Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102996
Name   oriT_p120899_50 in_silico
Organism   Escherichia coli strain 120899
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP025919 (12195..12546 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      192..198, 206..212  (TATAAAA..TTTTATA)
 104..110, 118..124  (TTTAAAT..ATTTAAA)
 106..111, 113..118  (TAAATC..GATTTA)
 93..98, 106..111  (GATTTA..TAAATC)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_p120899_50
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTATTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2247 GenBank   WP_126134456
Name   traI_CXW56_RS27320_p120899_50 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191830.29 Da        Isoelectric Point: 5.6943

>WP_126134456.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREVVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGSAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGIAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRSEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQNGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVTEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPRADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTATSEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   916 GenBank   WP_001151529
Name   WP_001151529_p120899_50 insolico UniProt ID   A0A7I0L277
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14497.49 Da        Isoelectric Point: 4.8662

>WP_001151529.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSAEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0L277


T4CP

ID   1934 GenBank   WP_001535744
Name   traC_CXW56_RS27215_p120899_50 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99314.21 Da        Isoelectric Point: 6.7390

>WP_001535744.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVKASWLAKKNQARIDDVVNFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-768)

  Protein structure



No available structure.



ID   1935 GenBank   WP_126134455
Name   traD_CXW56_RS27315_p120899_50 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82918.54 Da        Isoelectric Point: 5.0541

>WP_126134455.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGLSESGEVVDMAAYEAWQQENHPD
IQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 11624..40324

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CXW56_RS27085 6986..7240 + 255 WP_001230709 hypothetical protein -
CXW56_RS27090 7237..7479 + 243 WP_000151456 hypothetical protein -
CXW56_RS27100 8050..8343 + 294 WP_000673431 hypothetical protein -
CXW56_RS27105 8648..8935 + 288 WP_000606467 hypothetical protein -
CXW56_RS27110 9363..9596 + 234 WP_000093745 hypothetical protein -
CXW56_RS27115 9672..9974 + 303 WP_000379301 hypothetical protein -
CXW56_RS27120 10246..10395 + 150 WP_000903193 hypothetical protein -
CXW56_RS27125 10506..11327 + 822 WP_032283064 DUF932 domain-containing protein -
CXW56_RS27130 11624..12271 - 648 WP_072144024 transglycosylase SLT domain-containing protein virB1
CXW56_RS27135 12547..12930 + 384 WP_001151529 conjugal transfer relaxosome DNA-binding protein TraM -
CXW56_RS27140 13122..13769 + 648 WP_000332523 transcriptional regulator TraJ family protein -
CXW56_RS27145 13889..14116 + 228 WP_000589556 conjugal transfer relaxosome protein TraY -
CXW56_RS27150 14150..14512 + 363 WP_001098993 type IV conjugative transfer system pilin TraA -
CXW56_RS27155 14527..14838 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
CXW56_RS27160 14860..15426 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
CXW56_RS27165 15413..16141 + 729 WP_001230771 type-F conjugative transfer system secretin TraK traK
CXW56_RS27170 16141..17592 + 1452 WP_016235429 F-type conjugal transfer pilus assembly protein TraB traB
CXW56_RS27175 17582..18148 + 567 WP_000896598 conjugal transfer pilus-stabilizing protein TraP -
CXW56_RS27180 18135..18452 + 318 WP_001057297 conjugal transfer protein TrbD -
CXW56_RS27185 18452..18967 + 516 WP_000809872 type IV conjugative transfer system lipoprotein TraV traV
CXW56_RS27190 19102..19323 + 222 WP_001278695 conjugal transfer protein TraR -
CXW56_RS27195 19316..19729 + 414 WP_000549581 hypothetical protein -
CXW56_RS27200 19722..20195 + 474 WP_001620797 hypothetical protein -
CXW56_RS27205 20273..20491 + 219 WP_001377841 hypothetical protein -
CXW56_RS27210 20519..20866 + 348 WP_000836682 hypothetical protein -
CXW56_RS27215 20992..23622 + 2631 WP_001535744 type IV secretion system protein TraC virb4
CXW56_RS27220 23619..24005 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
CXW56_RS27225 24002..24634 + 633 WP_001203738 type-F conjugative transfer system protein TraW traW
CXW56_RS27230 24631..25623 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
CXW56_RS27235 25653..25958 + 306 WP_000224418 hypothetical protein -
CXW56_RS27240 25967..26605 + 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
CXW56_RS27245 26602..28452 + 1851 WP_032240955 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CXW56_RS27250 28479..28736 + 258 WP_000864347 conjugal transfer protein TrbE -
CXW56_RS27255 28729..29472 + 744 WP_001462109 type-F conjugative transfer system pilin assembly protein TraF traF
CXW56_RS27260 29486..29827 + 342 WP_000556795 conjugal transfer protein TrbA -
CXW56_RS27265 29808..30143 - 336 WP_001620807 hypothetical protein -
CXW56_RS27270 30224..30508 + 285 WP_042017850 type-F conjugative transfer system pilin chaperone TraQ -
CXW56_RS27275 30495..31040 + 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CXW56_RS27280 31030..31344 + 315 WP_001620812 P-type conjugative transfer protein TrbJ -
CXW56_RS27285 31298..31690 + 393 WP_032144618 F-type conjugal transfer protein TrbF -
CXW56_RS27290 31677..33050 + 1374 WP_001535740 conjugal transfer pilus assembly protein TraH traH
CXW56_RS27295 33047..35893 + 2847 WP_050009856 conjugal transfer mating-pair stabilization protein TraG traG
CXW56_RS27300 35890..36399 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
CXW56_RS27305 36413..37144 + 732 WP_042018826 conjugal transfer complement resistance protein TraT -
CXW56_RS27310 37347..38084 + 738 WP_000199909 hypothetical protein -
CXW56_RS27315 38135..40324 + 2190 WP_126134455 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3439 GenBank   NZ_CP025919
Plasmid name   p120899_50 Incompatibility group   -
Plasmid size   50268 bp Coordinate of oriT [Strand]   12195..12546 [+]
Host baterium   Escherichia coli strain 120899

Cargo genes

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