Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101578
Name   oriT_pMFDS1016183 in_silico
Organism   Escherichia coli strain MFDS1016183
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMVA010000002 (30225..30348 [+], 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_pMFDS1016183
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1045 GenBank   WP_001064245
Name   traC_V6L97_RS24420_pMFDS1016183 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   1046 GenBank   WP_062873762
Name   traD_V6L97_RS24510_pMFDS1016183 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: 29653..55791

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6L97_RS24305 24830..25177 + 348 WP_000624622 IS66 family insertion sequence element accessory protein TnpB -
V6L97_RS24310 25197..26768 + 1572 WP_332833059 IS66-like element ISCro1 family transposase -
V6L97_RS24315 26992..27141 + 150 Protein_37 plasmid maintenance protein Mok -
V6L97_RS24320 27083..27208 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6L97_RS24325 27428..27658 + 231 WP_074014914 hypothetical protein -
V6L97_RS24330 27656..27829 - 174 Protein_40 hypothetical protein -
V6L97_RS24335 27899..28105 + 207 WP_000547968 hypothetical protein -
V6L97_RS24340 28130..28416 + 287 Protein_42 hypothetical protein -
V6L97_RS24345 28535..29356 + 822 WP_074014913 DUF932 domain-containing protein -
V6L97_RS24350 29653..30300 - 648 WP_241363796 transglycosylase SLT domain-containing protein virB1
V6L97_RS24355 30577..30960 + 384 WP_040073112 conjugal transfer relaxosome DNA-binding protein TraM -
V6L97_RS24360 31150..31836 + 687 WP_000332492 PAS domain-containing protein -
V6L97_RS24365 31930..32157 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6L97_RS24370 32191..32556 + 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6L97_RS24375 32571..32882 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6L97_RS24380 32904..33470 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6L97_RS24385 33457..34185 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
V6L97_RS24390 34185..35612 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6L97_RS24395 35602..36192 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6L97_RS24400 36179..36376 + 198 WP_001324648 conjugal transfer protein TrbD -
V6L97_RS24405 36388..36638 + 251 Protein_55 conjugal transfer protein TrbG -
V6L97_RS24410 36635..37150 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
V6L97_RS24415 37285..37506 + 222 WP_001278689 conjugal transfer protein TraR -
V6L97_RS24420 37666..40293 + 2628 WP_001064245 type IV secretion system protein TraC virb4
V6L97_RS24425 40290..40676 + 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6L97_RS24430 40673..41305 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6L97_RS24435 41302..42294 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6L97_RS24440 42303..42941 + 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6L97_RS24445 42938..44746 + 1809 WP_032082947 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6L97_RS24450 44773..45030 + 258 WP_000864318 conjugal transfer protein TrbE -
V6L97_RS24455 45023..45766 + 744 WP_135460420 type-F conjugative transfer system pilin assembly protein TraF traF
V6L97_RS24460 45782..46129 + 348 WP_032082949 conjugal transfer protein TrbA -
V6L97_RS24465 46131..46406 - 276 WP_074430089 toxin ArtA -
V6L97_RS24470 46487..46771 + 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6L97_RS24475 46758..47303 + 546 WP_032082911 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6L97_RS24480 47233..47574 + 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6L97_RS24485 47561..47953 + 393 WP_032082924 F-type conjugal transfer protein TrbF -
V6L97_RS24490 47940..49313 + 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
V6L97_RS24495 49310..52135 + 2826 WP_062873763 conjugal transfer mating-pair stabilization protein TraG traG
V6L97_RS24500 52132..52641 + 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6L97_RS24505 52655..53386 + 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6L97_RS24510 53638..55791 + 2154 WP_062873762 type IV conjugative transfer system coupling protein TraD virb4
V6L97_RS24515 55800..56198 - 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6L97_RS24520 56198..56425 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2022 GenBank   NZ_JAQMVA010000002
Plasmid name   pMFDS1016183 Incompatibility group   IncFII
Plasmid size   97956 bp Coordinate of oriT [Strand]   30225..30348 [+]
Host baterium   Escherichia coli strain MFDS1016183

Cargo genes

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