Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100712
Name   oriT_pNCM3722-F in_silico
Organism   Escherichia coli strain NCM3722 isolate K-12
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP011496 (2243..2532 [-], 290 nt)
oriT length   290 nt
IRs (inverted repeats)      225..232, 235..242 n  (GCAAAAAC..GTTTTTGC)
Location of nic site      251..252
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 290 nt

>oriT_pNCM3722-F
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   784 GenBank   WP_000987005
Name   TraI_pNCM3722-F insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192015.91 Da        Isoelectric Point: 5.8951

>WP_000987005.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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

(575-625)

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

(633-712)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1681..28082

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AA953_RS27195 (AA953_23295) 14..133 + 120 WP_014106970 hypothetical protein -
AA953_RS23235 (AA953_23300) 158..445 + 288 WP_000107542 hypothetical protein -
AA953_RS23240 (AA953_23305) 564..1385 + 822 WP_001234417 DUF932 domain-containing protein -
AA953_RS23245 (AA953_23310) 1681..2283 - 603 WP_000243701 transglycosylase SLT domain-containing protein virB1
AA953_RS23250 (AA953_23315) 2604..2987 + 384 WP_001151527 conjugal transfer relaxosome DNA-binding protein TraM -
AA953_RS23255 (AA953_23320) 3174..3863 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
AA953_RS23260 (AA953_23325) 3962..4357 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
AA953_RS23265 (AA953_23330) 4390..4755 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
AA953_RS23270 (AA953_23335) 4770..5081 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
AA953_RS23275 (AA953_23340) 5103..5669 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
AA953_RS23280 (AA953_23345) 5656..6384 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
AA953_RS23285 (AA953_23350) 6384..7811 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
AA953_RS23290 (AA953_23355) 7801..8391 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
AA953_RS23295 (AA953_23360) 8378..8575 + 198 WP_001443030 conjugal transfer protein TrbD -
AA953_RS23300 (AA953_23365) 8587..8838 + 252 WP_001038342 conjugal transfer protein TrbG -
AA953_RS23305 (AA953_23370) 8835..9350 + 516 WP_000809843 type IV conjugative transfer system lipoprotein TraV traV
AA953_RS25570 (AA953_23375) 9485..9706 + 222 WP_001278689 conjugal transfer protein TraR -
AA953_RS23315 (AA953_23380) 9866..12493 + 2628 WP_001064243 type IV secretion system protein TraC virb4
AA953_RS23320 (AA953_23385) 12490..12876 + 387 WP_000099690 type-F conjugative transfer system protein TrbI -
AA953_RS23325 (AA953_23390) 12873..13505 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
AA953_RS23330 (AA953_23395) 13502..14494 + 993 WP_000830185 conjugal transfer pilus assembly protein TraU traU
AA953_RS23335 (AA953_23400) 14503..15141 + 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
AA953_RS23340 (AA953_23405) 15138..16946 + 1809 WP_000821835 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AA953_RS23345 (AA953_23410) 16973..17230 + 258 WP_000864318 conjugal transfer protein TrbE -
AA953_RS23350 (AA953_23415) 17223..17966 + 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
AA953_RS23355 (AA953_23420) 17982..18329 + 348 WP_001287913 conjugal transfer protein TrbA -
AA953_RS23360 (AA953_23425) 18331..18645 - 315 WP_000415566 protein ArtA -
AA953_RS23365 (AA953_23430) 18726..19010 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
AA953_RS23370 (AA953_23435) 18997..19542 + 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AA953_RS23375 (AA953_23440) 19472..19813 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
AA953_RS23380 (AA953_23445) 19800..20180 + 381 WP_001366201 F-type conjugal transfer protein TrbF -
AA953_RS23385 (AA953_23450) 20180..21553 + 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
AA953_RS23390 (AA953_23455) 21550..24366 + 2817 WP_001007055 conjugal transfer mating-pair stabilization protein TraG traG
AA953_RS25575 24399..24920 + 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
AA953_RS23400 (AA953_23465) 24945..25676 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
AA953_RS23405 (AA953_23470) 25929..28082 + 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
AA953_RS23410 (AA953_23475) 28091..28489 - 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
AA953_RS23415 (AA953_23480) 28489..28716 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1172 GenBank   NZ_CP011496
Plasmid name   pNCM3722-F Incompatibility group   IncFIC
Plasmid size   67545 bp Coordinate of oriT [Strand]   2243..2532 [-]
Host baterium   Escherichia coli strain NCM3722 isolate K-12

Cargo genes

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