Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   R3J28_RS03015 Genome accession   NZ_CP136971
Coordinates   698041..698487 (-) Length   148 a.a.
NCBI ID   WP_021358633.1    Uniprot ID   -
Organism   Xylella fastidiosa subsp. multiplex strain Santa29b     
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 691212..712997 698041..698487 within 0


Gene organization within MGE regions


Location: 691212..712997
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  R3J28_RS02975 (R3J28_02960) - 691212..692042 (-) 831 WP_004083974.1 ABC transporter ATP-binding protein -
  R3J28_RS02980 (R3J28_02965) - 692048..693166 (-) 1119 WP_004083972.1 ABC transporter permease -
  R3J28_RS02985 (R3J28_02970) - 693276..694538 (+) 1263 WP_012337721.1 threonine/serine exporter ThrE family protein -
  R3J28_RS02990 (R3J28_02975) - 695179..695385 (+) 207 WP_071869858.1 hypothetical protein -
  R3J28_RS02995 (R3J28_02980) - 695449..695661 (+) 213 WP_228304324.1 hypothetical protein -
  R3J28_RS03000 (R3J28_02985) - 695725..695934 (+) 210 WP_225621843.1 hypothetical protein -
  R3J28_RS03005 (R3J28_02990) xerC 696575..697747 (-) 1173 WP_004083967.1 tyrosine recombinase XerC -
  R3J28_RS03010 (R3J28_02995) - 697747..698019 (-) 273 WP_004083966.1 hypothetical protein -
  R3J28_RS03015 (R3J28_03000) ssb 698041..698487 (-) 447 WP_021358633.1 single-stranded DNA-binding protein Machinery gene
  R3J28_RS03020 (R3J28_03005) - 698471..698920 (-) 450 WP_154128301.1 DUF5131 family protein -
  R3J28_RS03025 (R3J28_03010) - 698913..699143 (-) 231 WP_021358635.1 hypothetical protein -
  R3J28_RS03030 (R3J28_03015) - 699143..699676 (-) 534 WP_004083962.1 hypothetical protein -
  R3J28_RS03035 (R3J28_03020) - 699673..700266 (-) 594 WP_004083960.1 DapH/DapD/GlmU-related protein -
  R3J28_RS03040 (R3J28_03025) - 700359..700892 (-) 534 WP_012337723.1 pilin -
  R3J28_RS03045 (R3J28_03030) - 701025..701291 (-) 267 WP_004084112.1 hypothetical protein -
  R3J28_RS03050 (R3J28_03035) - 701288..701566 (-) 279 WP_004083957.1 hypothetical protein -
  R3J28_RS03055 (R3J28_03040) - 701563..701784 (-) 222 WP_021358638.1 hypothetical protein -
  R3J28_RS03060 (R3J28_03045) - 701781..702239 (-) 459 WP_004084109.1 hypothetical protein -
  R3J28_RS03065 (R3J28_03050) - 702236..702700 (-) 465 WP_021358639.1 DUF1566 domain-containing protein -
  R3J28_RS03070 (R3J28_03055) - 702697..703194 (-) 498 WP_021358640.1 hypothetical protein -
  R3J28_RS03075 (R3J28_03060) - 703184..703807 (+) 624 WP_004083954.1 hypothetical protein -
  R3J28_RS03080 (R3J28_03065) - 703909..704310 (-) 402 WP_004084104.1 hypothetical protein -
  R3J28_RS03085 (R3J28_03070) - 704309..704797 (+) 489 WP_238836475.1 CHC2 zinc finger domain-containing protein -
  R3J28_RS03090 (R3J28_03075) - 704733..705377 (+) 645 WP_228762222.1 terminase gpA endonuclease subunit -
  R3J28_RS03095 (R3J28_03080) - 705454..705690 (+) 237 WP_375732123.1 hypothetical protein -
  R3J28_RS03100 (R3J28_03085) - 705687..706202 (+) 516 WP_192442536.1 phage portal protein -
  R3J28_RS03105 (R3J28_03090) - 706319..706609 (+) 291 WP_076613257.1 hypothetical protein -
  R3J28_RS03110 (R3J28_03095) - 706736..707164 (+) 429 WP_004086822.1 hypothetical protein -
  R3J28_RS03115 (R3J28_03100) - 707161..707397 (+) 237 WP_004083943.1 hypothetical protein -
  R3J28_RS03120 (R3J28_03105) - 707387..710212 (+) 2826 WP_169709956.1 phage tail protein -
  R3J28_RS03125 (R3J28_03110) - 710205..710717 (+) 513 WP_169709957.1 hypothetical protein -
  R3J28_RS03130 (R3J28_03115) - 710721..711140 (+) 420 WP_004083636.1 hypothetical protein -
  R3J28_RS03135 (R3J28_03120) - 711249..711911 (+) 663 WP_375732124.1 hypothetical protein -
  R3J28_RS03140 - 712092..712274 (-) 183 WP_021358562.1 hypothetical protein -
  R3J28_RS03150 (R3J28_03135) - 712746..712997 (+) 252 WP_004086775.1 Panacea domain-containing protein -

Sequence

Protein


Download         Length: 148 a.a.        Molecular weight: 16536.38 Da        Isoelectric Point: 6.4871

>NTDB_id=893892 R3J28_RS03015 WP_021358633.1 698041..698487(-) (ssb) [Xylella fastidiosa subsp. multiplex strain Santa29b]
MARGINKVILVGNLGNEPDIKYTQSGMTITSISLATSSGRKDREGNTQERTEWHRVKFFGKLGEIAAEYLHKGSQCYIEG
TIRYDKFTGQDGQERYVTEIIADQMHMLGGRGEGSSGITPQRQPAKVRNNDKAYAYAGDDFHDDDIPF

Nucleotide


Download         Length: 447 bp        

>NTDB_id=893892 R3J28_RS03015 WP_021358633.1 698041..698487(-) (ssb) [Xylella fastidiosa subsp. multiplex strain Santa29b]
ATGGCACGCGGAATTAACAAGGTGATCCTAGTCGGCAACCTGGGGAACGAACCGGATATCAAATACACCCAAAGCGGCAT
GACGATCACCAGCATTAGCCTAGCGACCAGCAGCGGACGCAAGGACAGAGAGGGCAATACCCAGGAGCGGACCGAATGGC
ACCGCGTCAAGTTTTTCGGAAAGCTTGGCGAGATTGCCGCCGAATATCTGCATAAGGGATCGCAGTGCTACATAGAGGGC
ACCATCCGTTACGACAAGTTCACCGGCCAGGACGGTCAGGAGCGTTATGTCACTGAGATTATTGCTGACCAAATGCACAT
GCTCGGCGGTCGCGGTGAAGGCTCCAGCGGTATCACGCCACAGCGGCAACCGGCAAAGGTCCGTAACAACGATAAAGCCT
ATGCGTATGCAGGCGACGACTTCCACGATGACGACATCCCGTTTTAG

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

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

41.477

100

0.493
  ssb Neisseria meningitidis MC58

38.728

100

0.453
  ssb Neisseria gonorrhoeae MS11

38.728

100

0.453
  ssb Glaesserella parasuis strain SC1401

41.304

93.243

0.385