Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   LDE01_RS00040 Genome accession   NZ_AP019750
Coordinates   9252..9830 (+) Length   192 a.a.
NCBI ID   WP_072546824.1    Uniprot ID   -
Organism   Lactobacillus delbrueckii subsp. delbrueckii strain NBRC 3202     
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 1546..33827 9252..9830 within 0


Gene organization within MGE regions


Location: 1546..33827
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LDE01_RS00010 (LDE01_00020) dnaN 1546..2673 (+) 1128 WP_099279015.1 DNA polymerase III subunit beta -
  LDE01_RS00015 (LDE01_00030) yaaA 2898..3128 (+) 231 WP_035176726.1 S4 domain-containing protein YaaA -
  LDE01_RS00020 (LDE01_00040) recF 3128..4273 (+) 1146 WP_002879425.1 DNA replication/repair protein RecF -
  LDE01_RS00025 (LDE01_00050) gyrB 4257..6218 (+) 1962 WP_002879426.1 DNA topoisomerase (ATP-hydrolyzing) subunit B -
  LDE01_RS00030 (LDE01_00060) gyrA 6231..8702 (+) 2472 WP_002879428.1 DNA gyrase subunit A -
  LDE01_RS00035 (LDE01_00070) rpsF 8918..9211 (+) 294 WP_072546823.1 30S ribosomal protein S6 -
  LDE01_RS00040 (LDE01_00080) ssb 9252..9830 (+) 579 WP_072546824.1 single-stranded DNA-binding protein Machinery gene
  LDE01_RS00045 (LDE01_00090) rpsR 9857..10093 (+) 237 WP_002879432.1 30S ribosomal protein S18 -
  LDE01_RS00050 (LDE01_00100) - 10234..12255 (+) 2022 WP_035182868.1 DHH family phosphoesterase -
  LDE01_RS00055 (LDE01_00110) rplI 12278..12733 (+) 456 WP_013438865.1 50S ribosomal protein L9 -
  LDE01_RS00060 (LDE01_00120) dnaB 12757..14127 (+) 1371 WP_072546825.1 replicative DNA helicase -
  LDE01_RS00065 (LDE01_00130) - 14176..15333 (-) 1158 WP_072546826.1 DUF2974 domain-containing protein -
  LDE01_RS00070 - 15605..16893 (-) 1289 Protein_13 RNA-guided endonuclease InsQ/TnpB family protein -
  LDE01_RS00075 (LDE01_00160) - 17263..17487 (+) 225 WP_072546829.1 hypothetical protein -
  LDE01_RS00080 (LDE01_00170) - 17598..18302 (-) 705 WP_072546830.1 MgtC/SapB family protein -
  LDE01_RS09845 (LDE01_00180) - 18699..19250 (+) 552 WP_231138997.1 helix-turn-helix domain-containing protein -
  LDE01_RS00100 - 19320..19727 (-) 408 WP_231138998.1 LytTR family transcriptional regulator DNA-binding domain-containing protein -
  LDE01_RS00105 (LDE01_00190) - 19905..20780 (+) 876 WP_141889008.1 ThiF family adenylyltransferase -
  LDE01_RS00110 (LDE01_00200) - 20792..22372 (+) 1581 WP_072546833.1 ABC transporter ATP-binding protein -
  LDE01_RS00115 (LDE01_00210) - 22362..23936 (+) 1575 WP_072546834.1 ABC transporter ATP-binding protein -
  LDE01_RS00125 (LDE01_00220) - 24227..24865 (+) 639 WP_072546835.1 ATP-binding cassette domain-containing protein -
  LDE01_RS00130 (LDE01_00230) fetB 24862..25629 (+) 768 WP_002880561.1 ABC transporter permease -
  LDE01_RS00135 (LDE01_00240) - 25632..25820 (+) 189 WP_168161980.1 hypothetical protein -
  LDE01_RS00140 (LDE01_00250) - 25913..26890 (+) 978 WP_310733910.1 RNA-guided endonuclease TnpB family protein -
  LDE01_RS00145 (LDE01_00260) - 27277..28431 (-) 1155 WP_099279037.1 SLAP domain-containing protein -
  LDE01_RS00150 (LDE01_00270) - 28691..29212 (+) 522 WP_002880554.1 GNAT family N-acetyltransferase -
  LDE01_RS00155 (LDE01_00280) - 29610..30443 (+) 834 WP_099279038.1 pyridoxamine kinase -
  LDE01_RS00160 (LDE01_00290) - 30478..31035 (+) 558 WP_002880550.1 ECF transporter S component -
  LDE01_RS00165 (LDE01_00300) - 31062..33827 (-) 2766 WP_099279039.1 DUF3427 domain-containing protein -

Sequence

Protein


Download         Length: 192 a.a.        Molecular weight: 20695.37 Da        Isoelectric Point: 4.5431

>NTDB_id=73778 LDE01_RS00040 WP_072546824.1 9252..9830(+) (ssb) [Lactobacillus delbrueckii subsp. delbrueckii strain NBRC 3202]
MINNVVLVGRLTRDPELRTTGSGISVATFTLAVDRQFTNASGQREADFISCVIWRKAAENFCNFTSKGSLVGIQGRIQTR
NYDNKDGQRVYVTEVLVDNFSLLESRRERESRQQNGGFGGQGQSQNTGFNTGFGGGSGYANDNAFGSPAQSNGPANAGFN
EDNKKDAGGDTNTNPFDSSDDVINVSNDDLPF

Nucleotide


Download         Length: 579 bp        

>NTDB_id=73778 LDE01_RS00040 WP_072546824.1 9252..9830(+) (ssb) [Lactobacillus delbrueckii subsp. delbrueckii strain NBRC 3202]
ATGATCAATAACGTTGTACTTGTTGGCCGTTTAACACGTGATCCTGAATTACGTACTACTGGGAGCGGCATCTCGGTTGC
TACGTTCACTTTGGCCGTTGACCGGCAGTTTACCAATGCATCAGGCCAGAGAGAAGCGGACTTCATCAGCTGCGTGATTT
GGCGCAAGGCTGCTGAGAACTTCTGCAACTTCACCAGCAAGGGCAGTTTGGTGGGCATCCAGGGCCGAATCCAGACCAGA
AACTATGATAACAAGGACGGCCAGCGAGTTTACGTGACAGAAGTCCTCGTGGACAACTTCTCACTGCTCGAATCACGCCG
CGAGCGTGAAAGCCGTCAGCAAAACGGCGGATTTGGCGGCCAAGGTCAAAGCCAAAACACCGGCTTCAACACCGGATTTG
GCGGCGGCAGCGGCTACGCCAACGACAACGCCTTCGGCAGCCCGGCCCAGTCAAACGGGCCAGCTAATGCCGGATTCAAT
GAAGATAACAAGAAAGATGCCGGCGGAGACACGAACACTAACCCGTTCGACAGCTCTGACGATGTAATCAACGTCTCAAA
TGACGATCTTCCATTTTAA

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

57.513

100

0.578
  ssbA Bacillus subtilis subsp. subtilis str. 168

47.396

100

0.474

Multiple sequence alignment