Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101777
Name   oriT_p2018n8362554_1 in_silico
Organism   Escherichia coli strain COL5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACYGD010000001 (6933..7284 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_p2018n8362554_1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTAGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   597 GenBank   WP_001369361
Name   WP_001369361_p2018n8362554_1 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   598 GenBank   WP_001151524
Name   WP_001151524_p2018n8362554_1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   1170 GenBank   WP_000009350
Name   traD_IYY12_RS00715_p2018n8362554_1 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81488.99 Da        Isoelectric Point: 5.0504

>WP_000009350.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWIKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCSEQLWSAFVLAAVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  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.



ID   1171 GenBank   WP_001064247
Name   traC_IYY12_RS00805_p2018n8362554_1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99187.86 Da        Isoelectric Point: 5.8486

>WP_001064247.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 186..7855

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IYY12_RS00010 186..701 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
IYY12_RS00015 698..949 - 252 WP_001038342 conjugal transfer protein TrbG -
IYY12_RS00020 961..1158 - 198 WP_001324648 conjugal transfer protein TrbD -
IYY12_RS00025 1145..1735 - 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
IYY12_RS00030 1725..3152 - 1428 WP_000146692 F-type conjugal transfer pilus assembly protein TraB traB
IYY12_RS00035 3152..3880 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
IYY12_RS00040 3867..4433 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
IYY12_RS00045 4455..4766 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
IYY12_RS00050 4781..5146 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
IYY12_RS00055 5179..5574 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
IYY12_RS00060 5673..6362 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
IYY12_RS00065 6549..6932 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
IYY12_RS00070 7253..7855 + 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
IYY12_RS00075 8152..8973 - 822 WP_001234471 DUF932 domain-containing protein -
IYY12_RS00080 9094..9381 - 288 WP_000107535 hypothetical protein -
IYY12_RS00085 9406..9612 - 207 WP_000547939 hypothetical protein -
IYY12_RS26025 9682..9855 + 174 Protein_17 hypothetical protein -
IYY12_RS26030 9853..10083 - 231 WP_001426396 hypothetical protein -
IYY12_RS00090 10303..10428 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
IYY12_RS26035 10370..10519 - 150 Protein_20 plasmid maintenance protein Mok -
IYY12_RS00095 10541..10729 + 189 WP_001299721 hypothetical protein -
IYY12_RS00100 10698..11460 - 763 Protein_22 plasmid SOS inhibition protein A -
IYY12_RS00105 11457..11891 - 435 WP_000845895 conjugation system SOS inhibitor PsiB -

Region 2: 127071..145288

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IYY12_RS00705 126437..126664 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
IYY12_RS00710 126664..127062 + 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
IYY12_RS00715 127071..129224 - 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
IYY12_RS00720 129477..130208 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
IYY12_RS00725 130233..130754 - 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
IYY12_RS00730 130787..133603 - 2817 WP_001007054 conjugal transfer mating-pair stabilization protein TraG traG
IYY12_RS00735 133600..134973 - 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
IYY12_RS00740 134973..135354 - 382 Protein_153 F-type conjugal transfer protein TrbF -
IYY12_RS00745 135341..135682 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
IYY12_RS00750 135612..136157 - 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IYY12_RS00755 136144..136428 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
IYY12_RS00760 136509..136823 + 315 WP_000415567 hypothetical protein -
IYY12_RS00765 136825..137172 - 348 WP_001287913 conjugal transfer protein TrbA -
IYY12_RS00770 137188..137931 - 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
IYY12_RS00775 137924..138181 - 258 WP_000864318 conjugal transfer protein TrbE -
IYY12_RS00780 138208..140016 - 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IYY12_RS00785 140013..140651 - 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
IYY12_RS00790 140660..141652 - 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
IYY12_RS00795 141649..142281 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
IYY12_RS00800 142278..142664 - 387 WP_000097319 type-F conjugative transfer system protein TrbI -
IYY12_RS00805 142661..145288 - 2628 WP_001064247 type IV secretion system protein TraC virb4

Host bacterium

ID   2221 GenBank   NZ_JACYGD010000001
Plasmid name   p2018n8362554_1 Incompatibility group   IncFIB
Plasmid size   145618 bp Coordinate of oriT [Strand]   6933..7284 [-]
Host baterium   Escherichia coli strain COL5

Cargo genes

Drug resistance gene   sitABCD, tet(A), blaTEM-1B
Virulence gene   iroB, iroC, iroD, iroE, iroN
Metal resistance gene   merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -