Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   XFASM12_RS02925 Genome accession   NC_010513
Coordinates   693884..694330 (-) Length   148 a.a.
NCBI ID   WP_021358633.1    Uniprot ID   -
Organism   Xylella fastidiosa M12     
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 684942..713273 693884..694330 within 0


Gene organization within MGE regions


Location: 684942..713273
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  XFASM12_RS02885 (Xfasm12_0624) - 684984..685568 (+) 585 WP_004083991.1 alpha-ketoglutarate-dependent dioxygenase AlkB -
  XFASM12_RS02890 (Xfasm12_0625) - 685763..686404 (-) 642 WP_004083987.1 ABC-type transport auxiliary lipoprotein family protein -
  XFASM12_RS02895 (Xfasm12_0626) - 686401..687327 (-) 927 WP_004083985.1 MlaD family protein -
  XFASM12_RS02900 (Xfasm12_0627) - 687331..688161 (-) 831 WP_004083974.1 ABC transporter ATP-binding protein -
  XFASM12_RS02905 (Xfasm12_0628) - 688167..689285 (-) 1119 WP_004083972.1 ABC transporter permease -
  XFASM12_RS02910 (Xfasm12_0629) - 689395..690657 (+) 1263 WP_012337721.1 threonine/serine exporter family protein -
  XFASM12_RS11290 - 691298..691504 (+) 207 WP_071869858.1 hypothetical protein -
  XFASM12_RS11295 - 691568..691777 (+) 210 WP_225621843.1 hypothetical protein -
  XFASM12_RS02915 (Xfasm12_0631) - 692418..693590 (-) 1173 WP_004083967.1 integrase -
  XFASM12_RS02920 (Xfasm12_0632) - 693590..693862 (-) 273 WP_004083966.1 hypothetical protein -
  XFASM12_RS02925 (Xfasm12_0633) ssb 693884..694330 (-) 447 WP_021358633.1 single-stranded DNA-binding protein Machinery gene
  XFASM12_RS11300 (Xfasm12_0634) - 694314..694784 (-) 471 WP_076613218.1 DUF5131 family protein -
  XFASM12_RS02930 (Xfasm12_0635) - 694777..695007 (-) 231 WP_021358635.1 hypothetical protein -
  XFASM12_RS02935 (Xfasm12_0636) - 695007..695540 (-) 534 WP_004083962.1 hypothetical protein -
  XFASM12_RS02940 (Xfasm12_0637) - 695537..696130 (-) 594 WP_004083960.1 DapH/DapD/GlmU-related protein -
  XFASM12_RS02945 (Xfasm12_0638) - 696223..696756 (-) 534 WP_012337723.1 pilin -
  XFASM12_RS02950 (Xfasm12_0639) - 696889..697155 (-) 267 WP_004084112.1 hypothetical protein -
  XFASM12_RS02955 (Xfasm12_0640) - 697152..697430 (-) 279 WP_004083957.1 hypothetical protein -
  XFASM12_RS02960 - 697427..697648 (-) 222 WP_021358638.1 hypothetical protein -
  XFASM12_RS02965 (Xfasm12_0642) - 697645..698103 (-) 459 WP_004084109.1 hypothetical protein -
  XFASM12_RS02970 - 698100..698564 (-) 465 WP_021358639.1 DUF1566 domain-containing protein -
  XFASM12_RS12730 (Xfasm12_0643) - 698561..698902 (-) 342 WP_228762220.1 hypothetical protein -
  XFASM12_RS02980 (Xfasm12_0644) - 699093..699671 (+) 579 WP_228762221.1 hypothetical protein -
  XFASM12_RS02985 - 699773..700174 (-) 402 WP_021358642.1 hypothetical protein -
  XFASM12_RS11305 (Xfasm12_0646) - 700173..700661 (+) 489 WP_021358643.1 CHC2 zinc finger domain-containing protein -
  XFASM12_RS02995 (Xfasm12_0647) - 700597..701241 (+) 645 WP_228762222.1 terminase gpA endonuclease subunit -
  XFASM12_RS03000 (Xfasm12_0648) - 701318..701554 (+) 237 WP_012337727.1 hypothetical protein -
  XFASM12_RS03005 (Xfasm12_0649) - 701551..702066 (+) 516 WP_004083947.1 phage portal protein -
  XFASM12_RS11310 (Xfasm12_0650) - 702183..702473 (+) 291 WP_076613257.1 hypothetical protein -
  XFASM12_RS13090 - 702487..702609 (+) 123 WP_324187556.1 hypothetical protein -
  XFASM12_RS10980 (Xfasm12_0651) - 702600..703028 (+) 429 WP_004086822.1 hypothetical protein -
  XFASM12_RS03020 (Xfasm12_0652) - 703025..703261 (+) 237 WP_004083943.1 hypothetical protein -
  XFASM12_RS03025 (Xfasm12_0653) - 703251..706076 (+) 2826 WP_012337728.1 phage tail protein -
  XFASM12_RS03030 (Xfasm12_0654) - 706069..706764 (+) 696 WP_228762224.1 hypothetical protein -
  XFASM12_RS03035 (Xfasm12_0655) - 706725..707003 (+) 279 WP_228762225.1 hypothetical protein -
  XFASM12_RS03040 (Xfasm12_0656) - 707112..707774 (+) 663 WP_228762226.1 hypothetical protein -
  XFASM12_RS13020 - 707834..707962 (-) 129 WP_256704593.1 hypothetical protein -
  XFASM12_RS12145 - 708010..708117 (+) 108 Protein_594 DNA adenine methylase -
  XFASM12_RS03050 (Xfasm12_0658) - 708169..708795 (+) 627 WP_038230952.1 IS607 family transposase -
  XFASM12_RS03055 (Xfasm12_0659) - 708789..709985 (+) 1197 WP_012337730.1 RNA-guided endonuclease TnpB family protein -
  XFASM12_RS03060 (Xfasm12_0660) - 709992..710696 (+) 705 WP_154123795.1 DNA adenine methylase -
  XFASM12_RS03070 (Xfasm12_0661) - 710953..711351 (-) 399 WP_012337731.1 hypothetical protein -
  XFASM12_RS03075 (Xfasm12_0662) - 711402..711701 (-) 300 WP_004084250.1 hypothetical protein -
  XFASM12_RS13025 - 711835..711966 (-) 132 WP_256704532.1 hypothetical protein -
  XFASM12_RS11315 (Xfasm12_0663) - 712061..712303 (-) 243 WP_012337732.1 hypothetical protein -
  XFASM12_RS03085 (Xfasm12_0664) - 712709..713026 (-) 318 WP_004084245.1 BrnA antitoxin family protein -
  XFASM12_RS03090 (Xfasm12_0665) - 712986..713273 (-) 288 WP_004083921.1 BrnT family toxin -

Sequence

Protein


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

>NTDB_id=30354 XFASM12_RS02925 WP_021358633.1 693884..694330(-) (ssb) [Xylella fastidiosa M12]
MARGINKVILVGNLGNEPDIKYTQSGMTITSISLATSSGRKDREGNTQERTEWHRVKFFGKLGEIAAEYLHKGSQCYIEG
TIRYDKFTGQDGQERYVTEIIADQMHMLGGRGEGSSGITPQRQPAKVRNNDKAYAYAGDDFHDDDIPF

Nucleotide


Download         Length: 447 bp        

>NTDB_id=30354 XFASM12_RS02925 WP_021358633.1 693884..694330(-) (ssb) [Xylella fastidiosa M12]
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

Multiple sequence alignment