Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103277
Name   oriT_pEC1188-NDM16 in_silico
Organism   Escherichia coli strain EC1188
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH213345 (42740..42863 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pEC1188-NDM16
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   2219 GenBank   WP_000069764
Name   traC_HTR95_RS00320_pEC1188-NDM16 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.



ID   2220 GenBank   WP_022630316
Name   traD_HTR95_RS00400_pEC1188-NDM16 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83920.60 Da        Isoelectric Point: 5.0524

>WP_022630316.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42168..69006

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTR95_RS00210 37270..37461 + 192 WP_039021874 hypothetical protein -
HTR95_RS00215 37775..39442 - 1668 WP_012372796 group II intron reverse transcriptase/maturase -
HTR95_RS00465 40171..40344 - 174 Protein_44 hypothetical protein -
HTR95_RS00470 40414..40620 + 207 WP_000547968 hypothetical protein -
HTR95_RS00225 40645..40932 + 288 WP_000107544 hypothetical protein -
HTR95_RS00230 41050..41871 + 822 WP_001234469 DUF932 domain-containing protein -
HTR95_RS00235 42168..42815 - 648 WP_031943493 transglycosylase SLT domain-containing protein virB1
HTR95_RS00240 43092..43475 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTR95_RS00245 43666..44352 + 687 WP_000332484 PAS domain-containing protein -
HTR95_RS00250 44446..44673 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTR95_RS00255 44707..45066 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
HTR95_RS00260 45081..45392 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTR95_RS00265 45414..45980 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTR95_RS00270 45967..46695 + 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
HTR95_RS00275 46695..48122 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HTR95_RS00280 48112..48702 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
HTR95_RS00285 48689..49009 + 321 WP_001057287 conjugal transfer protein TrbD virb4
HTR95_RS00290 49002..49253 + 252 WP_001038342 conjugal transfer protein TrbG -
HTR95_RS00295 49250..49765 + 516 WP_015059130 type IV conjugative transfer system lipoprotein TraV traV
HTR95_RS00300 49900..50121 + 222 WP_001278695 conjugal transfer protein TraR -
HTR95_RS00305 50114..50590 + 477 WP_015059129 hypothetical protein -
HTR95_RS00310 50670..50884 + 215 Protein_63 hypothetical protein -
HTR95_RS00315 50912..51274 + 363 WP_000836675 hypothetical protein -
HTR95_RS00320 51400..54030 + 2631 WP_000069764 type IV secretion system protein TraC virb4
HTR95_RS00325 54027..54413 + 387 WP_000214092 type-F conjugative transfer system protein TrbI -
HTR95_RS00330 54410..55042 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTR95_RS00335 55039..56031 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HTR95_RS00340 56040..56678 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTR95_RS00345 56675..58483 + 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTR95_RS00350 58509..58766 + 258 WP_000864352 conjugal transfer protein TrbE -
HTR95_RS00355 58759..59502 + 744 WP_001430248 type-F conjugative transfer system pilin assembly protein TraF traF
HTR95_RS00360 59518..59865 + 348 WP_001287891 conjugal transfer protein TrbA -
HTR95_RS00365 59984..60268 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HTR95_RS00370 60290..60799 + 510 WP_172693540 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTR95_RS00375 60729..61091 + 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HTR95_RS00380 61091..62464 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HTR95_RS00385 62461..65286 + 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
HTR95_RS00390 65283..65792 + 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
HTR95_RS00395 65806..66537 + 732 WP_094658456 conjugal transfer complement resistance protein TraT -
HTR95_RS00400 66790..69006 + 2217 WP_022630316 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3720 GenBank   NZ_MH213345
Plasmid name   pEC1188-NDM16 Incompatibility group   IncFII
Plasmid size   80215 bp Coordinate of oriT [Strand]   42740..42863 [+]
Host baterium   Escherichia coli strain EC1188

Cargo genes

Drug resistance gene   blaTEM-1B, rmtB, blaNDM-15, sul1, qacE, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11