Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   QRT02_RS03955 Genome accession   NZ_CP127867
Coordinates   777374..777805 (+) Length   143 a.a.
NCBI ID   WP_286103018.1    Uniprot ID   -
Organism   Pediococcus pentosaceus strain SMFM2016-WK1     
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 767857..807320 777374..777805 within 0


Gene organization within MGE regions


Location: 767857..807320
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QRT02_RS03880 - 767857..768732 (+) 876 WP_002833532.1 hypothetical protein -
  QRT02_RS03885 - 768725..769642 (+) 918 WP_002833533.1 hypothetical protein -
  QRT02_RS03890 - 769652..770191 (+) 540 WP_002833534.1 dUTP diphosphatase -
  QRT02_RS03895 - 770495..770722 (+) 228 WP_002833535.1 hypothetical protein -
  QRT02_RS03900 - 770862..771065 (-) 204 WP_023440273.1 membrane protein -
  QRT02_RS03905 - 771403..772551 (-) 1149 WP_286103011.1 tyrosine-type recombinase/integrase -
  QRT02_RS03910 - 772689..773564 (-) 876 WP_286103012.1 DUF5067 domain-containing protein -
  QRT02_RS03915 - 773623..773907 (-) 285 WP_286103013.1 hypothetical protein -
  QRT02_RS03920 - 773920..774255 (-) 336 WP_159270622.1 helix-turn-helix transcriptional regulator -
  QRT02_RS03925 - 774517..774723 (+) 207 WP_233671645.1 XRE family transcriptional regulator -
  QRT02_RS03930 - 774859..775581 (+) 723 WP_286103014.1 ORF6C domain-containing protein -
  QRT02_RS03935 - 775791..776129 (+) 339 WP_099299921.1 DUF771 domain-containing protein -
  QRT02_RS03940 - 776231..776491 (+) 261 WP_286103015.1 hypothetical protein -
  QRT02_RS03945 - 776511..776723 (+) 213 WP_286103016.1 hypothetical protein -
  QRT02_RS03950 - 776737..777369 (+) 633 WP_286103017.1 ERF family protein -
  QRT02_RS03955 ssb 777374..777805 (+) 432 WP_286103018.1 single-stranded DNA-binding protein Machinery gene
  QRT02_RS03960 - 777816..778493 (+) 678 WP_286103019.1 putative HNHc nuclease -
  QRT02_RS03965 - 778495..779259 (+) 765 WP_286103020.1 conserved phage C-terminal domain-containing protein -
  QRT02_RS03970 - 779240..780055 (+) 816 WP_286103021.1 ATP-binding protein -
  QRT02_RS03975 - 780172..780582 (+) 411 WP_094104450.1 RusA family crossover junction endodeoxyribonuclease -
  QRT02_RS03980 - 780579..780797 (+) 219 WP_286103022.1 hypothetical protein -
  QRT02_RS03985 - 780809..781015 (+) 207 WP_286103023.1 hypothetical protein -
  QRT02_RS03990 - 781023..781163 (+) 141 WP_286103024.1 hypothetical protein -
  QRT02_RS03995 - 781178..781549 (+) 372 WP_286103025.1 N-acetylmuramoyl-L-alanine amidase -
  QRT02_RS04000 - 781549..782310 (+) 762 WP_350149335.1 site-specific DNA-methyltransferase -
  QRT02_RS04005 - 782358..782825 (+) 468 WP_286103026.1 hypothetical protein -
  QRT02_RS04010 - 782860..783150 (+) 291 WP_286103027.1 hypothetical protein -
  QRT02_RS04015 - 783235..783477 (+) 243 WP_286103028.1 hypothetical protein -
  QRT02_RS04020 - 783481..783756 (+) 276 WP_286103029.1 hypothetical protein -
  QRT02_RS04025 - 783759..783956 (+) 198 WP_286103030.1 hypothetical protein -
  QRT02_RS04030 - 783957..784115 (+) 159 WP_286103031.1 hypothetical protein -
  QRT02_RS04035 - 784137..784499 (+) 363 WP_286103032.1 hypothetical protein -
  QRT02_RS04040 - 784576..785019 (+) 444 WP_286103033.1 ArpU family phage packaging/lysis transcriptional regulator -
  QRT02_RS04045 - 785508..785855 (+) 348 WP_286103034.1 phBC6A51 family helix-turn-helix protein -
  QRT02_RS04050 - 785848..787119 (+) 1272 WP_286103063.1 PBSX family phage terminase large subunit -
  QRT02_RS04055 - 787176..788675 (+) 1500 WP_286103035.1 phage portal protein -
  QRT02_RS04060 - 788659..789630 (+) 972 WP_286103036.1 minor capsid protein -
  QRT02_RS04065 - 789749..790327 (+) 579 WP_286103037.1 DUF4355 domain-containing protein -
  QRT02_RS04070 - 790345..791202 (+) 858 WP_286103038.1 capsid protein -
  QRT02_RS04075 - 791220..791486 (+) 267 WP_286103064.1 Ig-like domain-containing protein -
  QRT02_RS04080 - 791498..791848 (+) 351 WP_286103039.1 phage head-tail connector protein -
  QRT02_RS04085 - 791860..792168 (+) 309 WP_286103040.1 hypothetical protein -
  QRT02_RS04090 - 792161..792502 (+) 342 WP_286103041.1 HK97-gp10 family putative phage morphogenesis protein -
  QRT02_RS04095 - 792527..792910 (+) 384 WP_286103042.1 hypothetical protein -
  QRT02_RS04100 - 792923..793555 (+) 633 WP_286103043.1 phage major tail protein, TP901-1 family -
  QRT02_RS04105 - 793628..793969 (+) 342 WP_286103044.1 tail assembly chaperone -
  QRT02_RS04110 - 794074..794385 (+) 312 WP_286103045.1 hypothetical protein -
  QRT02_RS04115 - 794378..797398 (+) 3021 WP_286103046.1 phage tail tape measure protein -
  QRT02_RS04120 - 797398..798162 (+) 765 WP_286103047.1 phage tail protein -
  QRT02_RS04125 - 798162..801167 (+) 3006 WP_286103048.1 phage tail protein -
  QRT02_RS04130 - 801148..801513 (+) 366 WP_286103049.1 hypothetical protein -
  QRT02_RS04135 - 801515..804616 (+) 3102 WP_286103050.1 hypothetical protein -
  QRT02_RS04140 - 804660..804944 (+) 285 WP_286103051.1 hypothetical protein -
  QRT02_RS04145 - 804951..805193 (+) 243 WP_286103052.1 phage holin -
  QRT02_RS04150 - 805207..806307 (+) 1101 WP_286103065.1 N-acetylmuramoyl-L-alanine amidase -
  QRT02_RS04155 - 806569..806733 (+) 165 WP_286103053.1 hypothetical protein -
  QRT02_RS04160 - 806733..807320 (+) 588 WP_251974171.1 GNAT family N-acetyltransferase -

Sequence

Protein


Download         Length: 143 a.a.        Molecular weight: 16026.80 Da        Isoelectric Point: 9.0882

>NTDB_id=844853 QRT02_RS03955 WP_286103018.1 777374..777805(+) (ssb) [Pediococcus pentosaceus strain SMFM2016-WK1]
MINRTVLVGRLTKDPELRYTGSGTAVATFTIAVNRQFTNSNGKREADFINCVIWHKYAESFCNFTHKGSLVGIDGRIQTR
SYDNKQGQRVFITEVVAENFSLLESKNSNQNSQNKQSGQSSPSKNPNNAFNSMPDIKDDDLPF

Nucleotide


Download         Length: 432 bp        

>NTDB_id=844853 QRT02_RS03955 WP_286103018.1 777374..777805(+) (ssb) [Pediococcus pentosaceus strain SMFM2016-WK1]
ATGATTAATCGAACGGTATTAGTTGGACGTTTGACCAAAGACCCAGAACTTCGATACACAGGTAGTGGAACTGCAGTTGC
AACATTTACAATTGCCGTTAACCGTCAGTTTACTAACTCAAATGGCAAACGTGAAGCGGACTTTATCAACTGCGTCATAT
GGCATAAATATGCGGAAAGCTTTTGTAATTTCACTCACAAAGGTTCATTGGTTGGAATTGATGGACGAATTCAAACCAGG
TCATACGATAATAAACAAGGACAACGAGTTTTTATTACAGAAGTTGTAGCTGAAAACTTCTCACTACTTGAGTCCAAAAA
TAGCAATCAAAACAGTCAAAATAAGCAATCCGGTCAATCATCACCTAGCAAAAATCCTAACAATGCATTTAACAGCATGC
CAGATATAAAAGATGATGATTTGCCATTCTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(2-102)


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 Latilactobacillus sakei subsp. sakei 23K

58.824

100

0.699
  ssbA Bacillus subtilis subsp. subtilis str. 168

52.907

100

0.636
  ssbB Bacillus subtilis subsp. subtilis str. 168

54.717

74.126

0.406
  ssbB/cilA Streptococcus mitis NCTC 12261

40

100

0.406
  ssbB Streptococcus sobrinus strain NIDR 6715-7

40

100

0.406
  ssbB/cilA Streptococcus pneumoniae TIGR4

39.31

100

0.399
  ssbB/cilA Streptococcus pneumoniae Rx1

38.621

100

0.392
  ssbB/cilA Streptococcus pneumoniae D39

38.621

100

0.392
  ssbB/cilA Streptococcus pneumoniae R6

38.621

100

0.392
  ssbB/cilA Streptococcus mitis SK321

38.621

100

0.392
  ssb Neisseria meningitidis MC58

30.058

100

0.364
  ssb Neisseria gonorrhoeae MS11

30.058

100

0.364
  ssbA Streptococcus mutans UA159

35.862

100

0.364