Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116158
Name   oriT_pATCC-35471_1 in_silico
Organism   Escherichia fergusonii strain ATCC 35471
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP042943 (2771..2894 [+], 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_pATCC-35471_1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   12085 GenBank   WP_000069764
Name   traC_FV159_RS00110_pATCC-35471_1 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   12086 GenBank   WP_001610321
Name   traD_FV159_RS00190_pATCC-35471_1 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82846.44 Da        Isoelectric Point: 5.0504

>WP_001610321.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
IQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 2199..28756

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FV159_RS23735 1..205 + 205 WP_148049164 hypothetical protein -
FV159_RS23815 203..376 - 174 Protein_1 hypothetical protein -
FV159_RS00020 677..964 + 288 WP_000107538 hypothetical protein -
FV159_RS00025 1081..1902 + 822 WP_021573168 DUF932 domain-containing protein -
FV159_RS00030 2199..2846 - 648 WP_148049165 transglycosylase SLT domain-containing protein virB1
FV159_RS00035 3123..3506 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
FV159_RS00040 3697..4383 + 687 WP_000332484 PAS domain-containing protein -
FV159_RS00045 4477..4704 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
FV159_RS00050 4738..5097 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
FV159_RS00055 5112..5423 + 312 WP_000012103 type IV conjugative transfer system protein TraL traL
FV159_RS00060 5445..6011 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
FV159_RS00065 5998..6726 + 729 WP_001230798 type-F conjugative transfer system secretin TraK traK
FV159_RS00070 6726..8153 + 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
FV159_RS00075 8143..8733 + 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
FV159_RS00080 8720..9040 + 321 WP_001057307 conjugal transfer protein TrbD -
FV159_RS00085 9037..9552 + 516 WP_000809874 type IV conjugative transfer system lipoprotein TraV traV
FV159_RS00090 9687..9908 + 222 WP_001278695 conjugal transfer protein TraR -
FV159_RS00095 9901..10377 + 477 WP_000549579 hypothetical protein -
FV159_RS00100 10457..10674 + 218 Protein_18 hypothetical protein -
FV159_RS00105 10702..11049 + 348 WP_000802783 hypothetical protein -
FV159_RS00110 11176..13806 + 2631 WP_000069764 type IV secretion system protein TraC virb4
FV159_RS00115 13803..14189 + 387 WP_000214097 type-F conjugative transfer system protein TrbI -
FV159_RS00120 14186..14818 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
FV159_RS00125 14815..15807 + 993 WP_000830854 conjugal transfer pilus assembly protein TraU traU
FV159_RS00130 15816..16454 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
FV159_RS00135 16451..18259 + 1809 WP_000821843 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FV159_RS00140 18285..18542 + 258 WP_000864328 conjugal transfer protein TrbE -
FV159_RS00145 18535..19278 + 744 WP_001030390 type-F conjugative transfer system pilin assembly protein TraF traF
FV159_RS00150 19294..19641 + 348 WP_001287679 conjugal transfer protein TrbA -
FV159_RS00155 19760..20044 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
FV159_RS00160 20031..20576 + 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FV159_RS00165 20506..20868 + 363 WP_010379880 P-type conjugative transfer protein TrbJ -
FV159_RS00170 20868..22241 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
FV159_RS00175 22238..25063 + 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
FV159_RS00180 25060..25515 + 456 WP_148049166 conjugal transfer entry exclusion protein TraS -
FV159_RS00185 25584..26315 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
FV159_RS00190 26567..28756 + 2190 WP_001610321 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16591 GenBank   NZ_CP042943
Plasmid name   pATCC-35471_1 Incompatibility group   IncFII
Plasmid size   42599 bp Coordinate of oriT [Strand]   2771..2894 [+]
Host baterium   Escherichia fergusonii strain ATCC 35471

Cargo genes

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