Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   J417_RS17765 Genome accession   NZ_CP053012
Coordinates   3966622..3967170 (+) Length   182 a.a.
NCBI ID   WP_012886084.1    Uniprot ID   D2BVZ8
Organism   Dickeya zeae MS1     
Function   ssDNA binding (predicted from homology)   
DNA processing

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 3966622..3983630 3966622..3967170 within 0
IScluster/Tn 3968034..3968840 3966622..3967170 flank 864


Gene organization within MGE regions


Location: 3966622..3983630
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  J417_RS17765 (J417_17785) ssb 3966622..3967170 (+) 549 WP_012886084.1 single-stranded DNA-binding protein Machinery gene
  J417_RS17770 (J417_17790) - 3967276..3967464 (+) 189 WP_236377650.1 hypothetical protein -
  J417_RS17775 (J417_17795) - 3967575..3967899 (-) 325 Protein_3482 helix-turn-helix domain-containing protein -
  J417_RS17780 (J417_17800) - 3968070..3968840 (+) 771 Protein_3483 DDE-type integrase/transposase/recombinase -
  J417_RS17785 (J417_17805) - 3968871..3969986 (-) 1116 WP_019843453.1 hypothetical protein -
  J417_RS17790 (J417_17810) - 3970046..3971953 (-) 1908 WP_019843452.1 gas vesicle protein GvpD -
  J417_RS17795 (J417_17815) - 3972739..3973314 (-) 576 WP_019843451.1 flavin reductase family protein -
  J417_RS17800 (J417_17820) - 3973357..3973986 (-) 630 WP_019843450.1 NAD-dependent dehydratase -
  J417_RS17805 (J417_17825) - 3974162..3974749 (+) 588 WP_019843449.1 hypothetical protein -
  J417_RS17810 (J417_17830) - 3974794..3975258 (-) 465 WP_019843448.1 hypothetical protein -
  J417_RS17815 (J417_17835) - 3975493..3976074 (+) 582 WP_019843447.1 DUF4255 domain-containing protein -
  J417_RS17820 (J417_17840) - 3976071..3976880 (+) 810 WP_019843446.1 hypothetical protein -
  J417_RS17825 (J417_17845) - 3977017..3978570 (+) 1554 WP_019843445.1 phage tail sheath family protein -
  J417_RS17830 (J417_17850) - 3978632..3979102 (+) 471 WP_012886094.1 phage tail protein -
  J417_RS17835 (J417_17855) - 3979209..3979667 (+) 459 WP_236377651.1 phage tail protein -
  J417_RS17840 (J417_17860) - 3979688..3979888 (+) 201 WP_019843443.1 hypothetical protein -
  J417_RS17845 (J417_17865) - 3979903..3980550 (+) 648 WP_019843442.1 hypothetical protein -
  J417_RS17850 (J417_17870) vgrG 3980563..3982353 (+) 1791 WP_019843441.1 type VI secretion system tip protein VgrG -
  J417_RS17855 (J417_17875) - 3982909..3983208 (+) 300 WP_016940542.1 PAAR domain-containing protein -
  J417_RS17860 (J417_17880) - 3983211..3983630 (+) 420 WP_019843440.1 GPW/gp25 family protein -

Sequence

Protein


Download         Length: 182 a.a.        Molecular weight: 19464.46 Da        Isoelectric Point: 5.2440

>NTDB_id=442077 J417_RS17765 WP_012886084.1 3966622..3967170(+) (ssb) [Dickeya zeae MS1]
MASRGVNKVILIGNLGQDPEVRYMPNGGAVANLTLATSDSWRDKQTGEQKERTEWHRVALYGKLAEIAGEYLRKGSQVYI
EGQLRTRKWQDQGGQDRYTTEVVVDISGSMQMLGGRTGGGAPAGGNMGGNTGGGNAPQGGWGQPQQPQQANQFSGGGQSR
PQQSAPMPGNEPPMDFDDDIPF

Nucleotide


Download         Length: 549 bp        

>NTDB_id=442077 J417_RS17765 WP_012886084.1 3966622..3967170(+) (ssb) [Dickeya zeae MS1]
ATGGCCAGCAGAGGCGTTAACAAAGTGATTCTTATCGGGAATCTGGGTCAGGACCCGGAAGTCCGTTACATGCCGAATGG
CGGCGCAGTCGCTAACCTGACTCTGGCCACGTCGGACAGCTGGCGCGACAAGCAGACCGGCGAGCAGAAAGAGCGTACAG
AGTGGCACCGCGTCGCCCTCTACGGCAAGCTGGCGGAAATCGCCGGTGAGTACCTGCGCAAAGGCTCTCAGGTGTATATC
GAAGGTCAGTTGCGTACCCGTAAATGGCAGGATCAGGGCGGCCAGGATCGCTACACCACTGAAGTGGTGGTCGATATCTC
CGGCAGCATGCAAATGCTGGGCGGCCGTACCGGCGGCGGTGCACCTGCTGGTGGCAACATGGGCGGCAATACAGGTGGTG
GTAACGCACCACAAGGTGGTTGGGGTCAACCGCAACAGCCGCAGCAAGCCAACCAGTTCAGCGGTGGCGGCCAGTCACGT
CCGCAGCAAAGCGCCCCGATGCCGGGCAACGAACCGCCGATGGATTTTGACGACGATATTCCGTTCTGA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(6-112)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB D2BVZ8

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
  ssb Vibrio cholerae strain A1552

73.656

100

0.753
  ssb Glaesserella parasuis strain SC1401

55.319

100

0.571
  ssb Neisseria meningitidis MC58

45.263

100

0.473
  ssb Neisseria gonorrhoeae MS11

45.263

100

0.473