Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   M1B70_RS06545 Genome accession   NZ_CP096571
Coordinates   1313100..1313525 (-) Length   141 a.a.
NCBI ID   WP_248616949.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain BB2-4M     
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 1280479..1321076 1313100..1313525 within 0


Gene organization within MGE regions


Location: 1280479..1321076
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  M1B70_RS06330 (M1B70_06330) - 1280479..1281987 (-) 1509 WP_159215494.1 sodium:solute symporter -
  M1B70_RS06335 (M1B70_06335) - 1282241..1282972 (-) 732 WP_128211971.1 TIM barrel protein -
  M1B70_RS06340 (M1B70_06340) - 1282953..1283801 (-) 849 WP_075139827.1 ROK family protein -
  M1B70_RS06345 (M1B70_06345) - 1284545..1285873 (-) 1329 WP_248616916.1 GH25 family lysozyme -
  M1B70_RS06350 (M1B70_06350) - 1285854..1286105 (-) 252 WP_248616917.1 phage holin -
  M1B70_RS06355 (M1B70_06355) - 1286105..1286395 (-) 291 WP_248616918.1 hypothetical protein -
  M1B70_RS06360 (M1B70_06360) - 1286442..1287044 (-) 603 WP_248616919.1 hypothetical protein -
  M1B70_RS06365 (M1B70_06365) - 1287106..1287237 (-) 132 WP_248616920.1 XkdX family protein -
  M1B70_RS06370 (M1B70_06370) - 1287237..1287563 (-) 327 WP_248616921.1 DUF2977 domain-containing protein -
  M1B70_RS06375 (M1B70_06375) - 1287585..1288313 (-) 729 WP_248616922.1 hypothetical protein -
  M1B70_RS06380 (M1B70_06380) - 1288325..1290211 (-) 1887 WP_248616923.1 BppU family phage baseplate upper protein -
  M1B70_RS06385 (M1B70_06385) - 1290215..1290661 (-) 447 WP_248616924.1 hypothetical protein -
  M1B70_RS06390 (M1B70_06390) - 1290645..1293605 (-) 2961 WP_248616925.1 phage tail protein -
  M1B70_RS06395 (M1B70_06395) - 1293605..1294369 (-) 765 WP_248616926.1 phage tail protein -
  M1B70_RS06400 (M1B70_06400) - 1294369..1297020 (-) 2652 WP_248616927.1 phage tail tape measure protein -
  M1B70_RS06405 (M1B70_06405) - 1297004..1297282 (-) 279 WP_248616928.1 hypothetical protein -
  M1B70_RS06410 (M1B70_06410) - 1297429..1297770 (-) 342 WP_199874682.1 tail assembly chaperone -
  M1B70_RS06415 (M1B70_06415) - 1297842..1298474 (-) 633 WP_248616929.1 phage major tail protein, TP901-1 family -
  M1B70_RS06420 (M1B70_06420) - 1298487..1298894 (-) 408 WP_248616930.1 hypothetical protein -
  M1B70_RS06425 (M1B70_06425) - 1298895..1299236 (-) 342 WP_248616931.1 HK97-gp10 family putative phage morphogenesis protein -
  M1B70_RS06430 (M1B70_06430) - 1299229..1299546 (-) 318 WP_248616932.1 hypothetical protein -
  M1B70_RS06435 (M1B70_06435) - 1299551..1299925 (-) 375 WP_248616933.1 phage head-tail connector protein -
  M1B70_RS06440 (M1B70_06440) - 1299937..1300203 (-) 267 WP_128472106.1 Ig-like domain-containing protein -
  M1B70_RS06445 (M1B70_06445) - 1300221..1301039 (-) 819 WP_248616934.1 N4-gp56 family major capsid protein -
  M1B70_RS06450 (M1B70_06450) - 1301039..1301692 (-) 654 WP_248616935.1 DUF4355 domain-containing protein -
  M1B70_RS06455 (M1B70_06455) - 1301798..1302769 (-) 972 WP_248616936.1 minor capsid protein -
  M1B70_RS06460 (M1B70_06460) - 1302753..1304033 (-) 1281 WP_248617103.1 phage portal protein -
  M1B70_RS06465 (M1B70_06465) - 1304154..1305500 (-) 1347 WP_248616937.1 PBSX family phage terminase large subunit -
  M1B70_RS06470 (M1B70_06470) - 1305493..1305984 (-) 492 WP_248616938.1 terminase small subunit -
  M1B70_RS06475 (M1B70_06475) - 1306246..1306689 (-) 444 WP_248616939.1 hypothetical protein -
  M1B70_RS06480 (M1B70_06480) - 1306797..1307033 (-) 237 WP_248616940.1 hypothetical protein -
  M1B70_RS06485 (M1B70_06485) - 1307033..1307341 (-) 309 WP_248616941.1 hypothetical protein -
  M1B70_RS06490 (M1B70_06490) - 1307451..1307627 (-) 177 WP_159219778.1 hypothetical protein -
  M1B70_RS06495 (M1B70_06495) - 1307635..1308138 (-) 504 WP_248616942.1 DUF1642 domain-containing protein -
  M1B70_RS06500 (M1B70_06500) - 1308308..1308679 (-) 372 WP_248616943.1 N-acetylmuramoyl-L-alanine amidase -
  M1B70_RS06505 (M1B70_06505) - 1308666..1308815 (-) 150 WP_248616944.1 hypothetical protein -
  M1B70_RS06510 (M1B70_06510) - 1308818..1309000 (-) 183 WP_248616945.1 hypothetical protein -
  M1B70_RS06515 (M1B70_06515) - 1309000..1309227 (-) 228 WP_160185815.1 hypothetical protein -
  M1B70_RS06520 (M1B70_06520) - 1309439..1309909 (-) 471 WP_160185814.1 hypothetical protein -
  M1B70_RS06525 (M1B70_06525) - 1309906..1310313 (-) 408 WP_248617105.1 hypothetical protein -
  M1B70_RS06530 (M1B70_06530) - 1310322..1311554 (-) 1233 WP_248616946.1 DnaB-like helicase C-terminal domain-containing protein -
  M1B70_RS06535 (M1B70_06535) - 1311544..1312410 (-) 867 WP_248616947.1 conserved phage C-terminal domain-containing protein -
  M1B70_RS06540 (M1B70_06540) - 1312388..1313089 (-) 702 WP_248616948.1 putative HNHc nuclease -
  M1B70_RS06545 (M1B70_06545) ssb 1313100..1313525 (-) 426 WP_248616949.1 single-stranded DNA-binding protein Machinery gene
  M1B70_RS06550 (M1B70_06550) - 1313518..1314216 (-) 699 WP_248616950.1 ERF family protein -
  M1B70_RS06555 (M1B70_06555) - 1314217..1314672 (-) 456 WP_248616951.1 chromosome segregation protein SMC -
  M1B70_RS06560 (M1B70_06560) - 1314895..1315176 (+) 282 WP_002830747.1 hypothetical protein -
  M1B70_RS06565 (M1B70_06565) - 1315173..1315394 (-) 222 WP_193223205.1 hypothetical protein -
  M1B70_RS06570 (M1B70_06570) - 1315491..1315697 (-) 207 WP_036672525.1 hypothetical protein -
  M1B70_RS06575 (M1B70_06575) - 1315766..1316500 (-) 735 WP_248616952.1 Rha family transcriptional regulator -
  M1B70_RS06580 (M1B70_06580) - 1316515..1316703 (-) 189 WP_128688467.1 hypothetical protein -
  M1B70_RS06585 (M1B70_06585) - 1316969..1317307 (+) 339 WP_248616953.1 XRE family transcriptional regulator -
  M1B70_RS06590 (M1B70_06590) - 1317314..1317724 (+) 411 WP_248616954.1 hypothetical protein -
  M1B70_RS06595 (M1B70_06595) - 1317786..1318325 (+) 540 WP_248616955.1 Ltp family lipoprotein -
  M1B70_RS06600 (M1B70_06600) - 1318361..1318765 (+) 405 WP_195459564.1 hypothetical protein -
  M1B70_RS06605 (M1B70_06605) - 1318913..1319992 (+) 1080 WP_248616956.1 site-specific integrase -
  M1B70_RS06610 (M1B70_06610) - 1320387..1321076 (+) 690 WP_053906494.1 N-acetylmannosamine-6-phosphate 2-epimerase -

Sequence

Protein


Download         Length: 141 a.a.        Molecular weight: 15568.31 Da        Isoelectric Point: 7.9971

>NTDB_id=681802 M1B70_RS06545 WP_248616949.1 1313100..1313525(-) (ssb) [Pediococcus acidilactici strain BB2-4M]
MINRTVLIGRLTKDVELRHTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFVKYAQKGSLVGIDGRIQTR
SYENQQGQRVYVTEVVADNFSLLDSKPKGNQQNNARQASTPGDPFANGGQSIDIGDDSLPF

Nucleotide


Download         Length: 426 bp        

>NTDB_id=681802 M1B70_RS06545 WP_248616949.1 1313100..1313525(-) (ssb) [Pediococcus acidilactici strain BB2-4M]
ATGATTAATCGAACAGTACTAATAGGACGTTTAACTAAAGATGTTGAACTTCGCCACACAGCTAAAGGTGATGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGCGAAGCGGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGTTAAGTATGCACAAAAAGGTTCGTTGGTAGGTATTGACGGTCGAATTCAGACCCGT
TCATACGAAAACCAACAAGGACAACGAGTTTATGTAACTGAGGTTGTAGCTGATAACTTCTCGTTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAACGCACGGCAAGCATCAACGCCGGGAGATCCATTCGCTAATGGCGGGCAGTCAATTGATA
TTGGTGACGATAGTTTGCCTTTCTAA

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

57.647

100

0.695
  ssbA Bacillus subtilis subsp. subtilis str. 168

53.488

100

0.652
  ssbB Bacillus subtilis subsp. subtilis str. 168

61.111

76.596

0.468
  ssbB Streptococcus sobrinus strain NIDR 6715-7

42.958

100

0.433
  ssbB/cilA Streptococcus mitis NCTC 12261

42.254

100

0.426
  ssbB/cilA Streptococcus pneumoniae TIGR4

42.254

100

0.426
  ssbB/cilA Streptococcus pneumoniae Rx1

41.549

100

0.418
  ssbB/cilA Streptococcus pneumoniae D39

41.549

100

0.418
  ssbB/cilA Streptococcus pneumoniae R6

41.549

100

0.418
  ssbB/cilA Streptococcus mitis SK321

41.549

100

0.418
  ssbA Streptococcus mutans UA159

37.324

100

0.376