 1503 WP_016056168.1 distal tail protein Dit -
  K6972_RS00980 (K6972_00980) - 151616..155425 (+) 3810 WP_016056167.1 phage tail spike protein -
  K6972_RS00985 (K6972_00985) - 155439..157502 (+) 2064 WP_016056166.1 DUF859 family phage minor structural protein -
  K6972_RS00990 (K6972_00990) - 157564..157827 (+) 264 WP_024410576.1 hypothetical protein -
  K6972_RS00995 (K6972_00995) - 157840..158295 (+) 456 WP_016056164.1 hypothetical protein -
  K6972_RS01000 (K6972_01000) - 158270..158473 (+) 204 WP_016056163.1 putative holin protein -
  K6972_RS01005 (K6972_01005) - 158603..159313 (+) 711 WP_016056162.1 CHAP domain-containing protein -
  K6972_RS01010 (K6972_01010) prx 159461..159646 (+) 186 WP_016056161.1 hypothetical protein Regulator
  K6972_RS01015 (K6972_01015) - 159671..159973 (+) 303 Protein_168 ATPase, T2SS/T4P/T4SS family -
  K6972_RS01020 (K6972_01020) comYB 159885..160922 (+) 1038 WP_261984178.1 competence type IV pilus assembly protein ComGB Machinery gene

Sequence

Protein


Download         Length: 345 a.a.        Molecular weight: 38908.93 Da        Isoelectric Point: 9.1394

>NTDB_id=599916 K6972_RS01020 WP_261984178.1 159885..160922(+) (comYB) [Streptococcus suis strain NJ3]
MRKLIAFLQQDISVFGRQKQKKLPLARQRKVIELFNNLFASGFHLGEIVDFLKRSQLLADPYTQVLSDGLLAGKPFSSLL
ADLRFSDAVVTQVALAEVHGNTSLSLSHIQSYLENVSKVRKKLIEVATYPIILLGFLLLIMLGLKNYLLPQLEEGNAATM
LINHLPTIFLSLCGLSLVAVLAGLVWFRKTNKIKVFSCLAALPFFGKLIQTYLTAYYAREWGSLIGQGLDLPQIVGLMQE
QQSQLFREIGQDLEQSLSNGQSFHEHIKAYAFFKRELSLIVEYGQVKSKLGSELTVYAAECWEDFFSRVNRAMQLIQPLV
FLLVALMVVLIYAAMLLPIYQNMEL

Nucleotide


Download         Length: 1038 bp        

>NTDB_id=599916 K6972_RS01020 WP_261984178.1 159885..160922(+) (comYB) [Streptococcus suis strain NJ3]
ATGCGCAAATTGATCGCCTTTTTGCAGCAGGACATATCAGTCTTCGGCAGGCAGAAACAGAAAAAATTGCCCTTGGCTCG
CCAGCGTAAGGTCATTGAGCTTTTCAATAACCTTTTTGCTAGTGGTTTTCATCTGGGGGAGATTGTTGATTTCCTCAAAC
GCAGTCAGCTTCTGGCAGATCCCTATACCCAGGTCTTGTCAGACGGGCTGTTAGCAGGCAAACCCTTTTCGAGTTTGCTG
GCGGATTTGCGGTTTTCAGATGCGGTGGTCACGCAGGTGGCTCTGGCAGAAGTTCATGGCAATACCAGCCTGAGTTTGAG
CCATATCCAATCCTATTTGGAAAATGTCAGCAAGGTTCGTAAAAAACTGATTGAGGTGGCGACCTATCCGATTATTTTAC
TAGGTTTTCTGCTCTTGATTATGCTGGGCTTGAAAAACTATCTTCTGCCCCAGTTGGAGGAAGGCAATGCAGCGACCATG
CTAATTAATCATCTGCCGACTATCTTTTTATCCCTCTGTGGACTTAGTTTGGTGGCGGTCTTAGCTGGTCTTGTCTGGTT
TCGTAAAACTAACAAAATCAAGGTCTTTTCCTGCTTAGCAGCTCTGCCATTTTTCGGAAAACTCATCCAAACCTATCTGA
CGGCTTATTACGCCAGGGAGTGGGGGAGTTTGATTGGGCAAGGCTTGGACCTGCCGCAGATTGTGGGTTTGATGCAGGAG
CAGCAATCGCAGCTCTTTCGAGAGATTGGACAGGACCTGGAGCAGTCGCTTTCCAATGGTCAGAGTTTTCACGAACACAT
TAAGGCCTATGCCTTTTTTAAGCGGGAGCTGAGCTTGATTGTGGAGTATGGTCAGGTCAAGTCCAAGTTGGGGAGCGAGT
TGACAGTTTATGCAGCCGAGTGTTGGGAGGATTTTTTCTCTCGGGTCAATAGAGCCATGCAGCTGATTCAACCGCTGGTC
TTTCTCCTTGTGGCCTTAATGGTCGTTCTTATCTACGCAGCTATGTTGCTGCCGATTTATCAAAATATGGAGTTATAA

Domains

Predicted by InterproScan.

Type II secretion system (T2SS), protein F (T2SSF)

(218-338)

Type II secretion system (T2SS), protein F (T2SSF)

(33-150)


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
  comYB Streptococcus gordonii str. Challis substr. CH1

63.45

99.13

0.629
  comGB/cglB Streptococcus mitis NCTC 12261

60.597

97.101

0.588
  comGB/cglB Streptococcus mitis SK321

60.299

97.101

0.586
  comYB Streptococcus mutans UA140

58.892

99.42

0.586
  comYB Streptococcus mutans UA159

58.892

99.42

0.586
  comGB/cglB Streptococcus pneumoniae Rx1

60

97.101

0.583
  comGB/cglB Streptococcus pneumoniae D39

60

97.101

0.583
  comGB/cglB Streptococcus pneumoniae R6

60

97.101

0.583
  comGB/cglB Streptococcus pneumoniae TIGR4

60

97.101

0.583
  comGB Lactococcus lactis subsp. cremoris KW2

50.148

97.681

0.49