Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100951
Name   oriT_pXF-De_Donno in_silico
Organism   Xylella fastidiosa subsp. pauca strain De Donno
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP020871 (5956..6058 [-], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      53..70, 75..92  (GTGAAGAAGGAACACCGG..CCGGTGGGCCTACTTCAC)
Location of nic site      100..101
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 103 nt

>oriT_pXF-De_Donno
AGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1021 GenBank   WP_046417493
Name   TraI_pXF-De_Donno insolico UniProt ID   _
Length   830 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 830 a.a.        Molecular weight: 92904.89 Da        Isoelectric Point: 10.5707

>WP_046417493.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVMDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESHVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQAQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(463-550)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22462..32740

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
B9J09_RS11990 (B9J09_11990) 18192..18749 - 558 WP_046417502 recombinase family protein -
B9J09_RS11995 (B9J09_11995) 18837..19124 - 288 WP_004085905 type II toxin-antitoxin system RelE/ParE family toxin -
B9J09_RS12000 (B9J09_12000) 19117..19359 - 243 WP_004085758 type II toxin-antitoxin system ParD family antitoxin -
B9J09_RS13255 19554..19640 + 87 Protein_19 type II toxin-antitoxin system RelE/ParE family toxin -
B9J09_RS12005 (B9J09_12005) 19777..20097 + 321 WP_046417511 type II toxin-antitoxin system RelE/ParE family toxin -
B9J09_RS12010 (B9J09_12010) 20227..20553 + 327 WP_004091396 DNA-binding protein -
B9J09_RS12510 20928..21101 - 174 WP_155641416 hypothetical protein -
B9J09_RS12015 (B9J09_12015) 21103..21375 - 273 WP_046417513 type II toxin-antitoxin system RelE/ParE family toxin -
B9J09_RS12020 (B9J09_12020) 21347..21826 + 480 Protein_24 Tn3 family transposase -
B9J09_RS12025 (B9J09_12025) 21722..22456 - 735 WP_232755968 conjugal transfer protein TrbN -
B9J09_RS12030 (B9J09_12030) 22462..23859 - 1398 WP_046417516 P-type conjugative transfer protein TrbL virB6
B9J09_RS12515 (B9J09_12035) 23865..24179 - 315 WP_155561293 EexN family lipoprotein -
B9J09_RS12040 (B9J09_12040) 24192..24977 - 786 WP_046417519 P-type conjugative transfer protein TrbJ virB5
B9J09_RS12045 (B9J09_12045) 24996..26396 - 1401 WP_046417521 TrbI/VirB10 family protein virB10
B9J09_RS12050 (B9J09_12050) 26402..26878 - 477 WP_046417523 conjugal transfer protein TrbH -
B9J09_RS12055 (B9J09_12055) 26881..27771 - 891 WP_046417527 P-type conjugative transfer protein TrbG virB9
B9J09_RS12060 (B9J09_12060) 27788..28504 - 717 WP_046417528 conjugal transfer protein TrbF virB8
B9J09_RS12065 (B9J09_12065) 28501..31065 - 2565 WP_046417530 conjugal transfer protein TrbE virb4
B9J09_RS12070 (B9J09_12070) 31053..31373 - 321 WP_046417532 conjugal transfer protein TrbD virB3
B9J09_RS12075 (B9J09_12075) 31376..31768 - 393 WP_046417535 TrbC/VirB2 family protein virB2
B9J09_RS12080 (B9J09_12080) 31781..32740 - 960 WP_046417547 P-type conjugative transfer ATPase TrbB virB11
B9J09_RS12085 (B9J09_12085) 32938..33294 - 357 WP_012382841 transcriptional regulator -
B9J09_RS12090 (B9J09_12090) 33412..33771 + 360 WP_004091494 single-stranded DNA-binding protein -
B9J09_RS12095 (B9J09_12095) 33815..34162 + 348 WP_050812600 hypothetical protein -
B9J09_RS12100 (B9J09_12100) 34206..35117 + 912 WP_004091489 replication protein RepA -

Host bacterium

ID   1409 GenBank   NZ_CP020871
Plasmid name   pXF-De_Donno Incompatibility group   _
Plasmid size   35273 bp Coordinate of oriT [Strand]   5956..6058 [-]
Host baterium   Xylella fastidiosa subsp. pauca strain De Donno

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -