Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   SGW13_RS07255 Genome accession   NZ_CP138502
Coordinates   1428702..1429127 (-) Length   141 a.a.
NCBI ID   WP_323052058.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain AF2019     
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 1396171..1435572 1428702..1429127 within 0


Gene organization within MGE regions


Location: 1396171..1435572
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SGW13_RS07025 (SGW13_07025) - 1396171..1397034 (-) 864 WP_323052028.1 energy-coupling factor ABC transporter ATP-binding protein -
  SGW13_RS07030 (SGW13_07030) - 1397010..1397852 (-) 843 WP_193223283.1 energy-coupling factor transporter ATPase -
  SGW13_RS07035 (SGW13_07035) - 1398794..1399480 (-) 687 WP_070366309.1 DUF3800 domain-containing protein -
  SGW13_RS07040 (SGW13_07040) - 1399596..1400690 (-) 1095 WP_323052496.1 GH25 family lysozyme -
  SGW13_RS07045 (SGW13_07045) - 1400857..1401096 (-) 240 WP_323052029.1 phage holin -
  SGW13_RS07050 (SGW13_07050) - 1401096..1401380 (-) 285 WP_323052497.1 hypothetical protein -
  SGW13_RS07055 (SGW13_07055) - 1401430..1401588 (-) 159 WP_195918498.1 XkdX family protein -
  SGW13_RS07060 (SGW13_07060) - 1401591..1401926 (-) 336 WP_323052030.1 DUF2977 domain-containing protein -
  SGW13_RS07065 (SGW13_07065) - 1401926..1402663 (-) 738 WP_323052031.1 hypothetical protein -
  SGW13_RS07070 (SGW13_07070) - 1402679..1404523 (-) 1845 WP_323052032.1 phage baseplate upper protein -
  SGW13_RS07075 (SGW13_07075) - 1404527..1404940 (-) 414 WP_323052033.1 hypothetical protein -
  SGW13_RS07080 (SGW13_07080) - 1404940..1407852 (-) 2913 WP_323052034.1 phage tail protein -
  SGW13_RS07085 (SGW13_07085) - 1407852..1408613 (-) 762 WP_323052035.1 phage tail protein -
  SGW13_RS07090 (SGW13_07090) - 1408614..1411634 (-) 3021 WP_323052036.1 phage tail tape measure protein -
  SGW13_RS07095 (SGW13_07095) - 1411618..1411935 (-) 318 WP_008842042.1 hypothetical protein -
  SGW13_RS07100 (SGW13_07100) - 1412034..1412369 (-) 336 WP_204201436.1 tail assembly chaperone -
  SGW13_RS07105 (SGW13_07105) - 1412432..1412893 (-) 462 WP_323052037.1 Ig domain-containing protein -
  SGW13_RS07110 (SGW13_07110) - 1412902..1413177 (-) 276 WP_323052038.1 hypothetical protein -
  SGW13_RS07115 (SGW13_07115) - 1413255..1413857 (-) 603 WP_323052039.1 phage major tail protein, TP901-1 family -
  SGW13_RS07120 (SGW13_07120) - 1413878..1414279 (-) 402 WP_323052040.1 hypothetical protein -
  SGW13_RS07125 (SGW13_07125) - 1414280..1414621 (-) 342 WP_128472108.1 HK97-gp10 family putative phage morphogenesis protein -
  SGW13_RS07130 (SGW13_07130) - 1414614..1414919 (-) 306 WP_201197946.1 hypothetical protein -
  SGW13_RS07135 (SGW13_07135) - 1414924..1415298 (-) 375 WP_201197945.1 phage head-tail connector protein -
  SGW13_RS07140 (SGW13_07140) - 1415310..1415555 (-) 246 WP_236252672.1 Ig-like domain-containing protein -
  SGW13_RS07145 (SGW13_07145) - 1415594..1416508 (-) 915 WP_201197944.1 phage capsid protein -
  SGW13_RS07150 (SGW13_07150) - 1416521..1417171 (-) 651 WP_323052041.1 DUF4355 domain-containing protein -
  SGW13_RS07155 (SGW13_07155) - 1417268..1418251 (-) 984 WP_323052042.1 minor capsid protein -
  SGW13_RS07160 (SGW13_07160) - 1418220..1419551 (-) 1332 WP_323052498.1 phage portal protein -
  SGW13_RS07165 (SGW13_07165) - 1419657..1420925 (-) 1269 WP_323052043.1 PBSX family phage terminase large subunit -
  SGW13_RS07170 (SGW13_07170) - 1420915..1421388 (-) 474 WP_323052044.1 phBC6A51 family helix-turn-helix protein -
  SGW13_RS07175 (SGW13_07175) - 1421829..1422290 (-) 462 WP_002830416.1 ArpU family phage packaging/lysis transcriptional regulator -
  SGW13_RS07180 (SGW13_07180) - 1422429..1422593 (-) 165 WP_176582130.1 hypothetical protein -
  SGW13_RS07185 (SGW13_07185) - 1422590..1422790 (-) 201 WP_323052045.1 hypothetical protein -
  SGW13_RS07190 (SGW13_07190) - 1422793..1423080 (-) 288 WP_323052046.1 hypothetical protein -
  SGW13_RS07195 (SGW13_07195) - 1423081..1423341 (-) 261 WP_323052047.1 hypothetical protein -
  SGW13_RS07200 (SGW13_07200) - 1423341..1423625 (-) 285 WP_323052048.1 hypothetical protein -
  SGW13_RS07205 (SGW13_07205) - 1423639..1423959 (-) 321 WP_138492705.1 hypothetical protein -
  SGW13_RS07210 (SGW13_07210) - 1423964..1424158 (-) 195 WP_323052049.1 hypothetical protein -
  SGW13_RS07215 (SGW13_07215) - 1424155..1424466 (-) 312 WP_323052050.1 hypothetical protein -
  SGW13_RS07220 (SGW13_07220) - 1424459..1425007 (-) 549 WP_323052051.1 DUF1642 domain-containing protein -
  SGW13_RS07225 (SGW13_07225) - 1425176..1425547 (-) 372 WP_323052052.1 N-acetylmuramoyl-L-alanine amidase -
  SGW13_RS07230 (SGW13_07230) - 1425519..1425683 (-) 165 WP_323052053.1 hypothetical protein -
  SGW13_RS07235 (SGW13_07235) - 1425702..1426334 (-) 633 WP_323052054.1 RNA polymerase subunit sigma-70 -
  SGW13_RS07240 (SGW13_07240) - 1426452..1427096 (-) 645 WP_323052055.1 ATP-binding protein -
  SGW13_RS07245 (SGW13_07245) - 1427248..1428012 (-) 765 WP_323052056.1 conserved phage C-terminal domain-containing protein -
  SGW13_RS07250 (SGW13_07250) - 1427990..1428691 (-) 702 WP_323052057.1 putative HNHc nuclease -
  SGW13_RS07255 (SGW13_07255) ssb 1428702..1429127 (-) 426 WP_323052058.1 single-stranded DNA-binding protein Machinery gene
  SGW13_RS07260 (SGW13_07260) - 1429120..1429326 (-) 207 WP_058121226.1 hypothetical protein -
  SGW13_RS07265 (SGW13_07265) - 1429323..1430048 (-) 726 WP_323052059.1 ERF family protein -
  SGW13_RS07270 (SGW13_07270) - 1430049..1430513 (-) 465 WP_323052060.1 chromosome segregation protein SMC -
  SGW13_RS07275 (SGW13_07275) - 1430660..1430977 (-) 318 WP_159214831.1 hypothetical protein -
  SGW13_RS07280 (SGW13_07280) - 1431074..1431280 (-) 207 WP_036672525.1 hypothetical protein -
  SGW13_RS07285 (SGW13_07285) - 1431349..1432083 (-) 735 WP_248616952.1 Rha family transcriptional regulator -
  SGW13_RS07290 (SGW13_07290) - 1432098..1432286 (-) 189 WP_323052061.1 hypothetical protein -
  SGW13_RS07295 (SGW13_07295) - 1432552..1432890 (+) 339 WP_248616953.1 XRE family transcriptional regulator -
  SGW13_RS07300 (SGW13_07300) - 1432894..1433304 (+) 411 WP_075139781.1 hypothetical protein -
  SGW13_RS07305 (SGW13_07305) - 1433366..1433905 (+) 540 WP_195459567.1 Ltp family lipoprotein -
  SGW13_RS07310 (SGW13_07310) - 1433941..1434345 (+) 405 WP_323052062.1 hypothetical protein -
  SGW13_RS07315 (SGW13_07315) - 1434493..1435572 (+) 1080 WP_323052063.1 tyrosine-type recombinase/integrase -

Sequence

Protein


Download         Length: 141 a.a.        Molecular weight: 15626.35 Da        Isoelectric Point: 7.9559

>NTDB_id=903205 SGW13_RS07255 WP_323052058.1 1428702..1429127(-) (ssb) [Pediococcus acidilactici strain AF2019]
MINRTVLIGRLTKDVEVRYTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFAKYTQKGSLVGIEGRIQTR
SYENQQGQRVYVTEVVADNFSLLDSKPKGNQQNNTRQASTPGDPFANGGQSIDIGDDSLPF

Nucleotide


Download         Length: 426 bp        

>NTDB_id=903205 SGW13_RS07255 WP_323052058.1 1428702..1429127(-) (ssb) [Pediococcus acidilactici strain AF2019]
ATGATTAATAGGACAGTACTAATAGGACGCCTAACTAAAGATGTTGAGGTTCGCTACACAGCTAAAGGCGATGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGTGAAGCGGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGCTAAGTATACACAAAAAGGTTCGTTGGTAGGTATTGAAGGGCGGATTCAGACCCGT
TCATACGAAAACCAACAAGGACAACGAGTTTATGTAACTGAGGTTGTAGCGGATAACTTCTCGTTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAACACACGGCAAGCATCAACGCCAGGAGATCCATTCGCTAATGGCGGGCAGTCAATTGATA
TTGGTGACGATAGTTTGCCTTTCTAA

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

58.235

100

0.702
  ssbA Bacillus subtilis subsp. subtilis str. 168

53.488

100

0.652
  ssbB Bacillus subtilis subsp. subtilis str. 168

62.037

76.596

0.475
  ssbB/cilA Streptococcus mitis NCTC 12261

39.583

100

0.404
  ssbB/cilA Streptococcus pneumoniae TIGR4

39.583

100

0.404
  ssbB/cilA Streptococcus pneumoniae R6

38.889

100

0.397
  ssbB/cilA Streptococcus pneumoniae Rx1

38.889

100

0.397
  ssbB/cilA Streptococcus pneumoniae D39

38.889

100

0.397
  ssbB/cilA Streptococcus mitis SK321

38.889

100

0.397
  ssbB Streptococcus sobrinus strain NIDR 6715-7

46.957

81.56

0.383
  ssbA Streptococcus mutans UA159

37.324

100

0.376