Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101570
Name   oriT_pMFDS1013781 in_silico
Organism   Escherichia coli strain MFDS1013781
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMUS010000004 (72399..72522 [+], 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)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 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_pMFDS1013781
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   519 GenBank   WP_032083503
Name   WP_032083503_pMFDS1013781 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14584.63 Da        Isoelectric Point: 5.0278

>WP_032083503.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVERRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSIEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   520 GenBank   WP_001254386
Name   WP_001254386_pMFDS1013781 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1031 GenBank   WP_062873762
Name   traD_V6M00_RS26025_pMFDS1013781 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: 81434.90 Da        Isoelectric Point: 5.0485

>WP_062873762.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPDMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.



ID   1032 GenBank   WP_001064245
Name   traC_V6M00_RS26530_pMFDS1013781 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: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
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: 71827..87935

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M00_RS26415 67311..67658 + 348 WP_000624618 IS66 family insertion sequence element accessory protein TnpB -
V6M00_RS26420 67678..69249 + 1572 WP_332831964 IS66 family transposase -
V6M00_RS26425 69281..69333 + 53 Protein_89 Hok/Gef family protein -
V6M00_RS26430 69313..69378 + 66 WP_224156702 DUF5431 family protein -
V6M00_RS26435 69602..69832 + 231 WP_074014914 hypothetical protein -
V6M00_RS26440 69830..70003 - 174 Protein_92 hypothetical protein -
V6M00_RS26445 70073..70279 + 207 WP_000547968 hypothetical protein -
V6M00_RS26450 70304..70590 + 287 Protein_94 hypothetical protein -
V6M00_RS26455 70709..71530 + 822 WP_074014913 DUF932 domain-containing protein -
V6M00_RS26460 71827..72474 - 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6M00_RS26465 72751..73134 + 384 WP_032083503 conjugal transfer relaxosome DNA-binding protein TraM -
V6M00_RS26470 73324..74010 + 687 WP_000332492 PAS domain-containing protein -
V6M00_RS26475 74104..74331 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6M00_RS26480 74365..74730 + 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6M00_RS26485 74745..75056 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6M00_RS26490 75078..75644 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6M00_RS26495 75631..76359 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
V6M00_RS26500 76359..77781 + 1423 Protein_104 F-type conjugal transfer pilus assembly protein TraB -
V6M00_RS26505 77771..78361 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6M00_RS26510 78348..78545 + 198 WP_001324648 conjugal transfer protein TrbD -
V6M00_RS26515 78557..78807 + 251 Protein_107 conjugal transfer protein TrbG -
V6M00_RS26520 78804..79319 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
V6M00_RS26525 79454..79675 + 222 WP_001278689 conjugal transfer protein TraR -
V6M00_RS26530 79835..82462 + 2628 WP_001064245 type IV secretion system protein TraC virb4
V6M00_RS26535 82459..82845 + 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6M00_RS26540 82842..83474 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6M00_RS26545 83471..84463 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6M00_RS26550 84472..85110 + 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M00_RS26555 85107..86915 + 1809 WP_096111975 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6M00_RS26560 86942..87199 + 258 WP_000864318 conjugal transfer protein TrbE -
V6M00_RS26565 87192..87935 + 744 WP_123010632 type-F conjugative transfer system pilin assembly protein TraF traF
V6M00_RS26570 87951..88298 + 348 WP_032082949 conjugal transfer protein TrbA -
V6M00_RS26575 88300..88575 - 276 WP_001513501 hypothetical protein -
V6M00_RS26580 88656..88940 + 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -

Host bacterium

ID   2014 GenBank   NZ_JAQMUS010000004
Plasmid name   pMFDS1013781 Incompatibility group   IncFII
Plasmid size   89044 bp Coordinate of oriT [Strand]   72399..72522 [+]
Host baterium   Escherichia coli strain MFDS1013781

Cargo genes

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