Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116184
Name   oriT_pECD227_113 in_silico
Organism   Escherichia fergusonii ECD227
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM001144 (867..1218 [+], 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_pECD227_113
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTAGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10350 GenBank   WP_000987007
Name   traI_ECD227_RS23435_pECD227_113 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: 192218.18 Da        Isoelectric Point: 5.9371

>WP_000987007.1 conjugative transfer relaxase/helicase TraI [Escherichia fergusonii]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMVEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLIIDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAVSVKAGEESVAQVSGVREQAMLTQTIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMLVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

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

(633-711)

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   6099 GenBank   WP_001151524
Name   WP_001151524_pECD227_113 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   6100 GenBank   WP_001309237
Name   WP_001309237_pECD227_113 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   12095 GenBank   WP_001064247
Name   traC_ECD227_RS00700_pECD227_113 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: 99187.86 Da        Isoelectric Point: 5.8486

>WP_001064247.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   12096 GenBank   WP_000009350
Name   traD_ECD227_RS00630_pECD227_113 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: 81488.99 Da        Isoelectric Point: 5.0504

>WP_000009350.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWIKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCSEQLWSAFVLAAVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 296..26698

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ECD227_RS00765 (ECD227_4200) 296..898 - 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
ECD227_RS00760 (ECD227_4201) 1219..1602 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
ECD227_RS00755 (ECD227_4202) 1789..2478 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
ECD227_RS23410 2577..2972 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
ECD227_RS00750 (ECD227_4203) 3005..3370 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
ECD227_RS00745 (ECD227_4204) 3385..3696 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ECD227_RS00740 (ECD227_4205) 3718..4284 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
ECD227_RS00735 (ECD227_4206) 4271..4999 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ECD227_RS00730 (ECD227_4207) 4999..6426 + 1428 WP_000146692 F-type conjugal transfer pilus assembly protein TraB traB
ECD227_RS00725 (ECD227_4208) 6416..7006 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
ECD227_RS00720 (ECD227_4209) 6993..7190 + 198 WP_001324648 conjugal transfer protein TrbD -
ECD227_RS00715 (ECD227_4210) 7202..7453 + 252 WP_001038342 conjugal transfer protein TrbG -
ECD227_RS00710 (ECD227_4211) 7450..7965 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
ECD227_RS25310 (ECD227_4212) 8100..8321 + 222 WP_001278689 conjugal transfer protein TraR -
ECD227_RS00700 (ECD227_4213) 8481..11108 + 2628 WP_001064247 type IV secretion system protein TraC virb4
ECD227_RS00695 (ECD227_4214) 11105..11491 + 387 WP_000097319 type-F conjugative transfer system protein TrbI -
ECD227_RS00690 (ECD227_4215) 11488..12120 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
ECD227_RS00685 (ECD227_4216) 12117..13109 + 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
ECD227_RS00680 (ECD227_4217) 13118..13756 + 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
ECD227_RS00675 (ECD227_4218) 13753..15561 + 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ECD227_RS00670 (ECD227_4219) 15588..15845 + 258 WP_000864318 conjugal transfer protein TrbE -
ECD227_RS00665 (ECD227_4220) 15838..16581 + 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
ECD227_RS00660 (ECD227_4221) 16597..16944 + 348 WP_001287913 conjugal transfer protein TrbA -
ECD227_RS23415 16946..17260 - 315 WP_000415567 hypothetical protein -
ECD227_RS00655 (ECD227_4222) 17341..17625 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
ECD227_RS00650 (ECD227_4223) 17612..18157 + 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ECD227_RS00645 (ECD227_4224) 18087..18428 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
ECD227_RS23420 18415..18796 + 382 Protein_27 F-type conjugal transfer protein TrbF -
ECD227_RS00640 (ECD227_4225) 18796..20169 + 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
ECD227_RS00635 (ECD227_4226) 20166..22982 + 2817 WP_001007054 conjugal transfer mating-pair stabilization protein TraG traG
ECD227_RS25315 23015..23536 + 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
ECD227_RS23430 23561..24292 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
ECD227_RS00630 (ECD227_4227) 24545..26698 + 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
ECD227_RS00625 (ECD227_4228) 26707..27105 - 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
ECD227_RS00620 (ECD227_4229) 27105..27332 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   16617 GenBank   NZ_CM001144
Plasmid name   pECD227_113 Incompatibility group   IncFIB
Plasmid size   113216 bp Coordinate of oriT [Strand]   867..1218 [+]
Host baterium   Escherichia fergusonii ECD227

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   iutA, iucD, iucC, iucB, iucA, fdeC
Metal resistance gene   yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -