Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102411
Name   oriT_SMG001F2|unnamed1 in_silico
Organism   Escherichia coli strain SMG001F2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSM010000035 (44423..44774 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..46, 51..57  (GCAAAAA..TTTTTGC)
 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_SMG001F2|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAATTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATCATTTTATATTAGGGGCGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGTATTATGAATTTTAGTGTTCCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1805 GenBank   WP_016239093
Name   traI_ML351_RS18595_SMG001F2|unnamed1 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: 191754.53 Da        Isoelectric Point: 5.8515

>WP_016239093.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVES
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGMFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKTPDALALVDSVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   720 GenBank   WP_001369361
Name   WP_001369361_SMG001F2|unnamed1 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   721 GenBank   WP_001151538
Name   WP_001151538_SMG001F2|unnamed1 insolico UniProt ID   A0A8B3KK21
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14559.51 Da        Isoelectric Point: 4.8662

>WP_001151538.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINSIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A8B3KK21


T4CP

ID   1384 GenBank   WP_142457939
Name   traD_ML351_RS18600_SMG001F2|unnamed1 insolico UniProt ID   _
Length   756 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 756 a.a.        Molecular weight: 86067.87 Da        Isoelectric Point: 5.1044

>WP_142457939.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGHQGKQ
QSENEVTGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQ
LPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEMNINVHRERGEDVEPGDDF

  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   1385 GenBank   WP_015075088
Name   traC_ML351_RS18700_SMG001F2|unnamed1 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: 99232.78 Da        Isoelectric Point: 5.8689

>WP_015075088.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGINLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-764)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 16376..45345

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML351_RS18600 (ML351_18600) 16376..18646 - 2271 WP_142457939 type IV conjugative transfer system coupling protein TraD prgC
ML351_RS18605 (ML351_18605) 18697..19434 - 738 WP_016239096 hypothetical protein -
ML351_RS18610 (ML351_18610) 19637..20368 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
ML351_RS18615 (ML351_18615) 20400..20903 - 504 WP_000605510 hypothetical protein -
ML351_RS18620 (ML351_18620) 20918..23740 - 2823 WP_001007081 conjugal transfer mating-pair stabilization protein TraG traG
ML351_RS18625 (ML351_18625) 23737..25110 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
ML351_RS18630 (ML351_18630) 25097..25489 - 393 WP_000660700 F-type conjugal transfer protein TrbF -
ML351_RS18635 (ML351_18635) 25470..25817 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
ML351_RS18640 (ML351_18640) 25747..26292 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ML351_RS18645 (ML351_18645) 26279..26563 - 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
ML351_RS18650 (ML351_18650) 26644..26979 + 336 WP_000736414 hypothetical protein -
ML351_RS18655 (ML351_18655) 26960..27301 - 342 WP_000556795 conjugal transfer protein TrbA -
ML351_RS18660 (ML351_18660) 27315..28058 - 744 WP_001030385 type-F conjugative transfer system pilin assembly protein TraF traF
ML351_RS18665 (ML351_18665) 28051..28308 - 258 WP_000864309 conjugal transfer protein TrbE -
ML351_RS18670 (ML351_18670) 28335..30185 - 1851 WP_001570866 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ML351_RS18675 (ML351_18675) 30182..30820 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
ML351_RS18680 (ML351_18680) 30829..31134 - 306 WP_000224416 hypothetical protein -
ML351_RS18685 (ML351_18685) 31164..32156 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
ML351_RS18690 (ML351_18690) 32153..32785 - 633 WP_242428176 type-F conjugative transfer system protein TraW traW
ML351_RS18695 (ML351_18695) 32782..33168 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
ML351_RS18700 (ML351_18700) 33165..35795 - 2631 WP_015075088 type IV secretion system protein TraC virb4
ML351_RS18705 (ML351_18705) 35921..36268 - 348 WP_000836682 hypothetical protein -
ML351_RS18710 (ML351_18710) 36296..36514 - 219 WP_000556751 hypothetical protein -
ML351_RS18715 (ML351_18715) 36595..37068 - 474 WP_016249716 hypothetical protein -
ML351_RS18720 (ML351_18720) 37061..37473 - 413 Protein_42 hypothetical protein -
ML351_RS18725 (ML351_18725) 37466..37687 - 222 WP_001278689 conjugal transfer protein TraR -
ML351_RS18730 (ML351_18730) 37822..38337 - 516 WP_000809872 type IV conjugative transfer system lipoprotein TraV traV
ML351_RS18735 (ML351_18735) 38337..38654 - 318 WP_001057297 conjugal transfer protein TrbD -
ML351_RS18740 (ML351_18740) 38641..39207 - 567 WP_000896598 conjugal transfer pilus-stabilizing protein TraP -
ML351_RS18745 (ML351_18745) 39197..40648 - 1452 WP_016239102 F-type conjugal transfer pilus assembly protein TraB traB
ML351_RS18750 (ML351_18750) 40648..41376 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ML351_RS18755 (ML351_18755) 41363..41929 - 567 WP_016239103 type IV conjugative transfer system protein TraE traE
ML351_RS18760 (ML351_18760) 41951..42262 - 312 WP_000012113 type IV conjugative transfer system protein TraL traL
ML351_RS18765 (ML351_18765) 42277..42636 - 360 WP_016239104 type IV conjugative transfer system pilin TraA -
ML351_RS18770 (ML351_18770) 42669..43064 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
ML351_RS18775 (ML351_18775) 43163..43852 - 690 WP_016239105 conjugal transfer transcriptional regulator TraJ -
ML351_RS18780 (ML351_18780) 44039..44422 - 384 WP_001151538 conjugal transfer relaxosome DNA-binding protein TraM -
ML351_RS18785 (ML351_18785) 44743..45345 + 603 WP_077539848 transglycosylase SLT domain-containing protein virB1
ML351_RS18790 (ML351_18790) 45640..46461 - 822 WP_001234469 DUF932 domain-containing protein -
ML351_RS18795 (ML351_18795) 46581..46868 - 288 WP_000107535 hypothetical protein -
ML351_RS18800 (ML351_18800) 46870..47067 + 198 Protein_58 hypothetical protein -
ML351_RS18805 (ML351_18805) 47065..47295 - 231 WP_071593758 hypothetical protein -
ML351_RS18810 (ML351_18810) 47515..47640 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
ML351_RS18815 (ML351_18815) 47582..47731 - 150 Protein_61 plasmid maintenance protein Mok -
ML351_RS18820 (ML351_18820) 47753..47941 + 189 WP_001336239 hypothetical protein -
ML351_RS18825 (ML351_18825) 47910..48672 - 763 Protein_63 plasmid SOS inhibition protein A -
ML351_RS18830 (ML351_18830) 48669..49103 - 435 WP_000845923 conjugation system SOS inhibitor PsiB -
ML351_RS18835 (ML351_18835) 49158..49526 - 369 Protein_65 hypothetical protein -
ML351_RS18840 (ML351_18840) 49584..49652 + 69 WP_223277024 hypothetical protein -

Host bacterium

ID   2855 GenBank   NZ_JAKVSM010000035
Plasmid name   SMG001F2|unnamed1 Incompatibility group   IncFIC
Plasmid size   49652 bp Coordinate of oriT [Strand]   44423..44774 [-]
Host baterium   Escherichia coli strain SMG001F2

Cargo genes

Drug resistance gene   aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -