Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   GQS62_RS04535 Genome accession   NZ_CP046938
Coordinates   885934..886449 (+) Length   171 a.a.
NCBI ID   WP_158190603.1    Uniprot ID   -
Organism   Pediococcus pentosaceus strain GDIAS001     
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 874769..915224 885934..886449 within 0


Gene organization within MGE regions


Location: 874769..915224
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GQS62_RS04455 (GQS62_04450) - 874769..875941 (-) 1173 WP_158190590.1 tyrosine-type recombinase/integrase -
  GQS62_RS04460 (GQS62_04455) - 876037..876939 (-) 903 WP_158190591.1 DNA adenine methylase -
  GQS62_RS04465 (GQS62_04460) - 876983..878725 (-) 1743 WP_158190592.1 AIPR family protein -
  GQS62_RS04470 (GQS62_04465) - 878813..879751 (-) 939 WP_158190593.1 DUF3862 domain-containing protein -
  GQS62_RS04475 (GQS62_04470) - 879828..880220 (-) 393 WP_158190594.1 ImmA/IrrE family metallo-endopeptidase -
  GQS62_RS04480 (GQS62_04475) - 880227..880562 (-) 336 WP_099299649.1 helix-turn-helix domain-containing protein -
  GQS62_RS04485 (GQS62_04480) - 880711..880932 (+) 222 WP_158190595.1 helix-turn-helix domain-containing protein -
  GQS62_RS04490 (GQS62_04485) - 880964..881206 (+) 243 WP_158190596.1 hypothetical protein -
  GQS62_RS04495 (GQS62_04490) - 881280..881738 (+) 459 WP_233262826.1 helix-turn-helix domain-containing protein -
  GQS62_RS04500 (GQS62_04495) - 881739..882014 (+) 276 WP_158190597.1 helix-turn-helix domain-containing protein -
  GQS62_RS09330 - 882028..882159 (+) 132 WP_256677761.1 hypothetical protein -
  GQS62_RS04505 (GQS62_04500) - 882252..882533 (+) 282 WP_158190598.1 hypothetical protein -
  GQS62_RS04510 (GQS62_04505) bet 882526..883290 (+) 765 WP_158190599.1 phage recombination protein Bet -
  GQS62_RS04515 (GQS62_04510) - 883250..884095 (+) 846 WP_233262827.1 PD-(D/E)XK nuclease-like domain-containing protein -
  GQS62_RS04520 (GQS62_04515) - 884106..884981 (+) 876 WP_158190600.1 helix-turn-helix domain-containing protein -
  GQS62_RS04525 (GQS62_04520) - 884985..885686 (+) 702 WP_158190601.1 putative HNHc nuclease -
  GQS62_RS04530 (GQS62_04525) - 885691..885915 (+) 225 WP_233262828.1 hypothetical protein -
  GQS62_RS04535 (GQS62_04530) ssb 885934..886449 (+) 516 WP_158190603.1 single-stranded DNA-binding protein Machinery gene
  GQS62_RS04540 (GQS62_04535) - 886600..886917 (+) 318 WP_158190604.1 hypothetical protein -
  GQS62_RS04545 (GQS62_04540) - 887080..887277 (+) 198 WP_158190605.1 DUF6877 family protein -
  GQS62_RS04550 (GQS62_04545) - 887475..887717 (+) 243 WP_158190606.1 hypothetical protein -
  GQS62_RS04555 (GQS62_04550) - 888098..888541 (+) 444 WP_158190607.1 hypothetical protein -
  GQS62_RS04565 (GQS62_04560) - 888845..889465 (+) 621 WP_158190608.1 hypothetical protein -
  GQS62_RS09335 - 889455..889580 (+) 126 WP_267904096.1 hypothetical protein -
  GQS62_RS09255 - 889567..889731 (+) 165 WP_199267411.1 hypothetical protein -
  GQS62_RS04570 (GQS62_04565) - 889785..890261 (+) 477 WP_158190609.1 hypothetical protein -
  GQS62_RS04575 (GQS62_04570) - 890304..890840 (+) 537 WP_158190610.1 terminase small subunit -
  GQS62_RS04580 (GQS62_04575) - 890824..892095 (+) 1272 WP_158190611.1 PBSX family phage terminase large subunit -
  GQS62_RS04585 (GQS62_04580) - 892176..893495 (+) 1320 WP_158190981.1 phage portal protein -
  GQS62_RS04590 (GQS62_04585) - 893479..894444 (+) 966 WP_158190612.1 minor capsid protein -
  GQS62_RS04595 (GQS62_04590) - 894447..894815 (+) 369 WP_158190613.1 hypothetical protein -
  GQS62_RS04600 (GQS62_04595) - 894874..895119 (+) 246 WP_158190614.1 hypothetical protein -
  GQS62_RS04605 (GQS62_04600) - 895222..895917 (+) 696 WP_158190615.1 DUF4355 domain-containing protein -
  GQS62_RS04610 (GQS62_04605) - 895917..896735 (+) 819 WP_158190616.1 N4-gp56 family major capsid protein -
  GQS62_RS04615 (GQS62_04610) - 896753..897019 (+) 267 WP_158190982.1 Ig-like domain-containing protein -
  GQS62_RS04620 (GQS62_04615) - 897031..897402 (+) 372 WP_158190617.1 phage head-tail connector protein -
  GQS62_RS04625 (GQS62_04620) - 897407..897709 (+) 303 WP_158190618.1 hypothetical protein -
  GQS62_RS04630 (GQS62_04625) - 897702..898073 (+) 372 WP_158190619.1 HK97-gp10 family putative phage morphogenesis protein -
  GQS62_RS04635 (GQS62_04630) - 898074..898481 (+) 408 WP_158190620.1 hypothetical protein -
  GQS62_RS04640 (GQS62_04635) - 898499..899095 (+) 597 WP_141822621.1 phage major tail protein, TP901-1 family -
  GQS62_RS04645 (GQS62_04640) - 899173..899451 (+) 279 WP_158190621.1 hypothetical protein -
  GQS62_RS04650 (GQS62_04645) - 899531..899869 (+) 339 WP_158190622.1 tail assembly chaperone -
  GQS62_RS04655 (GQS62_04650) - 899971..900303 (+) 333 WP_229572677.1 hypothetical protein -
  GQS62_RS04660 (GQS62_04655) - 900296..903646 (+) 3351 WP_158190623.1 phage tail tape measure protein -
  GQS62_RS04665 (GQS62_04660) - 903646..904410 (+) 765 WP_158190624.1 phage tail protein -
  GQS62_RS04670 (GQS62_04665) - 904410..907370 (+) 2961 WP_158190625.1 peptidoglycan amidohydrolase family protein -
  GQS62_RS04675 (GQS62_04670) - 907354..907767 (+) 414 WP_158190626.1 hypothetical protein -
  GQS62_RS04680 (GQS62_04675) - 907771..909600 (+) 1830 WP_158190627.1 phage baseplate upper protein -
  GQS62_RS04685 (GQS62_04680) - 909612..910352 (+) 741 WP_158190563.1 hypothetical protein -
  GQS62_RS04690 (GQS62_04685) - 910352..910693 (+) 342 WP_158190628.1 DUF2977 domain-containing protein -
  GQS62_RS04695 (GQS62_04690) - 910690..910842 (+) 153 WP_158190629.1 XkdX family protein -
  GQS62_RS04700 (GQS62_04695) - 910881..911282 (+) 402 WP_158190630.1 phage holin family protein -
  GQS62_RS04705 (GQS62_04700) - 911266..912516 (+) 1251 WP_158190631.1 GH25 family lysozyme -
  GQS62_RS04710 (GQS62_04705) - 913072..913392 (+) 321 WP_069825307.1 acetyl-CoA carboxylase -
  GQS62_RS04715 (GQS62_04710) - 913848..915224 (+) 1377 WP_158190632.1 amino acid permease -

Sequence

Protein


Download         Length: 171 a.a.        Molecular weight: 19288.89 Da        Isoelectric Point: 4.9163

>NTDB_id=409552 GQS62_RS04535 WP_158190603.1 885934..886449(+) (ssb) [Pediococcus pentosaceus strain GDIAS001]
MINRTVLVGRLTRDPELKYTNSGRAVASFNIAVNRQFTNSQGEREADFINCVIWNKTAENFCNFTRKGSLVGIDGRIQTR
SYENQQGTRVYVTEVVAENFSLLESKNSSQIQKDGEHSNYQPQNSIPNQQNSQNDNLQPQNNSSNGQYGNYSNPNDPFSS
APQINDDDLPF

Nucleotide


Download         Length: 516 bp        

>NTDB_id=409552 GQS62_RS04535 WP_158190603.1 885934..886449(+) (ssb) [Pediococcus pentosaceus strain GDIAS001]
ATGATTAATCGAACTGTTTTAGTTGGCCGGTTGACGCGTGATCCAGAATTGAAATACACCAACAGTGGAAGGGCGGTAGC
TAGCTTTAACATAGCCGTTAACCGTCAATTTACAAATTCACAGGGCGAGCGCGAAGCGGACTTTATTAACTGCGTTATTT
GGAATAAAACGGCGGAAAACTTCTGTAACTTCACTCGCAAAGGGTCACTGGTTGGAATTGATGGACGAATTCAAACTCGA
TCATACGAAAATCAACAAGGAACACGAGTTTACGTTACTGAGGTCGTAGCTGAGAATTTCTCGCTACTTGAATCTAAAAA
CAGTAGTCAAATTCAAAAAGATGGCGAACATTCAAATTATCAACCACAGAATAGTATTCCAAATCAACAAAACAGCCAAA
ATGACAATTTACAACCACAAAATAACAGCTCAAATGGTCAATATGGAAATTACAGCAATCCTAATGACCCGTTTAGTAGT
GCACCACAGATTAATGATGACGATTTGCCGTTCTAG

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

59.777

100

0.626
  ssbA Bacillus subtilis subsp. subtilis str. 168

53.409

100

0.55

Multiple sequence alignment