Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   VNN47_RS06300 Genome accession   NZ_CP141709
Coordinates   1258030..1258524 (-) Length   164 a.a.
NCBI ID   WP_407350034.1    Uniprot ID   -
Organism   Lactococcus garvieae strain VC13     
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 1258030..1303938 1258030..1258524 within 0


Gene organization within MGE regions


Location: 1258030..1303938
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VNN47_RS06300 (VNN47_06275) ssb 1258030..1258524 (-) 495 WP_407350034.1 single-stranded DNA-binding protein Machinery gene
  VNN47_RS06305 (VNN47_06280) rpsF 1258562..1258855 (-) 294 WP_003133129.1 30S ribosomal protein S6 -
  VNN47_RS06310 (VNN47_06285) - 1259042..1259254 (-) 213 WP_016171080.1 hypothetical protein -
  VNN47_RS06315 (VNN47_06290) - 1259724..1261187 (+) 1464 WP_003133128.1 amino acid permease -
  VNN47_RS06320 (VNN47_06295) dnaX 1261221..1262879 (-) 1659 WP_407350035.1 DNA polymerase III subunit gamma/tau -
  VNN47_RS06325 (VNN47_06300) - 1262892..1263512 (-) 621 WP_407350036.1 phosphotransferase -
  VNN47_RS06330 (VNN47_06305) - 1263525..1264004 (-) 480 WP_014025504.1 GAF domain-containing protein -
  VNN47_RS06335 (VNN47_06310) - 1264476..1264688 (-) 213 WP_407350037.1 hypothetical protein -
  VNN47_RS06345 (VNN47_06320) - 1265741..1266514 (-) 774 WP_407350038.1 DUF3825 domain-containing protein -
  VNN47_RS06350 (VNN47_06325) - 1267088..1267789 (-) 702 WP_407350039.1 CHAP domain-containing protein -
  VNN47_RS06355 (VNN47_06330) - 1267796..1268041 (-) 246 WP_407350040.1 phage holin -
  VNN47_RS06360 (VNN47_06335) - 1268051..1268362 (-) 312 WP_339011347.1 hypothetical protein -
  VNN47_RS06365 (VNN47_06340) - 1268363..1269481 (-) 1119 WP_407350041.1 BppU family phage baseplate upper protein -
  VNN47_RS06370 (VNN47_06345) - 1269463..1271637 (-) 2175 WP_407350042.1 phage tail spike protein -
  VNN47_RS06375 (VNN47_06350) - 1271634..1272395 (-) 762 WP_407350043.1 distal tail protein Dit -
  VNN47_RS06380 (VNN47_06355) - 1272395..1275730 (-) 3336 WP_407350044.1 hypothetical protein -
  VNN47_RS06385 (VNN47_06360) - 1275730..1276320 (-) 591 WP_407350045.1 Gp15 family bacteriophage protein -
  VNN47_RS06390 (VNN47_06365) - 1276329..1276700 (-) 372 WP_407350046.1 hypothetical protein -
  VNN47_RS06395 (VNN47_06370) - 1276803..1277228 (-) 426 WP_407350047.1 phage tail tube protein -
  VNN47_RS06400 (VNN47_06375) - 1277231..1277629 (-) 399 WP_407350048.1 minor capsid protein -
  VNN47_RS06405 (VNN47_06380) - 1277629..1277982 (-) 354 WP_407350049.1 minor capsid protein -
  VNN47_RS06410 (VNN47_06385) - 1277982..1278320 (-) 339 WP_404883453.1 hypothetical protein -
  VNN47_RS06415 (VNN47_06390) - 1278320..1278703 (-) 384 WP_407350050.1 hypothetical protein -
  VNN47_RS06420 (VNN47_06395) - 1278748..1278969 (-) 222 WP_407350051.1 hypothetical protein -
  VNN47_RS06425 (VNN47_06400) - 1279039..1279863 (-) 825 WP_407350052.1 N4-gp56 family major capsid protein -
  VNN47_RS06430 (VNN47_06405) - 1279882..1280481 (-) 600 WP_407350053.1 phage scaffolding protein -
  VNN47_RS06440 (VNN47_06415) - 1280652..1281860 (-) 1209 WP_407350054.1 phage minor capsid protein -
  VNN47_RS06445 (VNN47_06420) - 1281863..1283344 (-) 1482 WP_407350055.1 phage portal protein -
  VNN47_RS06450 (VNN47_06425) - 1283355..1284650 (-) 1296 WP_407350986.1 PBSX family phage terminase large subunit -
  VNN47_RS06455 (VNN47_06430) - 1284647..1285180 (-) 534 WP_407350056.1 terminase small subunit -
  VNN47_RS06460 (VNN47_06435) - 1285227..1285823 (-) 597 WP_407350057.1 hypothetical protein -
  VNN47_RS06475 (VNN47_06450) - 1286723..1287118 (-) 396 WP_407350058.1 DUF722 domain-containing protein -
  VNN47_RS06480 (VNN47_06455) - 1287248..1287460 (-) 213 WP_407350060.1 hypothetical protein -
  VNN47_RS06485 (VNN47_06460) - 1287578..1287790 (-) 213 WP_407350061.1 hypothetical protein -
  VNN47_RS06490 (VNN47_06465) - 1287783..1288265 (-) 483 WP_407350999.1 hypothetical protein -
  VNN47_RS06495 (VNN47_06470) - 1288271..1288510 (-) 240 WP_407350062.1 helix-turn-helix domain-containing protein -
  VNN47_RS06500 (VNN47_06475) - 1288503..1288829 (-) 327 WP_407350063.1 hypothetical protein -
  VNN47_RS06505 (VNN47_06480) - 1288833..1288976 (-) 144 WP_407350064.1 hypothetical protein -
  VNN47_RS06510 (VNN47_06485) - 1289002..1289799 (-) 798 WP_407350065.1 DNA adenine methylase -
  VNN47_RS06515 (VNN47_06490) - 1289783..1290034 (-) 252 WP_407350066.1 hypothetical protein -
  VNN47_RS06520 (VNN47_06495) - 1290031..1290333 (-) 303 WP_407350067.1 hypothetical protein -
  VNN47_RS06525 (VNN47_06500) - 1290330..1290497 (-) 168 WP_407350987.1 DUF6877 family protein -
  VNN47_RS06530 (VNN47_06505) - 1290772..1290945 (-) 174 WP_407350068.1 hypothetical protein -
  VNN47_RS06535 (VNN47_06510) - 1291062..1291454 (-) 393 WP_407350069.1 RusA family crossover junction endodeoxyribonuclease -
  VNN47_RS06540 (VNN47_06515) - 1291451..1291735 (-) 285 WP_407350070.1 hypothetical protein -
  VNN47_RS06545 (VNN47_06520) - 1291719..1292507 (-) 789 WP_407350071.1 helix-turn-helix domain-containing protein -
  VNN47_RS06550 (VNN47_06525) - 1292510..1292674 (-) 165 WP_339011889.1 hypothetical protein -
  VNN47_RS06555 (VNN47_06530) - 1292687..1292905 (-) 219 WP_407350072.1 helix-turn-helix domain-containing protein -
  VNN47_RS06560 (VNN47_06535) - 1293136..1294131 (-) 996 WP_407350073.1 DUF1351 domain-containing protein -
  VNN47_RS06565 (VNN47_06540) bet 1294132..1294908 (-) 777 WP_407350074.1 phage recombination protein Bet -
  VNN47_RS06570 - 1294992..1295174 (-) 183 WP_407357373.1 hypothetical protein -
  VNN47_RS06575 (VNN47_06545) - 1295195..1295431 (-) 237 WP_407350075.1 DNA-binding protein -
  VNN47_RS06580 (VNN47_06550) - 1295595..1295792 (+) 198 WP_407350076.1 hypothetical protein -
  VNN47_RS06585 (VNN47_06555) - 1295831..1296100 (-) 270 WP_407350077.1 hypothetical protein -
  VNN47_RS06590 (VNN47_06560) - 1296112..1296360 (-) 249 WP_407350078.1 hypothetical protein -
  VNN47_RS06595 (VNN47_06565) - 1296589..1297389 (+) 801 WP_407350079.1 S24 family peptidase -
  VNN47_RS06600 (VNN47_06570) - 1297403..1297603 (+) 201 WP_407350081.1 hypothetical protein -
  VNN47_RS06605 (VNN47_06575) - 1297618..1297821 (+) 204 WP_407350082.1 hypothetical protein -
  VNN47_RS06610 (VNN47_06580) istB 1297873..1298631 (-) 759 WP_341485250.1 IS21-like element helper ATPase IstB -
  VNN47_RS06615 (VNN47_06585) istA 1298640..1299863 (-) 1224 WP_341485251.1 IS21 family transposase -
  VNN47_RS06620 (VNN47_06590) - 1300095..1300655 (+) 561 WP_407350083.1 hypothetical protein -
  VNN47_RS06625 (VNN47_06595) - 1300699..1301073 (+) 375 WP_407350084.1 PH domain-containing protein -
  VNN47_RS06630 (VNN47_06600) - 1301197..1302315 (+) 1119 WP_407350085.1 tyrosine-type recombinase/integrase -
  VNN47_RS06635 (VNN47_06605) - 1302544..1302837 (-) 294 WP_042218991.1 hypothetical protein -
  VNN47_RS06640 (VNN47_06610) - 1302839..1303105 (-) 267 WP_003133123.1 DUF2089 family protein -
  VNN47_RS06645 (VNN47_06615) - 1303245..1303514 (+) 270 WP_019299134.1 chorismate mutase -
  VNN47_RS06650 (VNN47_06620) - 1303507..1303938 (-) 432 WP_165706169.1 hypothetical protein -

Sequence

Protein


Download         Length: 164 a.a.        Molecular weight: 18035.94 Da        Isoelectric Point: 4.9533

>NTDB_id=918662 VNN47_RS06300 WP_407350034.1 1258030..1258524(-) (ssb) [Lactococcus garvieae strain VC13]
MINNVVLVGRVVRDPELRYTPQNTAVATFTIAVNRRFKNAQGEREADFINCVIWRQSAENLANWAKKGALIGVTGSIQMR
NYENKEGQRVYVTEVLADNFQMLESRAAREGGSGSYSAPQQQQSQNRPFAGSNSSAGNATPDFGRDADPFGGSPMEISDD
DLPF

Nucleotide


Download         Length: 495 bp        

>NTDB_id=918662 VNN47_RS06300 WP_407350034.1 1258030..1258524(-) (ssb) [Lactococcus garvieae strain VC13]
ATGATTAATAATGTTGTTTTGGTCGGACGCGTTGTGCGTGACCCTGAACTGCGATATACACCGCAAAATACTGCGGTTGC
TACATTTACGATTGCTGTTAACCGTCGTTTTAAAAACGCGCAAGGCGAACGTGAAGCTGATTTCATTAACTGTGTCATCT
GGCGTCAATCTGCTGAAAACTTGGCAAATTGGGCTAAAAAAGGTGCCTTGATTGGTGTAACAGGTAGCATTCAAATGCGA
AATTATGAGAACAAAGAAGGTCAACGTGTTTACGTGACTGAAGTATTGGCTGATAACTTCCAAATGCTTGAGAGTCGTGC
CGCACGTGAAGGTGGCTCTGGTTCATATTCTGCACCACAGCAACAACAATCACAAAATCGTCCTTTTGCTGGCTCTAACA
GCTCAGCAGGAAATGCAACACCTGATTTTGGTCGTGATGCAGATCCATTTGGTGGCTCACCAATGGAAATCTCAGATGAT
GATCTTCCATTCTAA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(2-103)


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

57.31

100

0.598
  ssbA Bacillus subtilis subsp. subtilis str. 168

53.933

100

0.585
  ssbB/cilA Streptococcus pneumoniae TIGR4

49.242

80.488

0.396
  ssbB/cilA Streptococcus pneumoniae D39

48.485

80.488

0.39
  ssbB/cilA Streptococcus pneumoniae R6

48.485

80.488

0.39
  ssbB/cilA Streptococcus mitis SK321

48.485

80.488

0.39
  ssbB/cilA Streptococcus mitis NCTC 12261

48.485

80.488

0.39
  ssbB/cilA Streptococcus pneumoniae Rx1

48.485

80.488

0.39
  ssbB Bacillus subtilis subsp. subtilis str. 168

57.547

64.634

0.372