Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   JYB87_RS11875 Genome accession   NZ_CP071503
Coordinates   2700736..2701302 (-) Length   188 a.a.
NCBI ID   WP_207353709.1    Uniprot ID   -
Organism   Shewanella avicenniae strain FJAT-51800     
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 2677053..2732504 2700736..2701302 within 0


Gene organization within MGE regions


Location: 2677053..2732504
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JYB87_RS11770 (JYB87_11770) dnaE 2677053..2680529 (-) 3477 WP_207353688.1 DNA polymerase III subunit alpha -
  JYB87_RS11775 (JYB87_11775) rnhB 2680612..2681232 (-) 621 WP_207353689.1 ribonuclease HII -
  JYB87_RS11780 (JYB87_11780) lpxB 2681236..2682396 (-) 1161 WP_407695848.1 lipid-A-disaccharide synthase -
  JYB87_RS11785 (JYB87_11785) - 2682609..2682884 (-) 276 WP_207353691.1 hypothetical protein -
  JYB87_RS11790 (JYB87_11790) - 2682896..2683114 (-) 219 WP_207353692.1 hypothetical protein -
  JYB87_RS11795 (JYB87_11795) - 2683228..2683572 (-) 345 WP_207353693.1 hypothetical protein -
  JYB87_RS11800 (JYB87_11800) - 2683572..2691098 (-) 7527 WP_207353694.1 hypothetical protein -
  JYB87_RS11805 (JYB87_11805) - 2691098..2691502 (-) 405 WP_207353695.1 DUF6950 family protein -
  JYB87_RS11810 (JYB87_11810) - 2691499..2692116 (-) 618 WP_207353696.1 hypothetical protein -
  JYB87_RS11815 (JYB87_11815) - 2692113..2692709 (-) 597 WP_207353697.1 hypothetical protein -
  JYB87_RS11820 (JYB87_11820) - 2692709..2694913 (-) 2205 WP_207353698.1 tape measure protein -
  JYB87_RS11825 (JYB87_11825) - 2694910..2695203 (-) 294 WP_207353699.1 hypothetical protein -
  JYB87_RS11830 (JYB87_11830) - 2695257..2695589 (-) 333 WP_207353700.1 hypothetical protein -
  JYB87_RS11835 (JYB87_11835) - 2695600..2696526 (-) 927 WP_207353701.1 phage tail tube protein -
  JYB87_RS11840 (JYB87_11840) - 2696533..2696979 (-) 447 WP_207353702.1 hypothetical protein -
  JYB87_RS11845 (JYB87_11845) - 2696969..2697508 (-) 540 WP_207353703.1 phage virion morphogenesis protein -
  JYB87_RS11850 (JYB87_11850) - 2697489..2697926 (-) 438 WP_207353704.1 gp436 family protein -
  JYB87_RS11855 (JYB87_11855) - 2697938..2698102 (-) 165 WP_207353705.1 hypothetical protein -
  JYB87_RS11860 (JYB87_11860) - 2698176..2699108 (-) 933 WP_207353706.1 hypothetical protein -
  JYB87_RS11865 (JYB87_11865) - 2699122..2699478 (-) 357 WP_207353707.1 capsid cement protein -
  JYB87_RS11870 (JYB87_11870) - 2699485..2700585 (-) 1101 WP_207353708.1 hypothetical protein -
  JYB87_RS11875 (JYB87_11875) ssb 2700736..2701302 (-) 567 WP_207353709.1 single-stranded DNA-binding protein Machinery gene
  JYB87_RS11880 (JYB87_11880) - 2701386..2701802 (-) 417 WP_207353710.1 antirestriction protein -
  JYB87_RS11885 (JYB87_11885) - 2701971..2702639 (-) 669 WP_207353711.1 HNH endonuclease family protein -
  JYB87_RS11890 (JYB87_11890) - 2702856..2703815 (-) 960 WP_207353712.1 integron integrase -
  JYB87_RS11895 (JYB87_11895) - 2704133..2704639 (+) 507 WP_207353713.1 hypothetical protein -
  JYB87_RS11900 (JYB87_11900) - 2705162..2705671 (+) 510 WP_207353714.1 DMP19 family protein -
  JYB87_RS11905 (JYB87_11905) ltrA 2705763..2707112 (-) 1350 WP_207353715.1 group II intron reverse transcriptase/maturase -
  JYB87_RS11910 (JYB87_11910) - 2707742..2708170 (+) 429 WP_228729853.1 DUF4844 domain-containing protein -
  JYB87_RS11915 (JYB87_11915) ltrA 2708252..2709601 (-) 1350 WP_207353715.1 group II intron reverse transcriptase/maturase -
  JYB87_RS11920 (JYB87_11920) - 2710225..2710683 (+) 459 WP_207353716.1 YcxB family protein -
  JYB87_RS11925 (JYB87_11925) - 2710878..2711651 (-) 774 WP_207353717.1 phage minor head protein -
  JYB87_RS11930 (JYB87_11930) - 2711659..2713170 (-) 1512 WP_207353718.1 DUF935 domain-containing protein -
  JYB87_RS18745 terL 2713173..2714807 (-) 1635 WP_228729854.1 phage terminase large subunit -
  JYB87_RS11940 (JYB87_11940) - 2714813..2715259 (-) 447 WP_207353719.1 hypothetical protein -
  JYB87_RS11945 (JYB87_11945) - 2715249..2716799 (-) 1551 WP_207353720.1 hypothetical protein -
  JYB87_RS11950 (JYB87_11950) - 2716847..2717155 (-) 309 WP_207353721.1 hypothetical protein -
  JYB87_RS11955 (JYB87_11955) - 2717226..2717468 (-) 243 WP_207353722.1 hypothetical protein -
  JYB87_RS11960 (JYB87_11960) - 2717461..2717973 (-) 513 WP_207353723.1 hypothetical protein -
  JYB87_RS11965 (JYB87_11965) - 2717970..2718290 (-) 321 WP_207353724.1 hypothetical protein -
  JYB87_RS11970 (JYB87_11970) - 2718262..2718660 (-) 399 WP_207353725.1 Mor transcription activator family protein -
  JYB87_RS11975 (JYB87_11975) - 2718657..2719082 (-) 426 WP_207353726.1 VRR-NUC domain-containing protein -
  JYB87_RS11980 (JYB87_11980) - 2719272..2719925 (-) 654 WP_207353727.1 replication protein P -
  JYB87_RS11985 (JYB87_11985) - 2719912..2720805 (-) 894 WP_207353728.1 hypothetical protein -
  JYB87_RS11990 (JYB87_11990) - 2720802..2721104 (-) 303 WP_207353729.1 hypothetical protein -
  JYB87_RS11995 (JYB87_11995) - 2721123..2721311 (-) 189 WP_207353730.1 Cro/CI family transcriptional regulator -
  JYB87_RS12000 (JYB87_12000) - 2721478..2722182 (+) 705 WP_207353731.1 helix-turn-helix domain-containing protein -
  JYB87_RS12005 (JYB87_12005) - 2722801..2723094 (+) 294 WP_207353732.1 hypothetical protein -
  JYB87_RS12010 (JYB87_12010) - 2723177..2723521 (+) 345 WP_207353733.1 hypothetical protein -
  JYB87_RS12015 (JYB87_12015) - 2723518..2724423 (+) 906 WP_207353734.1 PD-(D/E)XK nuclease-like domain-containing protein -
  JYB87_RS12020 (JYB87_12020) - 2724434..2725387 (+) 954 WP_207353735.1 RecT family recombinase -
  JYB87_RS12025 (JYB87_12025) - 2725432..2726034 (+) 603 WP_207353736.1 phage N-6-adenine-methyltransferase -
  JYB87_RS12030 (JYB87_12030) - 2726027..2726251 (+) 225 WP_207353737.1 hypothetical protein -
  JYB87_RS12035 (JYB87_12035) - 2726421..2726672 (+) 252 WP_207353738.1 type II toxin-antitoxin system Phd/YefM family antitoxin -
  JYB87_RS12040 (JYB87_12040) - 2726662..2726943 (+) 282 WP_207353739.1 type II toxin-antitoxin system RelE/ParE family toxin -
  JYB87_RS12045 (JYB87_12045) - 2727111..2728145 (+) 1035 WP_207353740.1 hypothetical protein -
  JYB87_RS12050 (JYB87_12050) - 2728230..2729180 (-) 951 WP_207353741.1 TerC family protein -
  JYB87_RS12055 (JYB87_12055) - 2729540..2729734 (-) 195 WP_207353742.1 hypothetical protein -
  JYB87_RS12060 (JYB87_12060) - 2729831..2730472 (-) 642 WP_207353743.1 hypothetical protein -
  JYB87_RS12065 (JYB87_12065) - 2730513..2731139 (-) 627 WP_207353744.1 DUF2026 family protein -
  JYB87_RS12070 (JYB87_12070) - 2731233..2732504 (-) 1272 WP_207353745.1 integrase arm-type DNA-binding domain-containing protein -

Sequence

Protein


Download         Length: 188 a.a.        Molecular weight: 21311.34 Da        Isoelectric Point: 6.8819

>NTDB_id=545750 JYB87_RS11875 WP_207353709.1 2700736..2701302(-) (ssb) [Shewanella avicenniae strain FJAT-51800]
MASRGINKVILVGNLGRDPEVKYTSNGNAVTNITLATSETWKDQHGQQQERTEWHRVVFFGKLAEIAGEYLRKGSQVYIE
GKLQTRKWQDQNGQDRYTTEVVVDINGTMQMLGSRGDSSGNQQSGQHNRQRTGYQDPALQPQYTQHAPQPKYVSQQQASD
IPNMQARNQPPAGWNNANSEDYWDDIPF

Nucleotide


Download         Length: 567 bp        

>NTDB_id=545750 JYB87_RS11875 WP_207353709.1 2700736..2701302(-) (ssb) [Shewanella avicenniae strain FJAT-51800]
ATGGCATCAAGAGGCATTAACAAAGTCATTTTAGTTGGCAATTTAGGGCGAGACCCCGAAGTAAAATACACATCAAACGG
AAACGCCGTTACCAACATCACACTGGCAACCAGCGAAACATGGAAAGACCAGCACGGCCAACAGCAAGAGCGCACCGAAT
GGCACCGCGTTGTGTTTTTTGGAAAGCTCGCTGAAATCGCCGGTGAGTACCTACGCAAAGGCTCGCAAGTTTACATCGAG
GGCAAGCTGCAAACTCGCAAATGGCAAGACCAAAACGGCCAAGACCGTTATACAACTGAGGTCGTTGTCGACATAAACGG
CACCATGCAAATGCTCGGTAGCCGAGGGGATAGCAGTGGCAACCAACAATCGGGACAACACAACCGGCAACGCACCGGCT
ACCAAGATCCAGCACTGCAACCGCAGTACACACAACACGCCCCGCAGCCCAAGTATGTGAGCCAGCAACAGGCTTCTGAT
ATTCCAAACATGCAAGCGCGTAACCAACCACCGGCAGGTTGGAACAACGCAAATTCTGAAGATTATTGGGACGATATACC
CTTTTAA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(6-111)


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

57.368

100

0.58
  ssb Glaesserella parasuis strain SC1401

48.454

100

0.5
  ssb Neisseria meningitidis MC58

45.55

100

0.463
  ssb Neisseria gonorrhoeae MS11

44.565

97.872

0.436