Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   PD_RS08430 Genome accession   NC_004556
Coordinates   1855136..1855582 (+) Length   148 a.a.
NCBI ID   WP_004088866.1    Uniprot ID   Q87B55
Organism   Xylella fastidiosa Temecula1     
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 1847783..1868933 1855136..1855582 within 0


Gene organization within MGE regions


Location: 1847783..1868933
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PD_RS08395 (PD1596) - 1847783..1848298 (-) 516 WP_004088839.1 phage portal protein -
  PD_RS13190 (PD1597) - 1848295..1848531 (-) 237 WP_004088842.1 hypothetical protein -
  PD_RS08405 (PD1598) - 1848608..1850707 (-) 2100 WP_004088845.1 phage terminase large subunit family protein -
  PD_RS08410 (PD1599) - 1850704..1851312 (-) 609 WP_004088848.1 hypothetical protein -
  PD_RS08415 (PD1600) - 1851709..1853178 (-) 1470 WP_004088851.1 VapE domain-containing protein -
  PD_RS08420 (PD1601) - 1853175..1854230 (-) 1056 WP_004088854.1 CHC2 zinc finger domain-containing protein -
  PD_RS08425 - 1854229..1854630 (+) 402 WP_004088857.1 hypothetical protein -
  PD_RS12775 - 1854732..1854905 (-) 174 WP_155115078.1 hypothetical protein -
  PD_RS12110 (PD1602) - 1854880..1855152 (+) 273 WP_004088863.1 DUF5131 family protein -
  PD_RS08430 (PD1603) ssb 1855136..1855582 (+) 447 WP_004088866.1 single-stranded DNA-binding protein Machinery gene
  PD_RS08435 (PD1604) - 1855601..1855876 (+) 276 WP_011098179.1 hypothetical protein -
  PD_RS08440 (PD1605) - 1855876..1857049 (+) 1174 Protein_1664 integrase -
  PD_RS08445 - 1857359..1857562 (+) 204 WP_004089756.1 DUF4102 domain-containing protein -
  PD_RS12780 - 1857629..1858036 (+) 408 WP_012382712.1 hypothetical protein -
  PD_RS13330 - 1858237..1858362 (-) 126 WP_256626233.1 hypothetical protein -
  PD_RS08455 (PD1607) - 1858516..1859970 (-) 1455 WP_004089759.1 SAM-dependent methyltransferase -
  PD_RS08460 (PD1608) - 1859967..1860656 (-) 690 WP_228446149.1 restriction endonuclease -
  PD_RS12510 - 1860731..1860940 (+) 210 WP_126709098.1 hypothetical protein -
  PD_RS08470 (PD1610) - 1861174..1861629 (-) 456 WP_012382713.1 type IV pilin protein -
  PD_RS08475 (PD1611) - 1861626..1866191 (-) 4566 WP_004089764.1 pilus assembly protein -
  PD_RS08480 (PD1612) - 1866195..1866689 (-) 495 WP_012382714.1 pilus assembly PilX family protein -
  PD_RS08485 (PD1613) - 1866689..1867945 (-) 1257 WP_004089768.1 PilW family protein -
  PD_RS08490 (PD1614) pilV 1867942..1868424 (-) 483 WP_004083567.1 type IV pilus modification protein PilV -
  PD_RS08495 (PD1615) - 1868421..1868933 (-) 513 WP_004089770.1 GspH/FimT family pseudopilin -

Sequence

Protein


Download         Length: 148 a.a.        Molecular weight: 16607.50 Da        Isoelectric Point: 7.3545

>NTDB_id=22657 PD_RS08430 WP_004088866.1 1855136..1855582(+) (ssb) [Xylella fastidiosa Temecula1]
MARGINKVILVGNLGNEPDIKYTQSGMTITSISLATSSKRKDREGNTQERTEWHRVKFFGKLGEIAAEYLHKGSQCYIEG
TIRYDKFTGNDGQDRYVTEIIADQMHMLGGRGEGSSGITPQRRPAKVRNNDKAYAYAGDDFHDDDIPF

Nucleotide


Download         Length: 447 bp        

>NTDB_id=22657 PD_RS08430 WP_004088866.1 1855136..1855582(+) (ssb) [Xylella fastidiosa Temecula1]
ATGGCACGCGGAATTAACAAGGTGATCCTAGTCGGAAACCTGGGAAACGAGCCAGATATTAAATACACCCAAAGCGGCAT
GACGATCACCAGTATTAGCCTAGCGACCAGCAGCAAACGCAAGGACAGAGAGGGCAATACCCAGGAGCGGACCGAATGGC
ACCGCGTCAAGTTTTTCGGAAAGCTGGGCGAGATTGCCGCTGAATATCTGCACAAGGGATCGCAGTGCTACATAGAGGGC
ACCATCCGTTACGACAAATTCACCGGCAATGATGGGCAGGACCGTTATGTCACTGAGATTATTGCTGACCAAATGCACAT
GCTCGGCGGTCGCGGCGAAGGCTCCAGCGGCATCACGCCACAGCGACGACCGGCAAAGGTCCGTAACAACGATAAAGCCT
ATGCGTATGCAGGCGACGACTTCCACGATGACGACATCCCGTTCTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(5-108)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q87B55

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

40.909

100

0.486
  ssb Neisseria meningitidis MC58

38.15

100

0.446
  ssb Neisseria gonorrhoeae MS11

38.15

100

0.446
  ssb Glaesserella parasuis strain SC1401

42.029

93.243

0.392

Multiple sequence alignment