Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   ID874_RS06035 Genome accession   NZ_CP061715
Coordinates   1244410..1244835 (-) Length   141 a.a.
NCBI ID   WP_024863114.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain HN9     
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 1215486..1253564 1244410..1244835 within 0


Gene organization within MGE regions


Location: 1215486..1253564
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ID874_RS05855 (ID874_05855) - 1215486..1216187 (-) 702 WP_159214808.1 type II toxin-antitoxin system antitoxin SocA domain-containing protein -
  ID874_RS05860 (ID874_05860) - 1216233..1216859 (-) 627 WP_159214809.1 hypothetical protein -
  ID874_RS05865 (ID874_05865) - 1216969..1218096 (-) 1128 WP_193223186.1 peptidoglycan recognition family protein -
  ID874_RS05870 (ID874_05870) - 1218080..1218619 (-) 540 WP_193223187.1 phage holin family protein -
  ID874_RS05875 (ID874_05875) - 1218654..1221737 (-) 3084 WP_193223188.1 phage baseplate upper protein -
  ID874_RS05880 (ID874_05880) - 1221737..1222066 (-) 330 WP_193223189.1 hypothetical protein -
  ID874_RS05885 (ID874_05885) - 1222050..1225010 (-) 2961 WP_193223190.1 phage tail protein -
  ID874_RS05890 (ID874_05890) - 1225010..1225771 (-) 762 WP_193223191.1 phage tail protein -
  ID874_RS05895 (ID874_05895) - 1225771..1228401 (-) 2631 WP_193223192.1 phage tail tape measure protein -
  ID874_RS05900 (ID874_05900) - 1228385..1228702 (-) 318 WP_008842042.1 hypothetical protein -
  ID874_RS05905 (ID874_05905) - 1228801..1229136 (-) 336 WP_193223193.1 tail assembly chaperone -
  ID874_RS05910 (ID874_05910) - 1229199..1229660 (-) 462 WP_098040733.1 Ig-like domain-containing protein -
  ID874_RS05915 (ID874_05915) - 1229669..1229944 (-) 276 WP_098040732.1 hypothetical protein -
  ID874_RS05920 (ID874_05920) - 1230022..1230627 (-) 606 WP_098040731.1 phage major tail protein, TP901-1 family -
  ID874_RS05925 (ID874_05925) - 1230648..1231049 (-) 402 WP_128472109.1 hypothetical protein -
  ID874_RS05930 (ID874_05930) - 1231050..1231391 (-) 342 WP_128472108.1 HK97-gp10 family putative phage morphogenesis protein -
  ID874_RS05935 (ID874_05935) - 1231384..1231689 (-) 306 WP_193223194.1 hypothetical protein -
  ID874_RS05940 (ID874_05940) - 1231694..1232068 (-) 375 WP_193223195.1 phage head-tail connector protein -
  ID874_RS05945 (ID874_05945) - 1232080..1232346 (-) 267 WP_128472106.1 Ig-like domain-containing protein -
  ID874_RS05950 (ID874_05950) - 1232364..1233182 (-) 819 WP_075139806.1 N4-gp56 family major capsid protein -
  ID874_RS05955 (ID874_05955) - 1233182..1233898 (-) 717 WP_058121207.1 DUF4355 domain-containing protein -
  ID874_RS05960 (ID874_05960) - 1234001..1234984 (-) 984 WP_176582124.1 minor capsid protein -
  ID874_RS05965 (ID874_05965) - 1234953..1236287 (-) 1335 WP_244138848.1 phage portal protein -
  ID874_RS05970 (ID874_05970) - 1236369..1237715 (-) 1347 WP_193223196.1 PBSX family phage terminase large subunit -
  ID874_RS05975 (ID874_05975) - 1237708..1238199 (-) 492 WP_002830732.1 terminase small subunit -
  ID874_RS05980 (ID874_05980) - 1238460..1238903 (-) 444 WP_193223197.1 hypothetical protein -
  ID874_RS05985 (ID874_05985) - 1239132..1239308 (-) 177 WP_164878527.1 hypothetical protein -
  ID874_RS05990 (ID874_05990) - 1239308..1239853 (-) 546 WP_193223198.1 DUF1642 domain-containing protein -
  ID874_RS05995 (ID874_05995) - 1240022..1240393 (-) 372 WP_193223199.1 N-acetylmuramoyl-L-alanine amidase -
  ID874_RS06000 (ID874_06000) - 1240380..1240529 (-) 150 WP_193223200.1 hypothetical protein -
  ID874_RS06005 (ID874_06005) - 1240560..1241180 (-) 621 WP_058121313.1 hypothetical protein -
  ID874_RS06010 (ID874_06010) - 1241180..1241407 (-) 228 WP_193223201.1 hypothetical protein -
  ID874_RS06015 (ID874_06015) - 1241407..1241838 (-) 432 WP_138492822.1 RusA family crossover junction endodeoxyribonuclease -
  ID874_RS06020 (ID874_06020) - 1241835..1242242 (-) 408 WP_244138895.1 hypothetical protein -
  ID874_RS06025 (ID874_06025) - 1242251..1243483 (-) 1233 WP_193223203.1 DnaB-like helicase C-terminal domain-containing protein -
  ID874_RS06030 (ID874_06030) - 1243473..1244390 (-) 918 WP_193223204.1 conserved phage C-terminal domain-containing protein -
  ID874_RS06035 (ID874_06035) ssb 1244410..1244835 (-) 426 WP_024863114.1 single-stranded DNA-binding protein Machinery gene
  ID874_RS06040 (ID874_06040) - 1244828..1245034 (-) 207 WP_024863113.1 hypothetical protein -
  ID874_RS06045 (ID874_06045) - 1245037..1245672 (-) 636 WP_002830745.1 ERF family protein -
  ID874_RS06050 (ID874_06050) - 1245682..1245894 (-) 213 WP_024863112.1 hypothetical protein -
  ID874_RS06055 (ID874_06055) - 1246043..1246324 (+) 282 WP_002830747.1 hypothetical protein -
  ID874_RS06060 (ID874_06060) - 1246321..1246542 (-) 222 WP_193223205.1 hypothetical protein -
  ID874_RS06065 (ID874_06065) - 1246642..1246971 (-) 330 WP_024863109.1 DUF771 domain-containing protein -
  ID874_RS06070 (ID874_06070) - 1246985..1247719 (-) 735 WP_193223206.1 Rha family transcriptional regulator -
  ID874_RS06075 (ID874_06075) - 1247832..1248020 (-) 189 WP_008842079.1 helix-turn-helix domain-containing protein -
  ID874_RS06080 (ID874_06080) - 1248310..1248642 (+) 333 WP_008842080.1 helix-turn-helix transcriptional regulator -
  ID874_RS06085 (ID874_06085) - 1248657..1248941 (+) 285 WP_008842081.1 hypothetical protein -
  ID874_RS06090 (ID874_06090) - 1249001..1249663 (+) 663 WP_193223207.1 hypothetical protein -
  ID874_RS10365 - 1249730..1250617 (+) 888 WP_066027433.1 DUF5067 domain-containing protein -
  ID874_RS06100 (ID874_06100) - 1250768..1250965 (+) 198 WP_193223208.1 hypothetical protein -
  ID874_RS06105 (ID874_06105) - 1251042..1251980 (+) 939 WP_193223209.1 hypothetical protein -
  ID874_RS06110 (ID874_06110) - 1251966..1252160 (-) 195 WP_060743626.1 hypothetical protein -
  ID874_RS06115 (ID874_06115) - 1252449..1253564 (+) 1116 WP_193223210.1 site-specific integrase -

Sequence

Protein


Download         Length: 141 a.a.        Molecular weight: 15678.43 Da        Isoelectric Point: 8.0263

>NTDB_id=484360 ID874_RS06035 WP_024863114.1 1244410..1244835(-) (ssb) [Pediococcus acidilactici strain HN9]
MINRTVLIGRLTKDVELRHTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFAKYTHKGSLVGIEGRIQTR
SYENQQGQRVYVTEIVADNFSLLDSKPKGNQQNNARQASTPGDPFANGGQSIDISDDQLPF

Nucleotide


Download         Length: 426 bp        

>NTDB_id=484360 ID874_RS06035 WP_024863114.1 1244410..1244835(-) (ssb) [Pediococcus acidilactici strain HN9]
ATGATTAATCGAACAGTACTAATAGGACGCCTAACTAAAGATGTTGAGCTTCGCCACACAGCTAAAGGCGATGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGCGAAGCGGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGCTAAGTATACACACAAGGGTTCGTTGGTAGGTATTGAAGGGCGGATTCAAACCCGT
TCGTACGAAAACCAACAAGGACAACGAGTATACGTTACCGAAATTGTAGCGGATAACTTCTCGTTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAACGCACGGCAAGCATCAACGCCGGGAGATCCATTCGCTAATGGCGGGCAGTCAATCGACA
TTTCAGACGATCAGCTTCCGTTCTAA

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

60.185

76.596

0.461
  ssbB Streptococcus sobrinus strain NIDR 6715-7

41.549

100

0.418
  ssbB/cilA Streptococcus mitis NCTC 12261

40.845

100

0.411
  ssbB/cilA Streptococcus pneumoniae TIGR4

40.845

100

0.411
  ssbB/cilA Streptococcus pneumoniae Rx1

40.141

100

0.404
  ssbB/cilA Streptococcus pneumoniae D39

40.141

100

0.404
  ssbB/cilA Streptococcus pneumoniae R6

40.141

100

0.404
  ssbB/cilA Streptococcus mitis SK321

40.141

100

0.404
  ssbA Streptococcus mutans UA159

36.62

100

0.369