Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102626
Name   oriT_pUMNturkey6_IncF in_silico
Organism   Escherichia coli strain UMNturkey6
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JRQB01000006 (39848..40199 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 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_pUMNturkey6_IncF
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATTGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1955 GenBank   WP_047402288
Name   traI_LS42_RS01780_pUMNturkey6_IncF insolico UniProt ID   A0A8S7Y2I9
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192292.94 Da        Isoelectric Point: 5.9169

>WP_047402288.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHSQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQVVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DTVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENCWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVLESKNLAFSHVDLLTEAKSFAAEGTSFTELGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAVTSERETALPESVLREPQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   781 GenBank   WP_001369361
Name   WP_001369361_pUMNturkey6_IncF insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   782 GenBank   WP_001151524
Name   WP_001151524_pUMNturkey6_IncF insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   1583 GenBank   WP_047402290
Name   traD_LS42_RS01785_pUMNturkey6_IncF 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: 81547.03 Da        Isoelectric Point: 5.0541

>WP_047402290.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDRYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDTQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   1584 GenBank   WP_001064265
Name   traC_LS42_RS01870_pUMNturkey6_IncF 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: 99296.07 Da        Isoelectric Point: 6.3032

>WP_001064265.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 14576..40770

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LS42_RS01785 (LS42_01785) 14576..16729 - 2154 WP_047402290 type IV conjugative transfer system coupling protein TraD virb4
LS42_RS01790 (LS42_01790) 16981..17712 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
LS42_RS01795 (LS42_01795) 17726..18235 - 510 WP_000628100 conjugal transfer entry exclusion protein TraS -
LS42_RS01800 (LS42_01800) 18232..21057 - 2826 WP_047402292 conjugal transfer mating-pair stabilization protein TraG traG
LS42_RS01805 (LS42_01805) 21054..22427 - 1374 WP_113444820 conjugal transfer pilus assembly protein TraH traH
LS42_RS01810 (LS42_01810) 22414..22806 - 393 WP_047402297 F-type conjugal transfer protein TrbF -
LS42_RS25520 22760..23074 - 315 WP_023149603 P-type conjugative transfer protein TrbJ -
LS42_RS01815 (LS42_01815) 23064..23618 - 555 WP_047402299 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LS42_RS01820 (LS42_01820) 23605..23889 - 285 WP_000624105 type-F conjugative transfer system pilin chaperone TraQ -
LS42_RS01825 (LS42_01825) 23970..24305 + 336 WP_000415571 hypothetical protein -
LS42_RS01830 (LS42_01830) 24286..24627 - 342 WP_047402303 conjugal transfer protein TrbA -
LS42_RS01835 (LS42_01835) 24641..25384 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
LS42_RS01840 (LS42_01840) 25377..25634 - 258 WP_000864320 conjugal transfer protein TrbE -
LS42_RS01845 (LS42_01845) 25661..27469 - 1809 WP_047402305 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LS42_RS01850 (LS42_01850) 27466..28104 - 639 WP_042047200 type-F conjugative transfer system pilin assembly protein TrbC trbC
LS42_RS01855 (LS42_01855) 28113..29105 - 993 WP_042047198 conjugal transfer pilus assembly protein TraU traU
LS42_RS01860 (LS42_01860) 29102..29734 - 633 WP_042047196 type-F conjugative transfer system protein TraW traW
LS42_RS01865 (LS42_01865) 29731..30117 - 387 WP_000099693 type-F conjugative transfer system protein TrbI -
LS42_RS01870 (LS42_01870) 30114..32741 - 2628 WP_001064265 type IV secretion system protein TraC virb4
LS42_RS25525 (LS42_01875) 32901..33122 - 222 WP_001278692 conjugal transfer protein TraR -
LS42_RS01880 (LS42_01880) 33257..33772 - 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
LS42_RS01885 (LS42_01885) 33769..34089 - 321 WP_001057283 conjugal transfer protein TrbD -
LS42_RS01890 (LS42_01890) 34076..34663 - 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
LS42_RS01895 (LS42_01895) 34653..36080 - 1428 WP_047402310 F-type conjugal transfer pilus assembly protein TraB traB
LS42_RS01900 (LS42_01900) 36080..36808 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
LS42_RS01905 (LS42_01905) 36795..37361 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
LS42_RS01910 (LS42_01910) 37383..37694 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
LS42_RS01915 (LS42_01915) 37699..38061 - 363 WP_000994784 type IV conjugative transfer system pilin TraA -
LS42_RS01920 (LS42_01920) 38094..38489 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
LS42_RS01925 (LS42_01925) 38588..39277 - 690 WP_047402313 conjugal transfer transcriptional regulator TraJ -
LS42_RS01930 (LS42_01930) 39464..39847 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
LS42_RS01935 (LS42_01935) 40180..40770 + 591 WP_001376243 transglycosylase SLT domain-containing protein virB1
LS42_RS01940 (LS42_01940) 41067..41888 - 822 WP_001234469 DUF932 domain-containing protein -
LS42_RS01945 (LS42_01945) 42007..42294 - 288 WP_000107548 hypothetical protein -
LS42_RS01950 (LS42_01950) 42545..43549 + 1005 WP_047402339 IS110 family transposase -
LS42_RS29150 (LS42_01955) 43643..43903 - 261 WP_042046747 hypothetical protein -
LS42_RS29155 (LS42_01960) 43973..44146 + 174 Protein_49 hypothetical protein -
LS42_RS29160 44144..44374 - 231 WP_113707887 hypothetical protein -
LS42_RS01965 (LS42_01965) 44594..44719 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
LS42_RS29165 44661..44810 - 150 Protein_52 plasmid maintenance protein Mok -
LS42_RS28730 (LS42_01970) 44832..45020 + 189 WP_001299721 hypothetical protein -
LS42_RS01975 (LS42_01975) 44989..45751 - 763 Protein_54 plasmid SOS inhibition protein A -

Host bacterium

ID   3070 GenBank   NZ_JRQB01000006
Plasmid name   pUMNturkey6_IncF Incompatibility group   IncFII
Plasmid size   66684 bp Coordinate of oriT [Strand]   39848..40199 [-]
Host baterium   Escherichia coli strain UMNturkey6

Cargo genes

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