Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102647
Name   oriT_LF236|unnamed 1 in_silico
Organism   Escherichia coli strain LF236
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LQWX02000052 (839..962 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 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_LF236|unnamed 1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTACTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   1595 GenBank   WP_001064258
Name   traC_AWH50_RS25145_LF236|unnamed 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: 99195.72 Da        Isoelectric Point: 5.8689

>WP_001064258.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLKSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNYKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFQPLQRDMIGKFGAARDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
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)

(467-763)

  Protein structure



No available structure.



ID   1596 GenBank   WP_045151360
Name   traD_AWH50_RS25255_LF236|unnamed 1 insolico UniProt ID   _
Length   623 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 623 a.a.        Molecular weight: 70819.41 Da        Isoelectric Point: 7.0363

>WP_045151360.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD, partial [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQ

  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: 267..28764

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AWH50_RS25085 (AWH50_027905) 267..857 - 591 WP_001376243 transglycosylase SLT domain-containing protein virB1
AWH50_RS25090 (AWH50_027910) 1200..1583 + 384 WP_001151566 conjugal transfer relaxosome DNA-binding protein TraM -
AWH50_RS25095 (AWH50_027915) 1717..2394 + 678 WP_001348626 PAS domain-containing protein -
AWH50_RS25100 (AWH50_027920) 2482..2709 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
AWH50_RS25105 (AWH50_027925) 2743..3105 + 363 WP_000338606 type IV conjugative transfer system pilin TraA -
AWH50_RS25110 (AWH50_027930) 3110..3421 + 312 WP_000012107 type IV conjugative transfer system protein TraL traL
AWH50_RS25115 (AWH50_027935) 3443..4009 + 567 WP_000399791 type IV conjugative transfer system protein TraE traE
AWH50_RS25120 (AWH50_027940) 3996..4724 + 729 WP_001230808 type-F conjugative transfer system secretin TraK traK
AWH50_RS25125 (AWH50_027945) 4724..6175 + 1452 WP_000146687 F-type conjugal transfer pilus assembly protein TraB traB
AWH50_RS25130 (AWH50_027950) 6165..6731 + 567 WP_001617877 conjugal transfer pilus-stabilizing protein TraP -
AWH50_RS25135 (AWH50_027955) 6718..7029 + 312 WP_001057272 conjugal transfer protein TrbD -
AWH50_RS25140 (AWH50_027960) 7029..7544 + 516 WP_000809886 type IV conjugative transfer system lipoprotein TraV traV
AWH50_RS30575 7679..7900 + 222 WP_001278694 conjugal transfer protein TraR -
AWH50_RS25145 (AWH50_027965) 8060..10687 + 2628 WP_001064258 type IV secretion system protein TraC virb4
AWH50_RS25150 (AWH50_027970) 10684..11070 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
AWH50_RS25155 (AWH50_027975) 11067..11699 + 633 WP_001203727 type-F conjugative transfer system protein TraW traW
AWH50_RS25160 (AWH50_027980) 11696..12688 + 993 WP_000830190 conjugal transfer pilus assembly protein TraU traU
AWH50_RS25165 (AWH50_027985) 12718..13023 + 306 WP_000224413 hypothetical protein -
AWH50_RS25170 (AWH50_027990) 13032..13670 + 639 WP_001080259 type-F conjugative transfer system pilin assembly protein TrbC trbC
AWH50_RS25175 (AWH50_027995) 13667..15517 + 1851 WP_000821866 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AWH50_RS25180 (AWH50_028000) 15544..15801 + 258 WP_000864347 conjugal transfer protein TrbE -
AWH50_RS25185 (AWH50_028005) 15794..16537 + 744 WP_001030401 type-F conjugative transfer system pilin assembly protein TraF traF
AWH50_RS25190 (AWH50_028010) 16667..17647 + 981 WP_000019450 IS5-like element ISKpn26 family transposase -
AWH50_RS31750 (AWH50_028020) 17802..18499 + 698 WP_225321517 IS1 family transposase -
AWH50_RS25205 (AWH50_028025) 18547..18867 + 321 WP_001348757 conjugal transfer protein TrbA -
AWH50_RS25210 (AWH50_028030) 18994..19278 + 285 WP_001617873 type-F conjugative transfer system pilin chaperone TraQ -
AWH50_RS25215 (AWH50_028035) 19265..19810 + 546 WP_000059829 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AWH50_RS25220 (AWH50_028040) 19740..20087 + 348 WP_071571857 P-type conjugative transfer protein TrbJ -
AWH50_RS25225 (AWH50_028045) 20068..20460 + 393 WP_000659962 F-type conjugal transfer protein TrbF -
AWH50_RS25230 (AWH50_028050) 20447..21820 + 1374 WP_000944328 conjugal transfer pilus assembly protein TraH traH
AWH50_RS25235 (AWH50_028055) 21817..24636 + 2820 WP_001007062 conjugal transfer mating-pair stabilization protein TraG traG
AWH50_RS25240 (AWH50_028060) 24655..25152 + 498 WP_000605862 entry exclusion protein -
AWH50_RS25245 (AWH50_028065) 25184..25915 + 732 WP_000850429 conjugal transfer complement resistance protein TraT -
AWH50_RS25250 (AWH50_028070) 26118..26897 + 780 WP_000199914 hypothetical protein -
AWH50_RS25255 (AWH50_028075) 26894..28764 + 1871 WP_045151360 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3091 GenBank   NZ_LQWX02000052
Plasmid name   LF236|unnamed 1 Incompatibility group   -
Plasmid size   28764 bp Coordinate of oriT [Strand]   839..962 [+]
Host baterium   Escherichia coli strain LF236

Cargo genes

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