Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102641
Name   oriT_SYAB4|unnamed1 in_silico
Organism   Escherichia coli strain SYAB4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LNUF01000043 (2193..2316 [+], 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_SYAB4|unnamed1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1591 GenBank   WP_001064268
Name   traC_AYM05_RS24590_SYAB4|unnamed1 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: 99248.97 Da        Isoelectric Point: 6.0801

>WP_001064268.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNKARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1621..15990

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AYM05_RS29120 1..69 + 69 Protein_0 single-stranded DNA-binding protein -
AYM05_RS24515 94..381 + 288 WP_000107535 hypothetical protein -
AYM05_RS24520 503..1324 + 822 WP_001234469 DUF932 domain-containing protein -
AYM05_RS24525 1621..2268 - 648 WP_000614936 transglycosylase SLT domain-containing protein virB1
AYM05_RS24530 2545..2928 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
AYM05_RS24535 3119..3805 + 687 WP_000332484 PAS domain-containing protein -
AYM05_RS24540 3899..4126 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
AYM05_RS24545 4160..4519 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
AYM05_RS24550 4534..4845 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
AYM05_RS24555 4867..5433 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
AYM05_RS24560 5420..6148 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
AYM05_RS24565 6148..7575 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
AYM05_RS24570 7565..8137 + 573 WP_000002780 conjugal transfer pilus-stabilizing protein TraP -
AYM05_RS24575 8134..8451 + 318 WP_001057292 conjugal transfer protein TrbD virb4
AYM05_RS24580 8448..8699 + 252 WP_001038341 conjugal transfer protein TrbG -
AYM05_RS24585 8696..9211 + 516 WP_000809906 type IV conjugative transfer system lipoprotein TraV traV
AYM05_RS27785 9346..9567 + 222 WP_001278689 conjugal transfer protein TraR -
AYM05_RS24590 9727..12354 + 2628 WP_001064268 type IV secretion system protein TraC virb4
AYM05_RS24595 12351..12737 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
AYM05_RS24600 12734..13366 + 633 WP_001203745 type-F conjugative transfer system protein TraW traW
AYM05_RS24605 13363..14355 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
AYM05_RS24610 14381..14842 + 462 WP_000277845 hypothetical protein -
AYM05_RS24615 14872..15324 + 453 WP_000069427 hypothetical protein -
AYM05_RS24620 15352..15990 + 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
AYM05_RS24625 15987..16847 + 861 Protein_24 conjugal transfer protein TraN -

Host bacterium

ID   3085 GenBank   NZ_LNUF01000043
Plasmid name   SYAB4|unnamed1 Incompatibility group   -
Plasmid size   16911 bp Coordinate of oriT [Strand]   2193..2316 [+]
Host baterium   Escherichia coli strain SYAB4

Cargo genes

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