Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101577
Name   oriT_pMFDS1013864 in_silico
Organism   Escherichia coli strain MFDS1013864
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMUV010000008 (12743..12866 [-], 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_pMFDS1013864
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   533 GenBank   WP_001254386
Name   WP_001254386_pMFDS1013864 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

ID   534 GenBank   WP_040073112
Name   WP_040073112_pMFDS1013864 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: 14556.62 Da        Isoelectric Point: 5.0278

>WP_040073112.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSIEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   1043 GenBank   WP_001064245
Name   traC_V6M12_RS19200_pMFDS1013864 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.



ID   1044 GenBank   WP_062873762
Name   traD_V6M12_RS19775_pMFDS1013864 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 151..13438

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M12_RS19180 151..789 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M12_RS19185 798..1790 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6M12_RS19190 1787..2419 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6M12_RS19195 2416..2802 - 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6M12_RS19200 2799..5426 - 2628 WP_001064245 type IV secretion system protein TraC virb4
V6M12_RS19205 5586..5807 - 222 WP_001278689 conjugal transfer protein TraR -
V6M12_RS19210 5942..6457 - 516 WP_332829757 type IV conjugative transfer system lipoprotein TraV traV
V6M12_RS19215 6454..6704 - 251 Protein_7 conjugal transfer protein TrbG -
V6M12_RS19220 6716..6913 - 198 WP_001324648 conjugal transfer protein TrbD -
V6M12_RS19225 6900..7490 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6M12_RS19230 7480..8907 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6M12_RS19235 8907..9634 - 728 Protein_11 type-F conjugative transfer system secretin TraK -
V6M12_RS19240 9621..10187 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6M12_RS19245 10209..10520 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6M12_RS19250 10535..10900 - 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6M12_RS19255 10934..11161 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6M12_RS19260 11255..11941 - 687 WP_000332492 PAS domain-containing protein -
V6M12_RS19265 12131..12514 - 384 WP_040073112 conjugal transfer relaxosome DNA-binding protein TraM -
V6M12_RS19270 12791..13438 + 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6M12_RS19275 13735..14556 - 822 WP_074014913 DUF932 domain-containing protein -
V6M12_RS19280 14675..14961 - 287 Protein_20 hypothetical protein -
V6M12_RS19285 14986..15192 - 207 WP_000547968 hypothetical protein -
V6M12_RS19290 15262..15435 + 174 Protein_22 hypothetical protein -
V6M12_RS19295 15433..15636 - 204 WP_332832966 hypothetical protein -
V6M12_RS19300 15639..17210 - 1572 WP_000381442 IS66 family transposase -
V6M12_RS19305 17230..17577 - 348 WP_000624618 IS66 family insertion sequence element accessory protein TnpB -
V6M12_RS19310 17577..18227 - 651 WP_000993956 IS66-like element accessory protein TnpA -

Region 2: 86973..99672

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M12_RS19765 86339..86566 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
V6M12_RS19770 86566..86964 + 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6M12_RS19775 86973..89126 - 2154 WP_062873762 type IV conjugative transfer system coupling protein TraD virb4
V6M12_RS19780 89378..90109 - 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6M12_RS19785 90123..90632 - 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6M12_RS19790 90629..93454 - 2826 WP_032082912 conjugal transfer mating-pair stabilization protein TraG traG
V6M12_RS19795 93451..94824 - 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
V6M12_RS19800 94811..95203 - 393 WP_032082924 F-type conjugal transfer protein TrbF -
V6M12_RS19805 95190..95531 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6M12_RS19810 95461..96006 - 546 WP_032082911 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6M12_RS19815 95993..96277 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6M12_RS19820 96358..96633 + 276 WP_001513501 hypothetical protein -
V6M12_RS19825 96635..96982 - 348 WP_032082949 conjugal transfer protein TrbA -
V6M12_RS19830 96998..97741 - 744 WP_032082948 type-F conjugative transfer system pilin assembly protein TraF traF
V6M12_RS19835 97734..97991 - 258 WP_000864318 conjugal transfer protein TrbE -
V6M12_RS19840 98018..99672 - 1655 WP_332832965 type-F conjugative transfer system mating-pair stabilization protein TraN traN

Host bacterium

ID   2021 GenBank   NZ_JAQMUV010000008
Plasmid name   pMFDS1013864 Incompatibility group   IncFII
Plasmid size   99672 bp Coordinate of oriT [Strand]   12743..12866 [-]
Host baterium   Escherichia coli strain MFDS1013864

Cargo genes

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