Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100434
Name   oriT_pTC1 in_silico
Organism   Escherichia coli F18+
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_018998 (51718..52267 [-], 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_pTC1
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAATGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCATGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   505 GenBank   YP_006940289
Name   TraI_pTC1 insolico UniProt ID   G7QEG1
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

>YP_006940289.1 TraI protein (plasmid) [Escherichia coli F18+]
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: 51330..79849

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
TC1_RS00305 (TC1_0062) 46510..47160 + 651 WP_000993956 IS66-like element accessory protein TnpA -
TC1_RS00310 (TC1_0063) 47160..47507 + 348 WP_000624618 IS66 family insertion sequence element accessory protein TnpB -
TC1_RS00315 (TC1_0064) 47527..49098 + 1572 WP_000381443 IS66 family transposase -
TC1_RS00320 49208..49504 - 297 Protein_65 hypothetical protein -
TC1_RS00325 (TC1_0066) 49805..50101 + 297 WP_001272251 hypothetical protein -
TC1_RS00330 (TC1_0067) 50212..51033 + 822 WP_001234445 DUF932 domain-containing protein -
TC1_RS00335 (TC1_0068) 51330..51932 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
TC1_RS00340 (TC1_0069) 52255..52638 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
TC1_RS00345 (TC1_0070) 52832..53503 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
TC1_RS00350 (TC1_0071) 53640..53867 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
TC1_RS00355 (TC1_0072) 53900..54259 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
TC1_RS00360 (TC1_0073) 54274..54585 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
TC1_RS00365 (TC1_0074) 54607..55173 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
TC1_RS00370 (TC1_0075) 55160..55888 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
TC1_RS00375 (TC1_0076) 55888..57339 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
TC1_RS00380 (TC1_0077) 57329..57895 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
TC1_RS00385 (TC1_0078) 57882..58202 + 321 WP_001057307 conjugal transfer protein TrbD -
TC1_RS00390 (TC1_0079) 58199..58714 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
TC1_RS00395 (TC1_0080) 58849..59070 + 222 WP_001278683 conjugal transfer protein TraR -
TC1_RS00400 (TC1_0081) 59063..59476 + 414 WP_000549589 hypothetical protein -
TC1_RS00405 59469..59942 + 474 WP_000549568 hypothetical protein -
TC1_RS00410 60022..60240 + 219 WP_000556745 hypothetical protein -
TC1_RS00415 (TC1_0083) 60268..60615 + 348 WP_000836682 hypothetical protein -
TC1_RS00420 (TC1_0084) 60741..63371 + 2631 WP_000069777 type IV secretion system protein TraC virb4
TC1_RS00425 (TC1_0085) 63368..63754 + 387 WP_015056478 type-F conjugative transfer system protein TrbI -
TC1_RS00430 (TC1_0086) 63751..64383 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
TC1_RS00435 (TC1_0087) 64380..65372 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
TC1_RS00440 (TC1_0088) 65402..65707 + 306 WP_000224416 hypothetical protein -
TC1_RS00445 (TC1_0089) 65716..66354 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
TC1_RS00450 (TC1_0090) 66351..68201 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
TC1_RS00455 68228..68485 + 258 WP_000864353 conjugal transfer protein TrbE -
TC1_RS00460 (TC1_0091) 68478..69221 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
TC1_RS00465 (TC1_0092) 69235..69579 + 345 WP_000556796 conjugal transfer protein TrbA -
TC1_RS00470 (TC1_0093) 69698..69982 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
TC1_RS00475 (TC1_0094) 69969..70514 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
TC1_RS00480 (TC1_0095) 70444..70791 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
TC1_RS00485 (TC1_0096) 70772..71164 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
TC1_RS00490 (TC1_0097) 71151..72524 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
TC1_RS00495 (TC1_0098) 72521..75343 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
TC1_RS00500 (TC1_0099) 75359..75844 + 486 WP_000605870 hypothetical protein -
TC1_RS00505 (TC1_0100) 75893..76624 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
TC1_RS00510 (TC1_0101) 76827..77564 + 738 WP_000199905 hypothetical protein -
TC1_RS00515 (TC1_0102) 77615..79849 + 2235 WP_000009330 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   895 GenBank   NC_018998
Plasmid name   pTC1 Incompatibility group   IncFII
Plasmid size   91019 bp Coordinate of oriT [Strand]   51718..52267 [-]
Host baterium   Escherichia coli F18+

Cargo genes

Drug resistance gene   tet(B)
Virulence gene   estIa
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -