Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   RFF16_RS09855 Genome accession   NZ_CP133642
Coordinates   2096472..2096927 (-) Length   151 a.a.
NCBI ID   WP_108575003.1    Uniprot ID   -
Organism   Pasteurella multocida strain Past3     
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 2091214..2138826 2096472..2096927 within 0


Gene organization within MGE regions


Location: 2091214..2138826
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RFF16_RS09805 (RFF16_09800) - 2091214..2092266 (-) 1053 WP_267894787.1 tyrosine-type recombinase/integrase -
  RFF16_RS09810 (RFF16_09805) - 2092176..2092508 (-) 333 WP_015691045.1 helix-turn-helix domain-containing protein -
  RFF16_RS09815 (RFF16_09810) - 2092644..2093081 (-) 438 WP_108575009.1 pyruvate kinase -
  RFF16_RS09820 (RFF16_09815) - 2093088..2093354 (-) 267 WP_064702824.1 hypothetical protein -
  RFF16_RS09825 (RFF16_09820) - 2093400..2093705 (-) 306 WP_108575008.1 hypothetical protein -
  RFF16_RS09830 (RFF16_09825) - 2093717..2094247 (-) 531 WP_108575007.1 DUF551 domain-containing protein -
  RFF16_RS09835 (RFF16_09830) rdgC 2094391..2095299 (-) 909 WP_108575023.1 recombination-associated protein RdgC -
  RFF16_RS09840 (RFF16_09835) - 2095308..2095691 (-) 384 WP_108575006.1 hypothetical protein -
  RFF16_RS09845 (RFF16_09840) - 2095772..2096116 (-) 345 WP_108575005.1 hypothetical protein -
  RFF16_RS09850 (RFF16_09845) - 2096137..2096400 (-) 264 WP_250190657.1 hypothetical protein -
  RFF16_RS09855 (RFF16_09850) ssb 2096472..2096927 (-) 456 WP_108575003.1 single-stranded DNA-binding protein Machinery gene
  RFF16_RS09860 (RFF16_09855) - 2096927..2097466 (-) 540 WP_108575002.1 HNH endonuclease signature motif containing protein -
  RFF16_RS09865 (RFF16_09860) - 2097470..2098081 (-) 612 WP_108575001.1 YqaJ viral recombinase family protein -
  RFF16_RS09870 (RFF16_09865) bet 2098074..2098925 (-) 852 WP_108575000.1 phage recombination protein Bet -
  RFF16_RS09875 (RFF16_09870) - 2098929..2099903 (-) 975 WP_108574999.1 hypothetical protein -
  RFF16_RS09880 (RFF16_09875) - 2099906..2100067 (-) 162 WP_165523898.1 hypothetical protein -
  RFF16_RS09885 (RFF16_09880) - 2100077..2100316 (-) 240 WP_108574998.1 hypothetical protein -
  RFF16_RS09890 (RFF16_09885) - 2100544..2100816 (+) 273 WP_071522856.1 CRISPR-associated protein Cas2 -
  RFF16_RS09895 (RFF16_09890) - 2100794..2101051 (-) 258 WP_108574997.1 hypothetical protein -
  RFF16_RS09900 (RFF16_09895) - 2101068..2101274 (-) 207 WP_108574996.1 hypothetical protein -
  RFF16_RS09905 (RFF16_09900) - 2101747..2102529 (+) 783 WP_108574995.1 sce7726 family protein -
  RFF16_RS09910 (RFF16_09905) - 2102530..2103642 (-) 1113 WP_159074468.1 beta family protein -
  RFF16_RS09915 (RFF16_09910) - 2103644..2104039 (-) 396 WP_108574993.1 hypothetical protein -
  RFF16_RS09920 (RFF16_09915) - 2104090..2104779 (-) 690 WP_108574992.1 XRE family transcriptional regulator -
  RFF16_RS09925 (RFF16_09920) - 2104907..2105116 (+) 210 WP_005720263.1 helix-turn-helix transcriptional regulator -
  RFF16_RS09930 (RFF16_09925) - 2105137..2105412 (+) 276 WP_005756640.1 hypothetical protein -
  RFF16_RS09935 (RFF16_09930) - 2105456..2105701 (+) 246 WP_005725517.1 helix-turn-helix domain-containing protein -
  RFF16_RS09940 (RFF16_09935) - 2105779..2106639 (+) 861 WP_108574991.1 DNA replication protein -
  RFF16_RS09945 (RFF16_09940) - 2106639..2108075 (+) 1437 WP_108574990.1 DnaB-like helicase C-terminal domain-containing protein -
  RFF16_RS09950 (RFF16_09945) - 2108079..2108504 (+) 426 WP_108574989.1 recombination protein NinB -
  RFF16_RS09955 (RFF16_09950) - 2108787..2109032 (+) 246 WP_108574987.1 hypothetical protein -
  RFF16_RS09960 (RFF16_09955) - 2109100..2109384 (+) 285 WP_108574986.1 DUF1364 domain-containing protein -
  RFF16_RS09965 (RFF16_09960) - 2109381..2109740 (+) 360 WP_108574985.1 RusA family crossover junction endodeoxyribonuclease -
  RFF16_RS09970 (RFF16_09965) - 2109737..2110426 (+) 690 WP_108574984.1 hypothetical protein -
  RFF16_RS09975 (RFF16_09970) - 2110423..2110791 (+) 369 WP_108574983.1 hypothetical protein -
  RFF16_RS09980 (RFF16_09975) - 2111007..2111351 (+) 345 WP_108574982.1 phage holin, lambda family -
  RFF16_RS09985 (RFF16_09980) - 2111344..2111757 (+) 414 WP_075266311.1 M15 family metallopeptidase -
  RFF16_RS09990 (RFF16_09985) - 2111729..2112097 (+) 369 WP_234409151.1 hypothetical protein -
  RFF16_RS09995 (RFF16_09990) - 2112299..2112523 (+) 225 WP_108574980.1 hypothetical protein -
  RFF16_RS10000 (RFF16_09995) - 2112564..2113283 (+) 720 WP_108574979.1 terminase -
  RFF16_RS10005 (RFF16_10000) - 2113283..2114830 (+) 1548 WP_108574978.1 TerL -
  RFF16_RS10010 (RFF16_10005) - 2114833..2117016 (+) 2184 WP_323995447.1 hypothetical protein -
  RFF16_RS10015 (RFF16_10010) - 2117080..2124054 (+) 6975 WP_323995450.1 LPD38 domain-containing protein -
  RFF16_RS10025 (RFF16_10020) - 2124633..2125508 (+) 876 WP_108574975.1 hypothetical protein -
  RFF16_RS10030 (RFF16_10025) - 2125539..2126537 (+) 999 WP_108574974.1 N4-gp56 family major capsid protein -
  RFF16_RS10035 (RFF16_10030) - 2126589..2127044 (+) 456 WP_108574973.1 SAP domain-containing protein -
  RFF16_RS10040 (RFF16_10035) - 2127041..2127427 (+) 387 WP_108574972.1 hypothetical protein -
  RFF16_RS10045 (RFF16_10040) - 2127471..2129402 (+) 1932 WP_108575021.1 hypothetical protein -
  RFF16_RS10050 (RFF16_10045) - 2129395..2131725 (+) 2331 WP_108574971.1 tail fiber protein -
  RFF16_RS10055 (RFF16_10050) - 2131735..2132334 (+) 600 WP_108574970.1 hypothetical protein -
  RFF16_RS10060 (RFF16_10055) - 2132337..2132591 (+) 255 WP_108574969.1 DNA helicase UvrD -
  RFF16_RS10065 (RFF16_10060) - 2132601..2133293 (+) 693 WP_108574968.1 hypothetical protein -
  RFF16_RS10070 (RFF16_10065) - 2133306..2133668 (+) 363 WP_108574967.1 hypothetical protein -
  RFF16_RS10075 (RFF16_10070) - 2133676..2134857 (+) 1182 WP_165544669.1 hypothetical protein -
  RFF16_RS10080 (RFF16_10075) - 2134866..2135363 (+) 498 WP_323995455.1 hypothetical protein -
  RFF16_RS10085 (RFF16_10080) - 2135363..2136103 (+) 741 WP_316727459.1 hypothetical protein -
  RFF16_RS10090 (RFF16_10085) - 2136242..2136898 (+) 657 WP_165544672.1 hypothetical protein -
  RFF16_RS10095 (RFF16_10090) - 2136935..2137597 (-) 663 WP_165544673.1 hypothetical protein -
  RFF16_RS10100 (RFF16_10095) - 2137990..2138826 (+) 837 WP_165544674.1 phage antirepressor N-terminal domain-containing protein -

Sequence

Protein


Download         Length: 151 a.a.        Molecular weight: 17013.96 Da        Isoelectric Point: 5.9220

>NTDB_id=875454 RFF16_RS09855 WP_108575003.1 2096472..2096927(-) (ssb) [Pasteurella multocida strain Past3]
MAGVNRVIILGNLGNDPDIRTMPNGDAVAKISVATSESWIDKNTGERKIQTEWHSIVFYRRQAEICEQYLKKGSKVYVEG
KIQTRKWQDQNGQERYLTEIIGNSLQMLDSRQDSQAQANAQAPQNNAYANAKAGKPVPQQVDNFEEDSIPF

Nucleotide


Download         Length: 456 bp        

>NTDB_id=875454 RFF16_RS09855 WP_108575003.1 2096472..2096927(-) (ssb) [Pasteurella multocida strain Past3]
ATGGCTGGGGTTAATCGTGTAATTATTTTAGGAAATTTAGGAAACGATCCTGATATCCGCACAATGCCAAATGGCGACGC
AGTGGCAAAAATCAGCGTCGCAACTAGTGAAAGCTGGATAGACAAAAACACTGGCGAACGCAAAATACAAACAGAATGGC
ATTCTATCGTGTTCTATCGCAGACAAGCAGAAATTTGTGAGCAGTATCTTAAAAAAGGTTCGAAAGTTTATGTAGAAGGT
AAAATTCAGACACGTAAATGGCAAGATCAGAACGGACAAGAGCGTTATTTAACAGAAATCATTGGTAATAGTCTACAAAT
GCTAGACAGTCGCCAAGATTCACAAGCTCAAGCTAATGCACAAGCACCACAAAACAATGCTTATGCGAATGCGAAAGCTG
GAAAGCCTGTACCGCAACAAGTAGATAACTTTGAAGAAGACAGCATACCATTTTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(4-108)


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 Glaesserella parasuis strain SC1401

58.564

100

0.702
  ssb Vibrio cholerae strain A1552

56.637

74.834

0.424
  ssb Neisseria gonorrhoeae MS11

46.715

90.728

0.424
  ssb Neisseria meningitidis MC58

52.174

76.159

0.397