Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   AB3212_RS01195 Genome accession   NZ_OZ061592
Coordinates   242648..243082 (-) Length   144 a.a.
NCBI ID   WP_367364916.1    Uniprot ID   -
Organism   Pediococcus parvulus isolate Pediococcus parvulus CIRM-BIA2501     
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 204645..253973 242648..243082 within 0


Gene organization within MGE regions


Location: 204645..253973
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AB3212_RS00990 - 204645..206402 (-) 1758 WP_260275082.1 ABC transporter ATP-binding protein -
  AB3212_RS00995 - 206428..208191 (-) 1764 WP_057782646.1 ABC transporter ATP-binding protein -
  AB3212_RS01000 - 208302..208529 (-) 228 WP_057782644.1 YneF family protein -
  AB3212_RS01005 - 208690..208941 (-) 252 WP_057782641.1 DUF896 domain-containing protein -
  AB3212_RS01010 lexA 209079..209708 (+) 630 WP_057782639.1 transcriptional repressor LexA -
  AB3212_RS01015 - 209748..210878 (-) 1131 WP_367364888.1 glycerate kinase -
  AB3212_RS01020 - 210887..211129 (-) 243 WP_157077587.1 hypothetical protein -
  AB3212_RS01025 - 211272..211907 (+) 636 WP_057782633.1 hypothetical protein -
  AB3212_RS01030 - 211958..213124 (-) 1167 WP_367364889.1 hydroxymethylglutaryl-CoA synthase -
  AB3212_RS01035 - 213353..214783 (+) 1431 WP_057782631.1 DHA2 family efflux MFS transporter permease subunit -
  AB3212_RS01040 - 215139..216464 (-) 1326 WP_367364890.1 GH25 family lysozyme -
  AB3212_RS01045 - 216476..216760 (-) 285 WP_367364891.1 phage holin -
  AB3212_RS01050 - 217090..217389 (-) 300 WP_367364892.1 hypothetical protein -
  AB3212_RS01055 - 217429..217650 (-) 222 WP_367364893.1 hypothetical protein -
  AB3212_RS01060 - 217643..217876 (-) 234 WP_367364894.1 hypothetical protein -
  AB3212_RS01065 - 217876..221448 (-) 3573 WP_367364895.1 hypothetical protein -
  AB3212_RS01070 - 221448..223991 (-) 2544 WP_367364896.1 phage tail spike protein -
  AB3212_RS01075 - 224008..225756 (-) 1749 WP_367364897.1 distal tail protein Dit -
  AB3212_RS01080 - 225753..230345 (-) 4593 WP_367364898.1 phage tail tape measure protein -
  AB3212_RS01085 - 230368..230505 (-) 138 WP_323708947.1 hypothetical protein -
  AB3212_RS01090 - 230583..230927 (-) 345 WP_323708948.1 phage tail assembly chaperone G -
  AB3212_RS01095 - 231045..231668 (-) 624 WP_367364899.1 major tail protein -
  AB3212_RS01100 - 231684..232094 (-) 411 WP_323708950.1 hypothetical protein -
  AB3212_RS01105 - 232091..232495 (-) 405 WP_323708951.1 hypothetical protein -
  AB3212_RS01110 - 232492..232878 (-) 387 WP_367364900.1 phage head-tail adapter protein -
  AB3212_RS01115 - 232871..233158 (-) 288 WP_367364901.1 phage gp6-like head-tail connector protein -
  AB3212_RS01120 - 233170..234489 (-) 1320 WP_367364902.1 phage major capsid protein -
  AB3212_RS01125 - 234512..235273 (-) 762 WP_367365413.1 head maturation protease, ClpP-related -
  AB3212_RS01130 - 235251..236405 (-) 1155 WP_367364903.1 phage portal protein -
  AB3212_RS01135 - 236429..238111 (-) 1683 WP_367364904.1 terminase TerL endonuclease subunit -
  AB3212_RS01140 - 238108..238440 (-) 333 WP_367364905.1 P27 family phage terminase small subunit -
  AB3212_RS01145 - 238557..238781 (-) 225 WP_367364906.1 hypothetical protein -
  AB3212_RS01150 - 238909..239235 (-) 327 WP_367364907.1 HNH endonuclease -
  AB3212_RS01155 - 239238..239501 (-) 264 WP_367364908.1 hypothetical protein -
  AB3212_RS01160 - 239902..240291 (-) 390 WP_367364909.1 ArpU family phage packaging/lysis transcriptional regulator -
  AB3212_RS01165 - 240381..240644 (-) 264 WP_367364910.1 hypothetical protein -
  AB3212_RS01170 - 240645..240881 (-) 237 WP_367364911.1 hypothetical protein -
  AB3212_RS01175 - 240899..241102 (-) 204 WP_367364912.1 hypothetical protein -
  AB3212_RS01180 - 241099..241554 (-) 456 WP_367364913.1 DUF1064 domain-containing protein -
  AB3212_RS01185 - 241551..241757 (-) 207 WP_367364914.1 helix-turn-helix domain-containing protein -
  AB3212_RS01190 - 241747..242631 (-) 885 WP_367364915.1 DnaD domain protein -
  AB3212_RS01195 ssb 242648..243082 (-) 435 WP_367364916.1 single-stranded DNA-binding protein Machinery gene
  AB3212_RS01200 - 243093..244028 (-) 936 WP_367365414.1 recombinase RecT -
  AB3212_RS01205 - 244036..244923 (-) 888 WP_367364917.1 YqaJ viral recombinase family protein -
  AB3212_RS01210 - 244907..245038 (-) 132 WP_323708969.1 hypothetical protein -
  AB3212_RS01215 - 245190..245477 (+) 288 WP_062909649.1 hypothetical protein -
  AB3212_RS01220 - 245457..245753 (-) 297 WP_367364918.1 hypothetical protein -
  AB3212_RS01225 - 245833..245994 (-) 162 WP_367364919.1 hypothetical protein -
  AB3212_RS01230 - 245997..246299 (-) 303 WP_367364920.1 DUF771 domain-containing protein -
  AB3212_RS01235 - 246280..247026 (-) 747 WP_367364921.1 phage regulatory protein/antirepressor Ant -
  AB3212_RS01240 - 247028..247237 (-) 210 WP_367364922.1 XRE family transcriptional regulator -
  AB3212_RS01245 - 247503..247838 (+) 336 WP_367364923.1 helix-turn-helix domain-containing protein -
  AB3212_RS01250 - 247848..248126 (+) 279 WP_367364924.1 hypothetical protein -
  AB3212_RS01255 - 248148..248456 (+) 309 WP_323708980.1 zinc-ribbon domain-containing protein -
  AB3212_RS01260 - 248510..249739 (+) 1230 WP_367364925.1 exonuclease domain-containing protein -
  AB3212_RS01265 - 249826..250377 (+) 552 WP_367364926.1 DUF5067 domain-containing protein -
  AB3212_RS01270 - 250464..251573 (+) 1110 WP_367364927.1 hypothetical protein -
  AB3212_RS01275 - 251591..251782 (-) 192 WP_367364928.1 hypothetical protein -
  AB3212_RS01280 - 251909..252592 (+) 684 WP_367364929.1 hypothetical protein -
  AB3212_RS01285 - 252846..253973 (+) 1128 WP_367364930.1 tyrosine-type recombinase/integrase -

Sequence

Protein


Download         Length: 144 a.a.        Molecular weight: 16167.88 Da        Isoelectric Point: 5.2403

>NTDB_id=1166342 AB3212_RS01195 WP_367364916.1 242648..243082(-) (ssb) [Pediococcus parvulus isolate Pediococcus parvulus CIRM-BIA2501]
MINRTVLIGRLTKEPDLRYTNSGTAVASFTLAVNRQFTNSDGEREADFINCVIWRKASENFANFTHKGSLVGIDGRIQTR
SYENQQGNKVYVTEVVVENFSLLEPKSHSDQSPQDSKKKTPPANQDPFASNGKQIDIDEDDLPF

Nucleotide


Download         Length: 435 bp        

>NTDB_id=1166342 AB3212_RS01195 WP_367364916.1 242648..243082(-) (ssb) [Pediococcus parvulus isolate Pediococcus parvulus CIRM-BIA2501]
ATGATAAATCGAACAGTTCTTATTGGACGCTTAACCAAGGAGCCAGATTTACGGTACACCAATAGTGGTACTGCAGTTGC
TAGTTTTACATTGGCAGTCAATCGCCAATTCACTAACTCTGATGGTGAACGTGAAGCTGATTTCATTAACTGCGTGATCT
GGCGAAAGGCATCCGAGAACTTTGCTAACTTTACCCATAAAGGTTCATTGGTTGGAATTGATGGACGGATTCAAACCCGT
TCTTACGAAAACCAACAAGGCAACAAAGTTTATGTAACGGAGGTTGTCGTTGAAAACTTCTCGTTGCTGGAACCCAAGTC
GCATTCTGACCAAAGCCCACAAGATAGTAAGAAAAAAACTCCGCCAGCTAATCAAGATCCATTTGCCAGTAACGGTAAGC
AAATTGATATTGATGAAGACGACTTGCCATTCTAA

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

59.649

100

0.708
  ssbA Bacillus subtilis subsp. subtilis str. 168

52.907

100

0.632
  ssbB Bacillus subtilis subsp. subtilis str. 168

60.377

73.611

0.444
  ssbB/cilA Streptococcus mitis NCTC 12261

40.278

100

0.403
  ssbB/cilA Streptococcus pneumoniae TIGR4

40.278

100

0.403
  ssbB Streptococcus sobrinus strain NIDR 6715-7

40.278

100

0.403
  ssbB/cilA Streptococcus pneumoniae Rx1

39.583

100

0.396
  ssbB/cilA Streptococcus pneumoniae D39

39.583

100

0.396
  ssbB/cilA Streptococcus pneumoniae R6

39.583

100

0.396
  ssbB/cilA Streptococcus mitis SK321

39.583

100

0.396
  ssbA Streptococcus mutans UA159

36.111

100

0.361

Multiple sequence alignment