Detailed information    

insolico Bioinformatically predicted

Overview

Name   radA   Type   Machinery gene
Locus tag   F7887_RS05910 Genome accession   NZ_CP044428
Coordinates   1470214..1471581 (-) Length   455 a.a.
NCBI ID   WP_005810649.1    Uniprot ID   -
Organism   Bacteroides fragilis strain DK1985     
Function   homologous recombination (predicted from homology)   
Homologous recombination

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)
Genomic island 1463695..1486583 1470214..1471581 within 0


Gene organization within MGE regions


Location: 1463695..1486583
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  F7887_RS05885 (F7887_06225) - 1463695..1464669 (+) 975 WP_122296901.1 zinc ribbon domain-containing protein -
  F7887_RS05890 (F7887_06230) - 1464911..1467313 (-) 2403 WP_122296900.1 TonB-dependent receptor -
  F7887_RS05895 (F7887_06235) - 1467561..1468160 (-) 600 WP_032531771.1 response regulator transcription factor -
  F7887_RS05900 (F7887_06240) - 1468169..1469758 (-) 1590 WP_032538157.1 NAD(P)/FAD-dependent oxidoreductase -
  F7887_RS05905 (F7887_06245) - 1469800..1470174 (-) 375 WP_032540283.1 GxxExxY protein -
  F7887_RS05910 (F7887_06250) radA 1470214..1471581 (-) 1368 WP_005810649.1 DNA repair protein RadA Machinery gene
  F7887_RS05915 (F7887_06255) - 1472405..1472812 (+) 408 WP_005778632.1 BT0820 family HAD-type phosphatase -
  F7887_RS22400 - 1472907..1473197 (-) 291 WP_239010769.1 hypothetical protein -
  F7887_RS05920 (F7887_06260) - 1473179..1475200 (-) 2022 WP_239010770.1 GumC family protein -
  F7887_RS05925 (F7887_06265) - 1475219..1476172 (-) 954 WP_005810643.1 polysaccharide biosynthesis/export family protein -
  F7887_RS05930 (F7887_06270) thrA 1476839..1479274 (+) 2436 WP_005778625.1 bifunctional aspartate kinase/homoserine dehydrogenase I -
  F7887_RS05935 (F7887_06275) - 1479285..1480496 (+) 1212 WP_122296898.1 cofactor-independent phosphoglycerate mutase -
  F7887_RS05940 (F7887_06280) thrC 1480646..1481947 (+) 1302 WP_032543353.1 threonine synthase -
  F7887_RS05945 (F7887_06285) - 1482277..1483224 (+) 948 WP_032531769.1 DMT family transporter -
  F7887_RS05950 (F7887_06290) - 1483178..1483801 (-) 624 WP_005810634.1 thiamine diphosphokinase -
  F7887_RS05955 (F7887_06295) pnuC 1483788..1484360 (-) 573 WP_005810632.1 nicotinamide riboside transporter PnuC -
  F7887_RS05960 (F7887_06300) - 1484364..1486583 (-) 2220 WP_122296897.1 TonB-dependent receptor -

Sequence

Protein


Download         Length: 455 a.a.        Molecular weight: 50199.95 Da        Isoelectric Point: 6.1360

>NTDB_id=389865 F7887_RS05910 WP_005810649.1 1470214..1471581(-) (radA) [Bacteroides fragilis strain DK1985]
MAKEKTVYVCSNCGQESPKWVGKCPSCGEWNTYVEEIVRKEVPNKRPVSGIESPKAKPVTLNEIEADEEPRIDMHDEELN
RVLGGGLVPGSLVLIGGEPGIGKSTLVLQTVLHMPERRILYISGEESARQLKLRADRLTQTSSDCLIVCETSLEQIYVHI
KNTRPDLVIIDSIQTISTESIESSPGSIAQVRECSASILRFAKETHTPVLLIGHINKEGSIAGPKVLEHIVDTVLQFEGD
QHYMYRILRSIKNRFGSTAELGIYEMRQDGLRQVSNPSELLLSQDHEGMSGVAIASAIEGVRPFLIETQALVSSAVYGNP
QRSATGFDIRRMNMLLAVLEKRVGFKLAQKDVFLNIAGGLKVNDPAIDLAVISAILSSNMDAAIEPEVCMAGEIGLSGEI
RPVNRIEQRIGEAEKLGFKRFILPKYNMQGIDMKKLKIELVPVRKVEEAFRGLFG

Nucleotide


Download         Length: 1368 bp        

>NTDB_id=389865 F7887_RS05910 WP_005810649.1 1470214..1471581(-) (radA) [Bacteroides fragilis strain DK1985]
ATGGCAAAAGAGAAAACCGTTTATGTATGCAGTAACTGCGGACAGGAATCACCCAAATGGGTGGGCAAGTGTCCTTCGTG
TGGCGAGTGGAATACTTATGTAGAAGAAATCGTACGCAAGGAGGTTCCGAATAAACGTCCGGTATCGGGCATCGAATCGC
CTAAAGCCAAACCTGTCACCCTGAACGAGATCGAAGCGGACGAGGAACCCCGCATCGACATGCACGACGAGGAGTTGAAC
CGGGTACTGGGCGGCGGACTGGTGCCGGGATCACTGGTGCTGATCGGTGGCGAACCGGGTATCGGAAAATCGACTCTGGT
ACTTCAAACCGTGCTCCACATGCCCGAACGCAGGATACTCTACATCTCCGGAGAAGAGAGTGCAAGGCAACTGAAGCTCC
GCGCGGACCGACTGACACAAACGTCGAGCGACTGCCTGATTGTGTGCGAAACGTCGTTGGAGCAGATCTATGTGCACATT
AAGAATACACGTCCGGATCTGGTAATCATCGACTCCATACAGACCATATCCACCGAAAGCATCGAGTCTTCGCCGGGAAG
TATCGCGCAAGTGCGGGAGTGCTCGGCCTCCATTCTCCGTTTTGCCAAAGAGACGCATACTCCGGTATTACTGATCGGGC
ATATCAACAAAGAAGGCAGCATTGCCGGTCCGAAGGTACTGGAACACATCGTAGACACCGTGCTCCAGTTTGAGGGGGAC
CAGCATTATATGTACCGTATCCTGCGCAGCATCAAGAACCGCTTTGGCAGTACGGCCGAACTGGGTATTTACGAGATGCG
GCAAGACGGGCTTCGCCAGGTCAGCAACCCATCGGAGCTGTTGCTGTCGCAAGATCACGAAGGCATGAGCGGGGTAGCCA
TCGCATCTGCCATCGAAGGAGTCAGGCCGTTCCTGATAGAAACACAGGCACTTGTCAGTTCTGCCGTTTACGGCAATCCG
CAACGTTCGGCAACCGGATTCGATATCCGCCGCATGAACATGCTGCTGGCTGTGCTCGAGAAACGTGTCGGCTTCAAGTT
AGCACAGAAAGATGTCTTTCTAAATATTGCCGGGGGGCTGAAGGTGAACGACCCTGCCATCGACCTGGCTGTTATCAGTG
CCATCCTTTCGTCCAATATGGATGCCGCCATCGAACCGGAAGTCTGTATGGCAGGTGAAATCGGGTTGTCCGGTGAAATC
CGTCCGGTAAACCGAATCGAACAACGTATCGGTGAAGCCGAGAAGCTTGGATTCAAACGGTTTATCCTGCCTAAGTATAA
TATGCAGGGAATCGACATGAAGAAGCTGAAGATAGAACTGGTGCCGGTGAGAAAGGTGGAAGAGGCGTTCCGGGGACTCT
TCGGATGA

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(341-427)

Rubredoxin metal binding domain (Zn_ribbon_LapB)

(8-35)

AAA domain (AAA_25)

(73-219)


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
  radA Bacillus subtilis subsp. subtilis str. 168

51.528

100

0.519
  radA Streptococcus pneumoniae Rx1

48.352

100

0.484
  radA Streptococcus pneumoniae D39

48.352

100

0.484
  radA Streptococcus pneumoniae R6

48.352

100

0.484
  radA Streptococcus pneumoniae TIGR4

48.352

100

0.484
  radA Streptococcus mitis NCTC 12261

48.352

100

0.484
  radA Streptococcus mitis SK321

48.132

100

0.481

Multiple sequence alignment