Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   QRT00_RS04245 Genome accession   NZ_CP127868
Coordinates   839344..839826 (+) Length   160 a.a.
NCBI ID   WP_257068211.1    Uniprot ID   -
Organism   Pediococcus pentosaceus strain SMFM2016-YK1     
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 830475..872835 839344..839826 within 0


Gene organization within MGE regions


Location: 830475..872835
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QRT00_RS04175 - 830475..831647 (-) 1173 WP_286120499.1 site-specific integrase -
  QRT00_RS04180 - 831745..831993 (-) 249 WP_286120501.1 hypothetical protein -
  QRT00_RS04185 - 832073..833056 (-) 984 WP_286120502.1 DUF308 domain-containing protein -
  QRT00_RS04190 - 833118..833525 (-) 408 WP_286120503.1 ImmA/IrrE family metallo-endopeptidase -
  QRT00_RS04195 - 833537..833908 (-) 372 WP_176932925.1 helix-turn-helix transcriptional regulator -
  QRT00_RS04200 - 834060..834311 (+) 252 WP_249704015.1 helix-turn-helix transcriptional regulator -
  QRT00_RS04205 - 834308..834550 (+) 243 WP_198467874.1 hypothetical protein -
  QRT00_RS04210 - 834624..835082 (+) 459 WP_286120504.1 helix-turn-helix transcriptional regulator -
  QRT00_RS04215 - 835083..835358 (+) 276 WP_286120505.1 hypothetical protein -
  QRT00_RS04220 - 835596..835877 (+) 282 WP_286120506.1 hypothetical protein -
  QRT00_RS04225 - 835870..836721 (+) 852 WP_138428639.1 RecT family recombinase -
  QRT00_RS04230 - 836681..837508 (+) 828 WP_286120507.1 PD-(D/E)XK nuclease-like domain-containing protein -
  QRT00_RS04235 - 837518..838471 (+) 954 WP_286120508.1 DnaD domain protein -
  QRT00_RS04240 - 838475..839170 (+) 696 WP_286120509.1 putative HNHc nuclease -
  QRT00_RS04245 ssb 839344..839826 (+) 483 WP_257068211.1 single-stranded DNA-binding protein Machinery gene
  QRT00_RS04250 - 839838..840302 (+) 465 WP_286120510.1 hypothetical protein -
  QRT00_RS04255 - 840299..840472 (+) 174 WP_286120511.1 hypothetical protein -
  QRT00_RS04260 - 840462..840824 (+) 363 WP_159270427.1 hypothetical protein -
  QRT00_RS04265 - 840824..841363 (+) 540 WP_286120512.1 DUF1642 domain-containing protein -
  QRT00_RS04270 - 841491..841751 (+) 261 WP_159270429.1 hypothetical protein -
  QRT00_RS04275 - 841902..842144 (+) 243 WP_286120513.1 hypothetical protein -
  QRT00_RS04280 - 842516..842959 (+) 444 WP_094104548.1 hypothetical protein -
  QRT00_RS04295 - 843724..843897 (+) 174 WP_286120515.1 hypothetical protein -
  QRT00_RS04300 - 843897..844466 (+) 570 WP_270217232.1 terminase small subunit -
  QRT00_RS04305 - 844472..845836 (+) 1365 WP_286120541.1 PBSX family phage terminase large subunit -
  QRT00_RS04310 - 845839..847386 (+) 1548 WP_286120516.1 phage portal protein -
  QRT00_RS04315 - 847383..848516 (+) 1134 WP_286120517.1 phage minor capsid protein -
  QRT00_RS04320 - 848616..849173 (+) 558 WP_286120518.1 phage scaffolding protein -
  QRT00_RS04325 - 849186..850097 (+) 912 WP_286120519.1 hypothetical protein -
  QRT00_RS04330 - 850165..850581 (+) 417 WP_286120520.1 hypothetical protein -
  QRT00_RS04335 - 850578..850925 (+) 348 WP_159270439.1 putative minor capsid protein -
  QRT00_RS04340 - 850925..851275 (+) 351 WP_286120521.1 minor capsid protein -
  QRT00_RS04345 - 851262..851657 (+) 396 WP_286120522.1 minor capsid protein -
  QRT00_RS04350 - 851661..852236 (+) 576 WP_233605433.1 capsid protein -
  QRT00_RS04355 - 852310..852747 (+) 438 WP_233671667.1 hypothetical protein -
  QRT00_RS04360 - 852754..853386 (+) 633 WP_286120523.1 Gp15 family bacteriophage protein -
  QRT00_RS04365 - 853390..858666 (+) 5277 WP_286120524.1 tape measure protein -
  QRT00_RS04370 - 858671..859516 (+) 846 WP_286120525.1 phage tail domain-containing protein -
  QRT00_RS04375 - 859525..860661 (+) 1137 WP_286120526.1 phage tail protein -
  QRT00_RS04380 - 860651..860974 (+) 324 WP_286120527.1 hypothetical protein -
  QRT00_RS04385 - 860967..861365 (+) 399 WP_286120528.1 hypothetical protein -
  QRT00_RS04390 - 861355..862392 (+) 1038 WP_286120529.1 BppU family phage baseplate upper protein -
  QRT00_RS04395 - 862405..863226 (+) 822 WP_286120531.1 collagen-like protein -
  QRT00_RS04400 - 863240..864730 (+) 1491 WP_286120532.1 hypothetical protein -
  QRT00_RS04405 - 864770..865075 (+) 306 WP_286120533.1 hypothetical protein -
  QRT00_RS04410 - 865078..865200 (+) 123 WP_286120534.1 hypothetical protein -
  QRT00_RS04415 - 865364..866428 (+) 1065 WP_286120542.1 peptidoglycan recognition family protein -
  QRT00_RS04420 - 866481..867167 (-) 687 WP_286120535.1 hypothetical protein -
  QRT00_RS04425 - 867335..867655 (+) 321 WP_286120537.1 acetyl-CoA carboxylase -
  QRT00_RS04430 - 868111..869487 (+) 1377 WP_002833594.1 amino acid permease -
  QRT00_RS04435 - 869648..870814 (+) 1167 WP_002833595.1 hydroxymethylglutaryl-CoA synthase -
  QRT00_RS04440 - 870854..871453 (-) 600 WP_002833596.1 hypothetical protein -
  QRT00_RS04445 lexA 871532..872161 (-) 630 WP_002833597.1 transcriptional repressor LexA -
  QRT00_RS04450 - 872295..872543 (+) 249 WP_002833598.1 DUF896 domain-containing protein -
  QRT00_RS04455 - 872614..872835 (+) 222 WP_002833599.1 YneF family protein -

Sequence

Protein


Download         Length: 160 a.a.        Molecular weight: 18320.13 Da        Isoelectric Point: 6.9556

>NTDB_id=844876 QRT00_RS04245 WP_257068211.1 839344..839826(+) (ssb) [Pediococcus pentosaceus strain SMFM2016-YK1]
MINRIVLVGRLTNDPELKYTGNDVAVATFTVAVNRQFTNSQGEREADFIRCQMWRKAAENFCNFTHKGSLVGIDGRIQTR
SYENQQGTRIFVTEVVAENFSLLESKNSNQNNQNEQFEQNRPKNNGQNYQNKQNGQSAPNRNPNNPFNSMPDIKDDDLPF

Nucleotide


Download         Length: 483 bp        

>NTDB_id=844876 QRT00_RS04245 WP_257068211.1 839344..839826(+) (ssb) [Pediococcus pentosaceus strain SMFM2016-YK1]
ATGATTAATCGAATAGTATTAGTCGGGCGGTTAACCAACGATCCAGAACTAAAATACACAGGCAATGATGTAGCAGTTGC
AACCTTCACAGTAGCCGTTAATCGGCAATTTACTAATTCGCAAGGCGAACGTGAAGCAGATTTTATTAGATGCCAAATGT
GGCGCAAAGCTGCTGAAAACTTCTGTAACTTCACTCACAAAGGTTCACTAGTTGGAATTGATGGACGAATTCAAACTCGC
TCATACGAAAATCAACAAGGAACACGAATTTTTGTTACTGAGGTCGTAGCTGAGAACTTCTCGCTGCTTGAATCTAAAAA
TAGTAATCAAAATAACCAAAATGAACAATTTGAACAGAATAGACCTAAAAACAACGGACAAAATTATCAGAATAAACAAA
ATGGTCAATCAGCACCCAACAGAAATCCTAACAACCCATTTAATAGCATGCCGGATATCAAGGATGACGATTTACCATTC
TAG

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

55.233

100

0.594
  ssbA Bacillus subtilis subsp. subtilis str. 168

54.286

100

0.594
  ssbB Bacillus subtilis subsp. subtilis str. 168

54.717

66.25

0.363