Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   PVS71_RS07900 Genome accession   NZ_CP118436
Coordinates   1600672..1601118 (-) Length   148 a.a.
NCBI ID   WP_274803643.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain GLP06     
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 1565792..1611739 1600672..1601118 within 0


Gene organization within MGE regions


Location: 1565792..1611739
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PVS71_RS07690 (PVS71_07690) dnaX 1565792..1567528 (-) 1737 WP_053906345.1 DNA polymerase III subunit gamma/tau -
  PVS71_RS07700 (PVS71_07700) tadA 1567743..1568228 (-) 486 WP_005916020.1 tRNA adenosine(34) deaminase TadA -
  PVS71_RS07705 (PVS71_07705) - 1568221..1568826 (-) 606 WP_002832340.1 class I SAM-dependent methyltransferase -
  PVS71_RS07710 (PVS71_07710) nrdH 1569048..1569278 (+) 231 WP_002832341.1 glutaredoxin-like protein NrdH -
  PVS71_RS07715 (PVS71_07715) nrdE 1569371..1571536 (+) 2166 WP_053906347.1 class 1b ribonucleoside-diphosphate reductase subunit alpha -
  PVS71_RS07720 (PVS71_07720) nrdF 1571555..1572508 (+) 954 WP_002832344.1 class 1b ribonucleoside-diphosphate reductase subunit beta -
  PVS71_RS07725 (PVS71_07725) - 1572958..1573374 (-) 417 WP_274803615.1 protein-export chaperone SecB -
  PVS71_RS07730 (PVS71_07730) - 1573375..1573704 (-) 330 WP_274803616.1 hypothetical protein -
  PVS71_RS07735 (PVS71_07735) - 1573728..1574288 (-) 561 WP_274803617.1 hypothetical protein -
  PVS71_RS07740 (PVS71_07740) - 1574417..1575538 (-) 1122 WP_274803618.1 peptidoglycan recognition family protein -
  PVS71_RS07745 (PVS71_07745) - 1575522..1575776 (-) 255 WP_159219753.1 phage holin -
  PVS71_RS07750 (PVS71_07750) - 1576110..1576262 (-) 153 WP_274803619.1 XkdX family protein -
  PVS71_RS07755 (PVS71_07755) - 1576259..1576618 (-) 360 WP_274803620.1 hypothetical protein -
  PVS71_RS07760 (PVS71_07760) - 1576632..1577354 (-) 723 WP_274803621.1 hypothetical protein -
  PVS71_RS07765 (PVS71_07765) - 1577370..1579211 (-) 1842 WP_274803622.1 BppU family phage baseplate upper protein -
  PVS71_RS07770 (PVS71_07770) - 1579211..1579534 (-) 324 WP_152688873.1 hypothetical protein -
  PVS71_RS07775 (PVS71_07775) - 1579537..1579788 (-) 252 WP_274803623.1 hypothetical protein -
  PVS71_RS07780 (PVS71_07780) - 1579781..1580896 (-) 1116 WP_274803624.1 prophage endopeptidase tail family protein -
  PVS71_RS07785 (PVS71_07785) - 1580909..1581733 (-) 825 WP_274803625.1 phage tail domain-containing protein -
  PVS71_RS07790 (PVS71_07790) - 1581733..1587294 (-) 5562 WP_274803626.1 tape measure protein -
  PVS71_RS07795 (PVS71_07795) - 1587328..1587948 (-) 621 WP_274803627.1 Gp15 family bacteriophage protein -
  PVS71_RS07800 (PVS71_07800) - 1587958..1588350 (-) 393 WP_065124790.1 hypothetical protein -
  PVS71_RS07805 (PVS71_07805) - 1588426..1588893 (-) 468 WP_274803628.1 Ig-like domain-containing protein -
  PVS71_RS07810 (PVS71_07810) - 1588967..1589503 (-) 537 WP_274803629.1 capsid protein -
  PVS71_RS07815 (PVS71_07815) - 1589516..1589911 (-) 396 WP_274803630.1 minor capsid protein -
  PVS71_RS07820 (PVS71_07820) - 1589911..1590255 (-) 345 WP_274803631.1 minor capsid protein -
  PVS71_RS07825 (PVS71_07825) - 1590255..1590605 (-) 351 WP_159208612.1 putative minor capsid protein -
  PVS71_RS07830 (PVS71_07830) - 1590602..1591018 (-) 417 WP_274803632.1 hypothetical protein -
  PVS71_RS07835 (PVS71_07835) - 1591092..1591961 (-) 870 WP_128472038.1 capsid protein -
  PVS71_RS07840 (PVS71_07840) - 1591974..1592546 (-) 573 WP_274803633.1 phage scaffolding protein -
  PVS71_RS07845 (PVS71_07845) - 1592645..1593778 (-) 1134 WP_274803634.1 phage minor capsid protein -
  PVS71_RS07850 (PVS71_07850) - 1593775..1595304 (-) 1530 WP_274803635.1 phage portal protein -
  PVS71_RS07855 (PVS71_07855) - 1595314..1596627 (-) 1314 WP_274803636.1 PBSX family phage terminase large subunit -
  PVS71_RS07860 (PVS71_07860) - 1596611..1597300 (-) 690 WP_274803637.1 terminase -
  PVS71_RS07865 (PVS71_07865) - 1597374..1597937 (-) 564 WP_274803638.1 hypothetical protein -
  PVS71_RS07880 (PVS71_07880) - 1598765..1599199 (-) 435 WP_274803639.1 ArpU family phage packaging/lysis transcriptional regulator -
  PVS71_RS07885 (PVS71_07885) - 1599462..1599695 (-) 234 WP_274803640.1 hypothetical protein -
  PVS71_RS07890 (PVS71_07890) - 1599832..1600431 (-) 600 WP_274803641.1 hypothetical protein -
  PVS71_RS07895 (PVS71_07895) - 1600436..1600660 (-) 225 WP_274803642.1 hypothetical protein -
  PVS71_RS07900 (PVS71_07900) ssb 1600672..1601118 (-) 447 WP_274803643.1 single-stranded DNA-binding protein Machinery gene
  PVS71_RS07905 (PVS71_07905) - 1601111..1601320 (-) 210 WP_274803644.1 hypothetical protein -
  PVS71_RS07910 (PVS71_07910) - 1601313..1601675 (-) 363 WP_274803645.1 hypothetical protein -
  PVS71_RS07915 (PVS71_07915) - 1601617..1602342 (-) 726 WP_274803646.1 putative HNHc nuclease -
  PVS71_RS07920 (PVS71_07920) - 1602347..1603183 (-) 837 WP_274803647.1 helix-turn-helix domain-containing protein -
  PVS71_RS07925 (PVS71_07925) - 1603176..1604012 (-) 837 WP_274803648.1 ERF family protein -
  PVS71_RS07930 (PVS71_07930) - 1604015..1604908 (-) 894 WP_274803649.1 DUF1351 domain-containing protein -
  PVS71_RS07935 (PVS71_07935) - 1605001..1605144 (-) 144 WP_274803650.1 hypothetical protein -
  PVS71_RS07940 (PVS71_07940) - 1605155..1605427 (-) 273 WP_128472030.1 hypothetical protein -
  PVS71_RS07945 (PVS71_07945) - 1605409..1605876 (-) 468 WP_128472029.1 helix-turn-helix transcriptional regulator -
  PVS71_RS07950 (PVS71_07950) - 1605959..1606174 (-) 216 WP_128472028.1 hypothetical protein -
  PVS71_RS07955 (PVS71_07955) - 1606209..1606430 (-) 222 WP_128472027.1 helix-turn-helix transcriptional regulator -
  PVS71_RS07960 (PVS71_07960) - 1606597..1606971 (+) 375 WP_128472026.1 helix-turn-helix transcriptional regulator -
  PVS71_RS07965 (PVS71_07965) - 1606983..1607387 (+) 405 WP_128472025.1 ImmA/IrrE family metallo-endopeptidase -
  PVS71_RS07970 (PVS71_07970) - 1607414..1608331 (+) 918 WP_159208654.1 SHOCT domain-containing protein -
  PVS71_RS07975 (PVS71_07975) - 1608538..1609080 (+) 543 WP_274803651.1 CvpA family protein -
  PVS71_RS07980 (PVS71_07980) - 1609166..1609396 (-) 231 WP_274803652.1 2-hydroxymuconic semialdehyde hydrolase -
  PVS71_RS07985 (PVS71_07985) - 1609410..1610183 (+) 774 WP_274803653.1 hypothetical protein -
  PVS71_RS07990 (PVS71_07990) - 1610654..1611739 (+) 1086 WP_274803654.1 site-specific integrase -

Sequence

Protein


Download         Length: 148 a.a.        Molecular weight: 16633.22 Da        Isoelectric Point: 5.1660

>NTDB_id=792514 PVS71_RS07900 WP_274803643.1 1600672..1601118(-) (ssb) [Pediococcus acidilactici strain GLP06]
MINRTVLVGRLTKDPEIRYTQSGTAVANFTMAVNRQFTNANGEREADFIGCIIWRKAAENFCNYTHKGSLVGIDGRIQTS
SYEKEGQRVYSTQVVVDSFSLLEPKQQSQQRGQQSNASDALHDNFGQPTNNYSQNNNDFGIDDNDLPF

Nucleotide


Download         Length: 447 bp        

>NTDB_id=792514 PVS71_RS07900 WP_274803643.1 1600672..1601118(-) (ssb) [Pediococcus acidilactici strain GLP06]
ATGATTAATCGAACCGTATTAGTTGGCCGGCTCACCAAAGATCCAGAAATCCGTTATACCCAATCAGGGACGGCGGTGGC
CAACTTTACCATGGCTGTGAACCGGCAGTTTACCAACGCTAATGGCGAGCGAGAAGCGGACTTTATTGGTTGTATCATTT
GGCGAAAGGCGGCCGAAAACTTCTGTAATTACACGCATAAAGGATCATTGGTCGGGATTGACGGTCGGATTCAAACGAGT
TCGTACGAGAAGGAAGGTCAGCGTGTTTACTCAACCCAGGTGGTTGTAGATAGCTTCTCGTTGTTGGAACCGAAACAACA
GAGCCAACAACGTGGCCAGCAATCTAACGCTAGCGATGCTTTGCATGACAATTTCGGCCAACCTACTAACAATTACAGCC
AGAATAATAACGATTTCGGCATTGACGATAACGATTTGCCGTTTTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(2-101)


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

54.706

100

0.628
  ssbA Bacillus subtilis subsp. subtilis str. 168

64.151

71.622

0.459
  ssbB Bacillus subtilis subsp. subtilis str. 168

56.364

74.324

0.419
  ssbB Streptococcus sobrinus strain NIDR 6715-7

39.189

100

0.392
  ssb Vibrio cholerae strain A1552

33.14

100

0.385
  ssbB/cilA Streptococcus pneumoniae TIGR4

38.514

100

0.385
  ssbB/cilA Streptococcus mitis NCTC 12261

38.514

100

0.385
  ssbB/cilA Streptococcus pneumoniae Rx1

37.838

100

0.378
  ssbB/cilA Streptococcus pneumoniae D39

37.838

100

0.378
  ssbB/cilA Streptococcus pneumoniae R6

37.838

100

0.378
  ssbB/cilA Streptococcus mitis SK321

37.838

100

0.378