Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   ACN08J_RS05025 Genome accession   NZ_CP183211
Coordinates   979504..979977 (-) Length   157 a.a.
NCBI ID   WP_419241952.1    Uniprot ID   -
Organism   Pediococcus pentosaceus strain NIBL1955     
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 946708..990508 979504..979977 within 0


Gene organization within MGE regions


Location: 946708..990508
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACN08J_RS04845 (ACN08J_04845) - 946708..946929 (-) 222 WP_002833599.1 YneF family protein -
  ACN08J_RS04850 (ACN08J_04850) - 947000..947248 (-) 249 WP_002833598.1 DUF896 domain-containing protein -
  ACN08J_RS04855 (ACN08J_04855) lexA 947382..948011 (+) 630 WP_002833597.1 transcriptional repressor LexA -
  ACN08J_RS04860 (ACN08J_04860) - 948090..948689 (+) 600 WP_011673312.1 hypothetical protein -
  ACN08J_RS04865 (ACN08J_04865) - 948729..949895 (-) 1167 WP_023440307.1 hydroxymethylglutaryl-CoA synthase -
  ACN08J_RS04870 (ACN08J_04870) - 950056..951432 (-) 1377 WP_201626886.1 amino acid permease -
  ACN08J_RS04875 (ACN08J_04875) - 952560..953684 (-) 1125 WP_419241927.1 peptidoglycan recognition family protein -
  ACN08J_RS04880 (ACN08J_04880) - 953668..953898 (-) 231 WP_419241928.1 phage holin -
  ACN08J_RS04885 (ACN08J_04885) - 954274..957141 (-) 2868 WP_419241929.1 glycerophosphodiester phosphodiesterase family protein -
  ACN08J_RS04890 (ACN08J_04890) - 957166..958263 (-) 1098 WP_419241930.1 SGNH/GDSL hydrolase family protein -
  ACN08J_RS04895 (ACN08J_04895) - 958263..958580 (-) 318 WP_419241931.1 hypothetical protein -
  ACN08J_RS04900 (ACN08J_04900) - 958570..959706 (-) 1137 WP_419241932.1 phage tail protein -
  ACN08J_RS04905 (ACN08J_04905) - 959715..960560 (-) 846 WP_419241933.1 phage tail domain-containing protein -
  ACN08J_RS04910 (ACN08J_04910) - 960565..965835 (-) 5271 WP_419241934.1 tape measure protein -
  ACN08J_RS04915 (ACN08J_04915) - 965839..966471 (-) 633 WP_419241935.1 Gp15 family bacteriophage protein -
  ACN08J_RS04920 (ACN08J_04920) - 966478..966915 (-) 438 WP_419241936.1 hypothetical protein -
  ACN08J_RS04925 (ACN08J_04925) - 966989..967534 (-) 546 WP_419241937.1 phage tail tube protein -
  ACN08J_RS04930 (ACN08J_04930) - 967538..967933 (-) 396 WP_195751793.1 minor capsid protein -
  ACN08J_RS04935 (ACN08J_04935) - 967920..968270 (-) 351 WP_419241938.1 minor capsid protein -
  ACN08J_RS04940 (ACN08J_04940) - 968270..968617 (-) 348 WP_419241939.1 putative minor capsid protein -
  ACN08J_RS04945 (ACN08J_04945) - 968614..969030 (-) 417 WP_419241940.1 hypothetical protein -
  ACN08J_RS04950 (ACN08J_04950) - 969042..969509 (-) 468 WP_419241941.1 Ig-like domain-containing protein -
  ACN08J_RS04955 (ACN08J_04955) - 969587..970477 (-) 891 WP_419241942.1 hypothetical protein -
  ACN08J_RS04960 (ACN08J_04960) - 970490..971044 (-) 555 WP_419241943.1 phage scaffolding protein -
  ACN08J_RS04965 (ACN08J_04965) - 971144..972277 (-) 1134 WP_419241944.1 phage minor capsid protein -
  ACN08J_RS04970 (ACN08J_04970) - 972274..973770 (-) 1497 WP_419241945.1 phage portal protein -
  ACN08J_RS04975 (ACN08J_04975) - 973824..975197 (-) 1374 WP_419241946.1 PBSX family phage terminase large subunit -
  ACN08J_RS04980 (ACN08J_04980) - 975194..975763 (-) 570 WP_419241947.1 terminase small subunit -
  ACN08J_RS04985 (ACN08J_04985) - 975763..975945 (-) 183 WP_419241948.1 hypothetical protein -
  ACN08J_RS04990 (ACN08J_04990) - 975956..977152 (-) 1197 WP_419241949.1 putative phage abortive infection protein -
  ACN08J_RS05000 (ACN08J_05000) - 977476..977907 (-) 432 WP_419241950.1 ArpU family phage packaging/lysis transcriptional regulator -
  ACN08J_RS05005 (ACN08J_05005) - 978282..978524 (-) 243 WP_195753226.1 hypothetical protein -
  ACN08J_RS05010 (ACN08J_05010) - 978677..978874 (-) 198 WP_029257899.1 DUF6877 family protein -
  ACN08J_RS05015 (ACN08J_05015) - 978867..979034 (-) 168 WP_155266534.1 hypothetical protein -
  ACN08J_RS05020 (ACN08J_05020) - 979037..979354 (-) 318 WP_419241951.1 DeoR family transcriptional regulator -
  ACN08J_RS05025 (ACN08J_05025) ssb 979504..979977 (-) 474 WP_419241952.1 single-stranded DNA-binding protein Machinery gene
  ACN08J_RS05030 (ACN08J_05030) - 979996..980256 (-) 261 WP_158190602.1 hypothetical protein -
  ACN08J_RS05035 (ACN08J_05035) - 980225..980926 (-) 702 WP_419241953.1 putative HNHc nuclease -
  ACN08J_RS05040 (ACN08J_05040) - 980930..981760 (-) 831 WP_419241954.1 helix-turn-helix domain-containing protein -
  ACN08J_RS05045 (ACN08J_05045) - 981770..982597 (-) 828 WP_419241955.1 PD-(D/E)XK nuclease-like domain-containing protein -
  ACN08J_RS05050 (ACN08J_05050) - 982557..983408 (-) 852 WP_419241956.1 recombinase RecT -
  ACN08J_RS05055 (ACN08J_05055) - 983401..983682 (-) 282 WP_141822573.1 hypothetical protein -
  ACN08J_RS05060 (ACN08J_05060) - 983920..984195 (-) 276 WP_251974206.1 hypothetical protein -
  ACN08J_RS05065 (ACN08J_05065) - 984196..984654 (-) 459 WP_419241957.1 XRE family transcriptional regulator -
  ACN08J_RS05070 (ACN08J_05070) - 984728..984949 (-) 222 WP_159254598.1 hypothetical protein -
  ACN08J_RS05075 (ACN08J_05075) - 984946..985209 (-) 264 WP_229573244.1 helix-turn-helix domain-containing protein -
  ACN08J_RS05080 (ACN08J_05080) - 985360..986025 (+) 666 WP_419241958.1 LexA family protein -
  ACN08J_RS05085 (ACN08J_05085) - 986088..986549 (+) 462 WP_229568445.1 hypothetical protein -
  ACN08J_RS05090 (ACN08J_05090) - 986623..987195 (+) 573 WP_419241959.1 AAA family ATPase -
  ACN08J_RS05095 (ACN08J_05095) - 987164..988312 (+) 1149 WP_419241960.1 AAA family ATPase -
  ACN08J_RS05100 (ACN08J_05100) - 988327..989235 (+) 909 WP_419241961.1 DNA adenine methylase -
  ACN08J_RS05105 (ACN08J_05105) - 989336..990508 (+) 1173 WP_419241962.1 tyrosine-type recombinase/integrase -

Sequence

Protein


Download         Length: 157 a.a.        Molecular weight: 17911.60 Da        Isoelectric Point: 6.3630

>NTDB_id=1104521 ACN08J_RS05025 WP_419241952.1 979504..979977(-) (ssb) [Pediococcus pentosaceus strain NIBL1955]
MINRTVLVGRLTRDPELKYTNSGRAVAGFNIAVNRQFTNSQGEREADFINCVIWNKTAENFCNFTRKGSLVGIDGRIQTR
SYENQQGTRIYVTEVVAENFSLLESKNSNQNEQFEQNRPQNNGQNYQNKQNGQSSPSRNPNDPFNSIPDIKDDDLPF

Nucleotide


Download         Length: 474 bp        

>NTDB_id=1104521 ACN08J_RS05025 WP_419241952.1 979504..979977(-) (ssb) [Pediococcus pentosaceus strain NIBL1955]
ATGATTAATCGAACTGTTTTAGTTGGCCGGTTGACGCGTGATCCAGAATTGAAATACACCAACAGTGGAAGGGCGGTAGC
TGGCTTTAACATAGCCGTTAACCGTCAATTTACAAATTCACAGGGCGAGCGCGAAGCGGACTTTATTAACTGCGTTATTT
GGAATAAAACGGCGGAAAACTTCTGTAACTTCACTCGCAAAGGGTCACTGGTTGGAATTGATGGACGAATTCAAACTCGA
TCATACGAAAATCAACAAGGAACACGAATTTACGTTACTGAAGTTGTAGCTGAGAACTTCTCGCTACTTGAGTCCAAAAA
CAGTAATCAAAATGAACAATTTGAACAGAATAGGCCTCAAAACAATGGACAAAATTATCAGAATAAACAAAATGGTCAAT
CATCACCTAGCAGAAATCCTAACGACCCATTTAATAGCATACCGGATATCAAGGATGACGATTTACCATTCTAG

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

58.824

100

0.637
  ssbA Bacillus subtilis subsp. subtilis str. 168

51.705

100

0.58
  ssbB Bacillus subtilis subsp. subtilis str. 168

56.604

67.516

0.382

Multiple sequence alignment