Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103074
Name   oriT_pEC13 in_silico
Organism   Escherichia coli
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU932024 (32635..32720 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pEC13
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2301 GenBank   WP_000948354
Name   traI_HTH56_RS00410_pEC13 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
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)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   958 GenBank   WP_001354030
Name   WP_001354030_pEC13 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   959 GenBank   WP_000089263
Name   WP_000089263_pEC13 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   2015 GenBank   WP_012917677
Name   traC_HTH56_RS00310_pEC13 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: 99204.83 Da        Isoelectric Point: 6.0793

>WP_012917677.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILRQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(469-764)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   2016 GenBank   WP_000009328
Name   traD_HTH56_RS00405_pEC13 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: 86020.84 Da        Isoelectric Point: 5.1644

>WP_000009328.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQ
LPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 32067..61958

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH56_RS00180 27393..27707 + 315 WP_000872086 hypothetical protein -
HTH56_RS00465 27897..28010 + 114 Protein_40 DUF5431 family protein -
HTH56_RS00185 27955..28077 + 123 WP_223412041 Hok/Gef family protein -
HTH56_RS00190 28378..28627 - 250 Protein_42 hypothetical protein -
HTH56_RS00195 28923..29246 + 324 WP_000533253 hypothetical protein -
HTH56_RS00200 29305..29547 + 243 WP_000540588 hypothetical protein -
HTH56_RS00470 29813..30073 + 261 WP_071600428 hypothetical protein -
HTH56_RS00205 30544..30840 + 297 WP_001272251 hypothetical protein -
HTH56_RS00210 30950..31771 + 822 WP_181727871 DUF932 domain-containing protein -
HTH56_RS00215 32067..32669 - 603 WP_000243715 transglycosylase SLT domain-containing protein virB1
HTH56_RS00220 32992..33375 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTH56_RS00225 33569..34240 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTH56_RS00230 34377..34604 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTH56_RS00235 34637..34996 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTH56_RS00240 35011..35322 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTH56_RS00245 35344..35910 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTH56_RS00250 35897..36625 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTH56_RS00255 36625..38076 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTH56_RS00260 38066..38632 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTH56_RS00265 38619..38939 + 321 WP_001057307 conjugal transfer protein TrbD -
HTH56_RS00270 38936..39451 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTH56_RS00275 39586..39807 + 222 WP_001278683 conjugal transfer protein TraR -
HTH56_RS00280 39800..40213 + 414 WP_000549589 hypothetical protein -
HTH56_RS00285 40206..40679 + 474 WP_000549568 hypothetical protein -
HTH56_RS00290 40759..40977 + 219 WP_000556745 hypothetical protein -
HTH56_RS00295 40978..41154 + 177 WP_172693362 hypothetical protein -
HTH56_RS00300 41243..42471 + 1229 WP_088895425 IS3-like element IS2 family transposase -
HTH56_RS00305 42482..42688 + 207 Protein_66 hypothetical protein -
HTH56_RS00310 42814..45444 + 2631 WP_012917677 type IV secretion system protein TraC virb4
HTH56_RS00315 45441..45827 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTH56_RS00320 45824..46456 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTH56_RS00325 46453..47445 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTH56_RS00330 47475..47780 + 306 WP_000224416 hypothetical protein -
HTH56_RS00335 47789..48427 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTH56_RS00340 48424..50274 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTH56_RS00345 50301..50558 + 258 WP_181727872 conjugal transfer protein TrbE -
HTH56_RS00350 50551..51294 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HTH56_RS00355 51308..51652 + 345 WP_000556796 conjugal transfer protein TrbA -
HTH56_RS00360 51771..52055 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTH56_RS00365 52042..52587 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTH56_RS00370 52517..52864 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTH56_RS00375 52845..53237 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTH56_RS00380 53224..54597 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HTH56_RS00385 54594..57416 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTH56_RS00390 57432..57917 + 486 WP_000605870 hypothetical protein -
HTH56_RS00395 57966..58697 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTH56_RS00400 58900..59637 + 738 WP_000199905 hypothetical protein -
HTH56_RS00405 59688..61958 + 2271 WP_000009328 type IV conjugative transfer system coupling protein TraD prgC

Host bacterium

ID   3517 GenBank   NZ_KU932024
Plasmid name   pEC13 Incompatibility group   IncFII
Plasmid size   71656 bp Coordinate of oriT [Strand]   32635..32720 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7