Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100247
Name   oriT_pC15-1a in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_005327 (50301..50850 [-], 550 nt)
oriT length   550 nt
IRs (inverted repeats)      243..255, 257..269  (TATTTAATAATTC..GAATTATTAAATA)
 311..318, 321..328  (GCAAAAAC..GTTTTTGC)
Location of nic site      337..338
Conserved sequence flanking the
  nic site    		  GTAGTGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 550 nt

>oriT_pC15-1a
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAATGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCATGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   318 GenBank   NP_957632
Name   TraI_pC15-1a insolico UniProt ID   Q6SIZ4
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>NP_957632.1 conjugal transfer nickase/helicase TraI (plasmid) [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 49913..77993

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS369_RS00270 (pC15-1a_045) 45290..45715 + 426 WP_000422741 transposase -
HS369_RS00275 (pC15-1a_046) 45712..46062 + 351 WP_000624722 IS66 family insertion sequence element accessory protein TnpB -
HS369_RS00280 (pC15-1a_047) 46093..47706 + 1614 WP_000080200 IS66-like element ISEc23 family transposase -
HS369_RS00570 47791..48087 - 297 Protein_57 hypothetical protein -
HS369_RS00285 48158..48364 + 207 WP_001087957 hypothetical protein -
HS369_RS00290 (pC15-1a_049) 48388..48684 + 297 WP_001272251 hypothetical protein -
HS369_RS00295 (pC15-1a_050) 48795..49616 + 822 WP_001234445 DUF932 domain-containing protein -
HS369_RS00300 (pC15-1a_051) 49913..50515 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HS369_RS00305 (pC15-1a_052) 50838..51221 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HS369_RS00310 (pC15-1a_053) 51415..52086 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HS369_RS00315 (pC15-1a_054) 52223..52450 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HS369_RS00320 (pC15-1a_055) 52483..52842 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HS369_RS00325 (pC15-1a_056) 52857..53168 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HS369_RS00330 (pC15-1a_057) 53190..53756 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HS369_RS00335 (pC15-1a_058) 53743..54471 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HS369_RS00340 (pC15-1a_059) 54471..55922 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HS369_RS00345 (pC15-1a_060) 55912..56478 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HS369_RS00350 (pC15-1a_061) 56465..56785 + 321 WP_001057307 conjugal transfer protein TrbD -
HS369_RS00355 (pC15-1a_062) 56782..57297 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HS369_RS00360 (pC15-1a_063) 57432..57653 + 222 WP_001278683 conjugal transfer protein TraR -
HS369_RS00365 (pC15-1a_064) 57646..58122 + 477 WP_000549587 hypothetical protein -
HS369_RS00370 (pC15-1a_065) 58202..58420 + 219 WP_000556745 hypothetical protein -
HS369_RS00375 (pC15-1a_066) 58448..58795 + 348 WP_000836682 hypothetical protein -
HS369_RS00380 (pC15-1a_067) 58921..61551 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HS369_RS00385 (pC15-1a_068) 61548..61934 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HS369_RS00390 (pC15-1a_069) 61931..62563 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HS369_RS00395 (pC15-1a_070) 62560..63552 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HS369_RS00400 (pC15-1a_071) 63582..63887 + 306 WP_000224416 hypothetical protein -
HS369_RS00405 (pC15-1a_072) 63896..64534 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS369_RS00410 (pC15-1a_073) 64531..66381 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS369_RS00415 (pC15-1a_074) 66408..66665 + 258 WP_000864353 conjugal transfer protein TrbE -
HS369_RS00420 (pC15-1a_075) 66658..67401 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HS369_RS00425 (pC15-1a_076) 67415..67759 + 345 WP_000556796 conjugal transfer protein TrbA -
HS369_RS00430 (pC15-1a_077) 67878..68162 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HS369_RS00435 (pC15-1a_078) 68149..68694 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS369_RS00440 (pC15-1a_079) 68624..68971 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HS369_RS00445 (pC15-1a_080) 68952..69344 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HS369_RS00450 (pC15-1a_081) 69331..70704 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HS369_RS00455 (pC15-1a_082) 70701..73523 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HS369_RS00460 (pC15-1a_083) 73539..74024 + 486 WP_000605870 hypothetical protein -
HS369_RS00465 (pC15-1a_084) 74073..74804 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HS369_RS00470 (pC15-1a_085) 75007..75744 + 738 WP_000199905 hypothetical protein -
HS369_RS00475 (pC15-1a_086) 75795..77993 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   709 GenBank   NC_005327
Plasmid name   pC15-1a Incompatibility group   IncFII
Plasmid size   92353 bp Coordinate of oriT [Strand]   50301..50850 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   tet(A), blaOXA-1, aac(6')-Ib-cr, aac(3)-IIa, blaCTX-M-15, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -