Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101546
Name   oriT_DSM 30083|unnamed in_silico
Organism   Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 strain DSM 30083
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AGSE01000004 (97861..98213 [+], 353 nt)
oriT length   353 nt
IRs (inverted repeats)      256..263, 272..279  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 134..141, 152..159  (TCGGCGCG..CGCGCCGA)
 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: 353 nt

>oriT_DSM 30083|unnamed
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTATCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1370 GenBank   WP_000986993
Name   traI_ESCCO_RS0100645_DSM 30083|unnamed insolico UniProt ID   A0A7G8AEP4
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191812.64 Da        Isoelectric Point: 6.0533

>WP_000986993.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQVILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ESGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGGQQTRVIRPAQVRAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDTPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DSKTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREVARENLLQERLQQMEQDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

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

(633-712)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   484 GenBank   WP_001151524
Name   WP_001151524_DSM 30083|unnamed 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

ID   485 GenBank   WP_001309237
Name   WP_001309237_DSM 30083|unnamed insolico UniProt ID   A0A5W1N5T0
Length   131 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15183.38 Da        Isoelectric Point: 9.9240

>WP_001309237.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-59)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W1N5T0


T4CP

ID   999 GenBank   WP_001064252
Name   traC_ESCCO_RS0100560_DSM 30083|unnamed 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: 99164.84 Da        Isoelectric Point: 5.8486

>WP_001064252.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRESGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1000 GenBank   WP_001350920
Name   traD_ESCCO_RS0100640_DSM 30083|unnamed 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: 81420.87 Da        Isoelectric Point: 5.0524

>WP_001350920.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGSSESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  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: 97290..123047

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ESCCO_RS01000000124595 93281..93715 + 435 Protein_93 conjugation system SOS inhibitor PsiB -
ESCCO_RS0100470 93712..94498 + 787 Protein_94 plasmid SOS inhibition protein A -
ESCCO_RS1000000130015 94688..94801 + 114 Protein_95 DUF5431 family protein -
ESCCO_RS01000000124605 94746..94868 + 123 WP_223195199 Hok/Gef family protein -
ESCCO_RS1000000129925 95169..95466 - 298 Protein_97 hypothetical protein -
ESCCO_RS0100480 95767..96054 + 288 WP_000107520 hypothetical protein -
ESCCO_RS0100485 96173..96994 + 822 WP_001234468 DUF932 domain-containing protein -
ESCCO_RS0100490 97290..97799 - 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
ESCCO_RS0100495 98214..98597 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
ESCCO_RS0100500 98784..99473 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
ESCCO_RS0100505 99572..99967 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
ESCCO_RS0100510 100000..100365 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
ESCCO_RS0100515 100380..100691 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ESCCO_RS0100520 100713..101279 + 567 WP_000399785 type IV conjugative transfer system protein TraE traE
ESCCO_RS0100525 101266..101994 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ESCCO_RS0100530 101994..103421 + 1428 WP_025857813 F-type conjugal transfer pilus assembly protein TraB traB
ESCCO_RS0100535 103411..104001 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
ESCCO_RS0100540 103988..104185 + 198 WP_001324648 conjugal transfer protein TrbD -
ESCCO_RS0100545 104197..104448 + 252 WP_001038342 conjugal transfer protein TrbG -
ESCCO_RS0100550 104445..104960 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
ESCCO_RS1000000126845 105095..105316 + 222 WP_001278689 conjugal transfer protein TraR -
ESCCO_RS0100560 105476..108103 + 2628 WP_001064252 type IV secretion system protein TraC virb4
ESCCO_RS0100565 108100..108486 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
ESCCO_RS0100570 108483..109115 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
ESCCO_RS0100575 109112..110104 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
ESCCO_RS0100580 110113..110751 + 639 WP_000777693 type-F conjugative transfer system pilin assembly protein TrbC trbC
ESCCO_RS0100585 110748..112556 + 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ESCCO_RS0100590 112583..112840 + 258 WP_000864325 conjugal transfer protein TrbE -
ESCCO_RS0100595 112833..113576 + 744 WP_001030389 type-F conjugative transfer system pilin assembly protein TraF traF
ESCCO_RS0100600 113592..113939 + 348 WP_001287676 conjugal transfer protein TrbA -
ESCCO_RS0100605 114058..114342 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
ESCCO_RS0100610 114329..114874 + 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ESCCO_RS0100615 114804..115166 + 363 WP_002430925 P-type conjugative transfer protein TrbJ -
ESCCO_RS0100620 115166..116539 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
ESCCO_RS0100625 116536..119361 + 2826 WP_001622731 conjugal transfer mating-pair stabilization protein TraG traG
ESCCO_RS0100630 119376..119879 + 504 WP_000605510 hypothetical protein -
ESCCO_RS0100635 119911..120642 + 732 WP_001447147 conjugal transfer complement resistance protein TraT -
ESCCO_RS0100640 120894..123047 + 2154 WP_001350920 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1990 GenBank   NZ_AGSE01000004
Plasmid name   DSM 30083|unnamed Incompatibility group   IncFIB
Plasmid size   131289 bp Coordinate of oriT [Strand]   97861..98213 [+]
Host baterium   Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 strain DSM 30083

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   iroN, iroE, iroD, iroC, iroB, iucA, iucB, iucC, iutA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -