Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   PSL001_RS00205 Genome accession   NZ_CP039378
Coordinates   32728..33252 (-) Length   174 a.a.
NCBI ID   WP_146419232.1    Uniprot ID   -
Organism   Pediococcus pentosaceus strain SL001     
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 818..49663 32728..33252 within 0


Gene organization within MGE regions


Location: 818..49663
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PSL001_RS00020 (PSL001_00020) lexA 818..1447 (+) 630 WP_002833597.1 transcriptional repressor LexA -
  PSL001_RS00025 (PSL001_00025) - 1526..2125 (+) 600 WP_060743702.1 hypothetical protein -
  PSL001_RS00030 (PSL001_00030) - 2165..3331 (-) 1167 WP_128886914.1 hydroxymethylglutaryl-CoA synthase -
  PSL001_RS00035 (PSL001_00035) - 3491..4867 (-) 1377 WP_128886915.1 amino acid permease -
  PSL001_RS00040 (PSL001_00040) - 6048..7190 (-) 1143 WP_146419204.1 N-acetylmuramoyl-L-alanine amidase -
  PSL001_RS00045 (PSL001_00045) - 7174..7425 (-) 252 WP_146419205.1 phage holin -
  PSL001_RS00050 (PSL001_00050) - 7425..7715 (-) 291 WP_233605431.1 hypothetical protein -
  PSL001_RS00055 (PSL001_00055) - 7759..7905 (-) 147 WP_146419206.1 XkdX family protein -
  PSL001_RS00060 (PSL001_00060) - 7905..8213 (-) 309 WP_146419207.1 DUF2977 domain-containing protein -
  PSL001_RS00065 (PSL001_00065) - 8225..8992 (-) 768 WP_146419208.1 hypothetical protein -
  PSL001_RS00070 (PSL001_00070) - 8982..10811 (-) 1830 WP_146419209.1 metallophosphoesterase -
  PSL001_RS00075 (PSL001_00075) - 10811..11086 (-) 276 WP_146419210.1 hypothetical protein -
  PSL001_RS00080 (PSL001_00080) - 11076..11402 (-) 327 WP_146419211.1 hypothetical protein -
  PSL001_RS00085 (PSL001_00085) - 11392..12528 (-) 1137 WP_146419212.1 phage tail protein -
  PSL001_RS00090 (PSL001_00090) - 12537..13382 (-) 846 WP_233605432.1 phage tail domain-containing protein -
  PSL001_RS00095 (PSL001_00095) - 13387..18654 (-) 5268 WP_146419213.1 tape measure protein -
  PSL001_RS00100 (PSL001_00100) - 18658..19290 (-) 633 WP_146419214.1 Gp15 family bacteriophage protein -
  PSL001_RS00105 (PSL001_00105) - 19297..19734 (-) 438 WP_146419215.1 hypothetical protein -
  PSL001_RS00110 (PSL001_00110) - 19808..20383 (-) 576 WP_233605433.1 capsid protein -
  PSL001_RS00115 (PSL001_00115) - 20387..20782 (-) 396 WP_146419216.1 minor capsid protein -
  PSL001_RS00120 (PSL001_00120) - 20769..21119 (-) 351 WP_146419217.1 minor capsid protein -
  PSL001_RS00125 (PSL001_00125) - 21119..21466 (-) 348 WP_146419218.1 putative minor capsid protein -
  PSL001_RS00130 (PSL001_00130) - 21463..21879 (-) 417 WP_146419219.1 hypothetical protein -
  PSL001_RS00135 (PSL001_00135) - 21978..22889 (-) 912 WP_146419220.1 hypothetical protein -
  PSL001_RS00140 (PSL001_00140) - 22902..23459 (-) 558 WP_158632712.1 phage scaffolding protein -
  PSL001_RS00145 (PSL001_00145) - 23559..24692 (-) 1134 WP_146419222.1 phage minor capsid protein -
  PSL001_RS00150 (PSL001_00150) - 24689..26236 (-) 1548 WP_199753527.1 phage portal protein -
  PSL001_RS00155 (PSL001_00155) - 26239..27603 (-) 1365 WP_233605461.1 PBSX family phage terminase large subunit -
  PSL001_RS00160 (PSL001_00160) - 27609..28109 (-) 501 WP_146419224.1 terminase small subunit -
  PSL001_RS00165 (PSL001_00165) - 28261..29370 (-) 1110 WP_146419225.1 hypothetical protein -
  PSL001_RS00175 (PSL001_00175) - 29737..30180 (-) 444 WP_146419226.1 hypothetical protein -
  PSL001_RS09670 - 30552..30695 (-) 144 WP_158632713.1 hypothetical protein -
  PSL001_RS00180 (PSL001_00180) - 30871..31107 (-) 237 WP_146419227.1 hypothetical protein -
  PSL001_RS00185 (PSL001_00185) - 31100..31345 (-) 246 WP_146419228.1 hypothetical protein -
  PSL001_RS00190 (PSL001_00190) - 31338..31871 (-) 534 WP_146419229.1 DUF1642 domain-containing protein -
  PSL001_RS00195 (PSL001_00195) - 31871..32233 (-) 363 WP_146419230.1 hypothetical protein -
  PSL001_RS00200 (PSL001_00200) - 32399..32716 (-) 318 WP_146419231.1 hypothetical protein -
  PSL001_RS00205 (PSL001_00205) ssb 32728..33252 (-) 525 WP_146419232.1 single-stranded DNA-binding protein Machinery gene
  PSL001_RS00210 (PSL001_00210) - 33272..33532 (-) 261 WP_146419233.1 hypothetical protein -
  PSL001_RS00215 (PSL001_00215) - 33501..34202 (-) 702 WP_146419234.1 putative HNHc nuclease -
  PSL001_RS00220 (PSL001_00220) - 34206..35078 (-) 873 WP_146419235.1 helix-turn-helix domain-containing protein -
  PSL001_RS00225 (PSL001_00225) - 35085..35852 (-) 768 WP_146419236.1 ERF family protein -
  PSL001_RS00230 (PSL001_00230) - 35852..36745 (-) 894 WP_146419237.1 DUF1351 domain-containing protein -
  PSL001_RS00235 (PSL001_00235) - 37104..37349 (-) 246 WP_146419238.1 hypothetical protein -
  PSL001_RS00240 (PSL001_00240) - 37350..37808 (-) 459 WP_233605434.1 helix-turn-helix domain-containing protein -
  PSL001_RS00245 (PSL001_00245) - 37882..38103 (-) 222 WP_146419239.1 hypothetical protein -
  PSL001_RS00250 (PSL001_00250) - 38172..38459 (+) 288 WP_146419240.1 hypothetical protein -
  PSL001_RS00255 (PSL001_00255) - 38586..38807 (-) 222 WP_146419241.1 helix-turn-helix transcriptional regulator -
  PSL001_RS00260 (PSL001_00260) - 38951..39274 (+) 324 WP_146419242.1 helix-turn-helix transcriptional regulator -
  PSL001_RS00265 (PSL001_00265) - 39281..39673 (+) 393 WP_146419243.1 ImmA/IrrE family metallo-endopeptidase -
  PSL001_RS09800 - 39752..40216 (+) 465 WP_233605435.1 hypothetical protein -
  PSL001_RS00275 (PSL001_00275) - 40292..41119 (+) 828 WP_158632714.1 DUF4393 domain-containing protein -
  PSL001_RS00280 (PSL001_00280) - 41416..41664 (+) 249 WP_146419245.1 hypothetical protein -
  PSL001_RS00285 (PSL001_00285) - 41681..42934 (+) 1254 WP_233605436.1 site-specific integrase -
  PSL001_RS00290 (PSL001_00290) fabI 43073..43831 (-) 759 WP_060743755.1 enoyl-ACP reductase FabI -
  PSL001_RS00295 (PSL001_00295) accA 43848..44615 (-) 768 WP_002833592.1 carboxyltransferase subunit alpha -
  PSL001_RS00300 (PSL001_00300) - 44629..45459 (-) 831 WP_002833591.1 acetyl-CoA carboxylase carboxyltransferase subunit beta -
  PSL001_RS00305 (PSL001_00305) - 45449..46816 (-) 1368 WP_029257879.1 acetyl-CoA carboxylase biotin carboxylase subunit -
  PSL001_RS00310 (PSL001_00310) - 46834..47247 (-) 414 WP_011673308.1 3-hydroxyacyl-ACP dehydratase FabZ family protein -
  PSL001_RS00315 (PSL001_00315) - 47247..47684 (-) 438 WP_060743756.1 biotin/lipoyl-containing protein -
  PSL001_RS00320 (PSL001_00320) fabF 47690..48916 (-) 1227 WP_060743707.1 beta-ketoacyl-ACP synthase II -
  PSL001_RS00325 (PSL001_00325) fabG 48935..49663 (-) 729 WP_011673305.1 3-oxoacyl-ACP reductase FabG -

Sequence

Protein


Download         Length: 174 a.a.        Molecular weight: 19585.26 Da        Isoelectric Point: 5.2149

>NTDB_id=358281 PSL001_RS00205 WP_146419232.1 32728..33252(-) (ssb) [Pediococcus pentosaceus strain SL001]
MINRTVLVGRLTRDPELKYTNSGRAVASFNIAVNRQFTNSQGEREADFINCVIWNKTAENFCNFTRKGSLVGIDGRIQTR
SYENQQGTRIFVTEVVAENFSLLESKNSNQIQKDGKHSNYQPQNSIPNQQNSQNDNLQPQNNSSNGQYGNYSNPNDPFTN
GGQGIDINDDDLPF

Nucleotide


Download         Length: 525 bp        

>NTDB_id=358281 PSL001_RS00205 WP_146419232.1 32728..33252(-) (ssb) [Pediococcus pentosaceus strain SL001]
ATGATTAATCGAACTGTTTTAGTTGGCCGGTTGACGCGTGATCCAGAATTGAAATACACCAACAGTGGAAGGGCGGTAGC
TAGCTTTAACATAGCCGTTAACCGTCAATTTACAAATTCACAGGGCGAGCGCGAAGCGGACTTTATTAACTGCGTTATTT
GGAATAAAACGGCGGAAAACTTCTGTAACTTCACTCGCAAAGGGTCACTGGTTGGAATTGATGGACGAATTCAAACTCGA
TCATACGAAAATCAACAAGGAACACGAATTTTTGTTACTGAGGTCGTAGCGGAGAACTTCTCACTACTTGAGTCCAAAAA
CAGTAATCAAATTCAAAAAGATGGCAAACATTCAAATTATCAACCACAGAATAGTATTCCAAATCAACAAAACAGCCAAA
ATGACAATTTACAACCACAAAATAACAGCTCAAATGGTCAATATGGAAATTACAGCAATCCTAATGACCCATTCACTAAT
GGCGGCCAAGGAATTGATATTAATGACGATGATTTACCGTTTTAG

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

60.894

100

0.626
  ssbA Bacillus subtilis subsp. subtilis str. 168

55.682

100

0.563

Multiple sequence alignment