Detailed information    

insolico Bioinformatically predicted

Overview

Name   sbcB   Type   Machinery gene
Locus tag   OCV04_RS09140 Genome accession   NZ_AP024893
Coordinates   1953195..1954619 (+) Length   474 a.a.
NCBI ID   WP_171137474.1    Uniprot ID   -
Organism   Vibrio plantisponsor strain CECT 7581     
Function   promote 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)
Prophage 1912780..1955034 1953195..1954619 within 0


Gene organization within MGE regions


Location: 1912780..1955034
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OCV04_RS08880 - 1912780..1913370 (+) 591 WP_171137425.1 phage antirepressor N-terminal domain-containing protein -
  OCV04_RS08885 - 1913444..1914148 (-) 705 WP_171137426.1 phospholipase D-like domain-containing protein -
  OCV04_RS08890 - 1914188..1915123 (-) 936 WP_171137427.1 hypothetical protein -
  OCV04_RS08895 - 1915126..1915569 (-) 444 WP_390631883.1 DUF6932 family protein -
  OCV04_RS08900 - 1916063..1916635 (-) 573 WP_171137429.1 hypothetical protein -
  OCV04_RS08905 - 1916653..1916940 (-) 288 WP_171137430.1 MarR family transcriptional regulator -
  OCV04_RS08910 - 1916991..1918268 (-) 1278 WP_171137431.1 tyrosine-type recombinase/integrase -
  OCV04_RS08915 - 1918268..1919239 (-) 972 WP_171137432.1 hypothetical protein -
  OCV04_RS08920 - 1919239..1919442 (-) 204 WP_171137433.1 hypothetical protein -
  OCV04_RS08925 - 1919442..1919807 (-) 366 WP_171137434.1 phage tail protein -
  OCV04_RS08930 - 1919810..1922551 (-) 2742 WP_171137435.1 phage tail tape measure protein -
  OCV04_RS08935 - 1922663..1923370 (-) 708 WP_240956653.1 phage tail assembly protein -
  OCV04_RS08940 - 1923430..1923906 (-) 477 WP_171137436.1 phage major tail tube protein -
  OCV04_RS08945 - 1923899..1925068 (-) 1170 WP_171137437.1 phage tail protein -
  OCV04_RS08950 - 1925071..1925274 (-) 204 WP_171137438.1 hypothetical protein -
  OCV04_RS08955 - 1925357..1926055 (-) 699 WP_171137439.1 DUF4376 domain-containing protein -
  OCV04_RS08960 - 1926048..1927157 (-) 1110 WP_171137440.1 phage tail protein -
  OCV04_RS08965 - 1927150..1927767 (-) 618 WP_171137441.1 phage tail protein -
  OCV04_RS08970 - 1927751..1928731 (-) 981 WP_171137442.1 baseplate J/gp47 family protein -
  OCV04_RS08975 - 1928728..1929060 (-) 333 WP_171137443.1 phage baseplate protein -
  OCV04_RS08980 - 1929057..1929758 (-) 702 WP_171137444.1 phage baseplate assembly protein V -
  OCV04_RS08985 - 1929715..1930227 (-) 513 WP_171137445.1 hypothetical protein -
  OCV04_RS08990 - 1930193..1930723 (-) 531 WP_171137446.1 phage tail protein -
  OCV04_RS08995 - 1930695..1931036 (-) 342 WP_171137447.1 hypothetical protein -
  OCV04_RS09000 - 1931039..1931377 (-) 339 WP_171137448.1 hypothetical protein -
  OCV04_RS09005 - 1931442..1933616 (-) 2175 WP_171137449.1 head maturation protease, ClpP-related -
  OCV04_RS09010 - 1933609..1935099 (-) 1491 WP_171137450.1 phage portal protein -
  OCV04_RS09015 - 1935092..1935310 (-) 219 WP_171137451.1 hypothetical protein -
  OCV04_RS09020 - 1935307..1937397 (-) 2091 WP_171137452.1 terminase gpA endonuclease subunit -
  OCV04_RS09025 - 1937378..1937848 (-) 471 WP_171137453.1 hypothetical protein -
  OCV04_RS09030 - 1938175..1938453 (-) 279 WP_171137454.1 HP1 family phage holin -
  OCV04_RS09035 - 1938459..1938938 (-) 480 WP_171137455.1 lysis protein -
  OCV04_RS09040 - 1938935..1939414 (-) 480 WP_261881145.1 lysozyme -
  OCV04_RS09045 - 1939676..1941007 (+) 1332 WP_171137457.1 AAA family ATPase -
  OCV04_RS09050 - 1941012..1941893 (+) 882 WP_171137458.1 DUF4435 domain-containing protein -
  OCV04_RS09055 - 1941938..1942519 (-) 582 WP_171137459.1 hypothetical protein -
  OCV04_RS09060 - 1942519..1943091 (-) 573 WP_171137460.1 MT-A70 family methyltransferase -
  OCV04_RS09065 - 1943088..1943801 (-) 714 WP_240956654.1 ATP-binding protein -
  OCV04_RS09070 - 1943807..1944664 (-) 858 WP_171137462.1 hypothetical protein -
  OCV04_RS09075 - 1944856..1945404 (-) 549 WP_171137463.1 hypothetical protein -
  OCV04_RS09080 - 1945454..1945687 (-) 234 WP_171137464.1 helix-turn-helix transcriptional regulator -
  OCV04_RS09085 - 1945778..1946446 (+) 669 WP_171137465.1 LexA family transcriptional regulator -
  OCV04_RS09090 - 1946469..1947269 (+) 801 WP_171137466.1 hypothetical protein -
  OCV04_RS09095 - 1947492..1947767 (+) 276 WP_171137467.1 hypothetical protein -
  OCV04_RS09100 - 1947922..1948182 (+) 261 WP_171137468.1 hypothetical protein -
  OCV04_RS09105 - 1948179..1948553 (+) 375 WP_171137469.1 hypothetical protein -
  OCV04_RS09110 - 1948617..1948853 (+) 237 WP_171137470.1 hypothetical protein -
  OCV04_RS09115 - 1948894..1949748 (+) 855 WP_240956655.1 3'-5' exonuclease -
  OCV04_RS09120 - 1949806..1950066 (+) 261 WP_171137393.1 hypothetical protein -
  OCV04_RS09125 - 1950125..1950424 (+) 300 WP_171137471.1 AlpA family transcriptional regulator -
  OCV04_RS09130 - 1950421..1951800 (-) 1380 WP_171137472.1 HEPN domain-containing protein -
  OCV04_RS09135 - 1951830..1953014 (-) 1185 WP_171137473.1 site-specific integrase -
  OCV04_RS09140 sbcB 1953195..1954619 (+) 1425 WP_171137474.1 exodeoxyribonuclease I Machinery gene
  OCV04_RS09145 - 1954669..1955034 (+) 366 WP_102940531.1 CidA/LrgA family protein -

Sequence

Protein


Download         Length: 474 a.a.        Molecular weight: 54677.17 Da        Isoelectric Point: 5.2619

>NTDB_id=89210 OCV04_RS09140 WP_171137474.1 1953195..1954619(+) (sbcB) [Vibrio plantisponsor strain CECT 7581]
MKTDEQPTFFFFDYETWGTNPAKDRPSQFAGVRTDMDFNIIGEPLIIYCQLPSDYLPAPEAALITGITPQKAMAQGLPEP
EFIARIHQELSQPNTTSLGYNSIRFDDEVTRYTCYRNFFDPYSWSWQNGNSRWDLLDVMRACHALRPEGIVWPENGEGFT
SFKLEHLSKANGIEHENAHDAMADVIATIELAKKVKAAQPKLFDYFFTMRHKRKLNELVDIVNMTPLMHVSGMLGRECQY
TSWIVPIAWHPTNQNAVIVADLAKDPQPLIELSSEELHTRLYTKRDELAPDELPVPVKLVHLNKCPILAPAKTLTAENAE
KIGINREQCLANLALIRQHPEIREKLVALFSIEREFEQSTDVDTQLYDGFFSPADKASMEIIRSTPPENLAALGITFADK
RIEPLLFRYRARHFPWTLDENEQRRWANHCRDFYESRIEDYMLNLENLVHEHESDEKKIAILKSVYQYVSKLVS

Nucleotide


Download         Length: 1425 bp        

>NTDB_id=89210 OCV04_RS09140 WP_171137474.1 1953195..1954619(+) (sbcB) [Vibrio plantisponsor strain CECT 7581]
ATGAAAACTGATGAACAACCAACATTCTTCTTCTTCGATTATGAGACTTGGGGCACTAACCCAGCGAAAGATCGTCCTAG
TCAGTTTGCTGGCGTACGTACCGATATGGATTTTAATATTATCGGCGAACCATTAATTATCTACTGCCAATTACCTAGCG
ATTATTTACCTGCACCAGAGGCAGCGCTAATAACGGGTATCACCCCGCAGAAGGCGATGGCTCAAGGTCTACCTGAGCCC
GAGTTCATTGCTCGTATTCATCAAGAACTTTCTCAGCCAAATACCACCAGCCTTGGTTACAACAGCATTCGCTTCGATGA
CGAAGTCACGCGTTACACTTGCTATCGCAACTTTTTCGATCCGTATTCTTGGAGCTGGCAGAACGGCAATTCACGTTGGG
ACTTACTCGATGTGATGCGTGCTTGCCATGCCCTTCGTCCTGAAGGCATTGTTTGGCCTGAAAACGGAGAAGGGTTTACA
AGTTTCAAACTGGAACATCTGTCAAAAGCCAATGGTATTGAACACGAAAATGCGCATGATGCGATGGCTGACGTGATTGC
TACTATTGAGCTGGCTAAGAAAGTCAAAGCTGCACAACCAAAGCTGTTTGATTACTTTTTTACCATGCGCCATAAACGCA
AACTCAATGAGTTAGTGGATATCGTCAACATGACACCACTGATGCATGTTTCTGGAATGTTAGGCAGAGAATGCCAATAC
ACCAGTTGGATAGTACCTATTGCTTGGCATCCAACTAATCAAAATGCTGTGATTGTGGCTGACTTAGCCAAAGATCCTCA
GCCTTTAATTGAGCTTTCCAGTGAAGAACTGCATACGCGTCTTTATACCAAACGTGATGAACTTGCGCCCGACGAACTGC
CTGTTCCTGTCAAATTGGTTCATCTCAACAAGTGCCCTATTCTTGCACCAGCTAAGACGTTGACCGCTGAAAACGCTGAG
AAGATAGGCATCAATCGCGAACAGTGTTTAGCGAACTTAGCACTGATTCGCCAGCATCCTGAGATCCGAGAAAAGCTGGT
TGCACTGTTTTCGATTGAACGTGAATTTGAACAGAGCACCGATGTTGATACGCAGTTATACGATGGTTTCTTCTCTCCTG
CGGACAAAGCGTCGATGGAGATTATTCGCAGTACCCCACCGGAAAATTTGGCGGCACTGGGCATCACTTTTGCCGACAAA
AGAATCGAGCCTTTATTATTCCGTTATCGTGCTCGTCACTTCCCATGGACACTGGATGAAAATGAACAGCGCCGCTGGGC
GAATCACTGTCGTGATTTTTATGAGTCGCGAATTGAAGATTACATGCTCAATTTAGAAAACTTAGTTCATGAGCATGAGA
GTGACGAAAAGAAAATCGCTATTTTAAAATCTGTCTATCAATACGTCTCAAAACTCGTTTCCTAG

Domains

Predicted by InterproScan.

Exonuclease (RNase_T)

(11-191)

Exonuclease C-terminal (Exonuc_X-T_C)

(210-470)


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
  sbcB Vibrio cholerae O1 biovar El Tor strain E7946

82.875

99.789

0.827

Multiple sequence alignment