Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102966
Name   oriT_pAPEC-O2-211A-ColV in_silico
Organism   Escherichia coli APEC O2-211
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP030791 (146491..146614 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 57..62, 70..75  (TGATTT..AAATCA)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pAPEC-O2-211A-ColV
GGTTGGTGGTTCTCACCACCAAAAGTACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTAAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2223 GenBank   WP_114637674
Name   traI_APECO2_RS27290_pAPEC-O2-211A-ColV 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: 192030.00 Da        Isoelectric Point: 6.1910

>WP_114637674.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKISLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFKSAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLWGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   913 GenBank   WP_001254385
Name   WP_001254385_pAPEC-O2-211A-ColV insolico UniProt ID   A0A1Q9L2K4
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8975.08 Da        Isoelectric Point: 10.1422

>WP_001254385.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVAEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A1Q9L2K4

ID   914 GenBank   WP_000124981
Name   WP_000124981_pAPEC-O2-211A-ColV insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9


T4CP

ID   1914 GenBank   WP_039025869
Name   traD_APECO2_RS27305_pAPEC-O2-211A-ColV 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: 81513.13 Da        Isoelectric Point: 5.1761

>WP_039025869.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKNMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAGTLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGREMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGENVEPGDDF

  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   1915 GenBank   WP_001064245
Name   traC_APECO2_RS27400_pAPEC-O2-211A-ColV 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: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 121052..147186

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
APECO2_RS27295 (APECO2_28395) 120418..120645 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
APECO2_RS27300 (APECO2_28400) 120645..121043 + 399 WP_000911333 tRNA(fMet)-specific endonuclease VapC -
APECO2_RS27305 (APECO2_28405) 121052..123205 - 2154 WP_039025869 type IV conjugative transfer system coupling protein TraD virb4
APECO2_RS27310 (APECO2_28410) 123458..124189 - 732 WP_000850416 conjugal transfer complement resistance protein TraT -
APECO2_RS27315 (APECO2_28415) 124203..124712 - 510 WP_000628105 conjugal transfer entry exclusion protein TraS -
APECO2_RS27320 (APECO2_28420) 124709..127534 - 2826 WP_001007036 conjugal transfer mating-pair stabilization protein TraG traG
APECO2_RS27325 (APECO2_28425) 127531..128904 - 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
APECO2_RS28710 128891..129283 - 393 Protein_127 F-type conjugal transfer protein TrbF -
APECO2_RS27340 (APECO2_28440) 129270..129611 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
APECO2_RS27345 (APECO2_28445) 129541..130086 - 546 WP_000059833 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
APECO2_RS27350 (APECO2_28450) 130073..130357 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
APECO2_RS28225 (APECO2_28455) 130438..130713 + 276 WP_114637675 toxin ArtA -
APECO2_RS27360 (APECO2_28460) 130715..131062 - 348 WP_001287907 conjugal transfer protein TrbA -
APECO2_RS27365 (APECO2_28465) 131078..131821 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
APECO2_RS27370 (APECO2_28470) 131814..132071 - 258 WP_000864318 conjugal transfer protein TrbE -
APECO2_RS27375 (APECO2_28475) 132098..133906 - 1809 WP_000821867 type-F conjugative transfer system mating-pair stabilization protein TraN traN
APECO2_RS27380 (APECO2_28480) 133903..134541 - 639 WP_000777703 type-F conjugative transfer system pilin assembly protein TrbC trbC
APECO2_RS27385 (APECO2_28485) 134550..135542 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
APECO2_RS27390 (APECO2_28490) 135539..136171 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
APECO2_RS27395 (APECO2_28495) 136168..136554 - 387 WP_000099688 type-F conjugative transfer system protein TrbI -
APECO2_RS27400 (APECO2_28500) 136551..139178 - 2628 WP_001064245 type IV secretion system protein TraC virb4
APECO2_RS27405 (APECO2_28505) 139338..139559 - 222 WP_001278690 conjugal transfer protein TraR -
APECO2_RS27410 (APECO2_28510) 139694..140209 - 516 WP_000809834 type IV conjugative transfer system lipoprotein TraV traV
APECO2_RS27415 (APECO2_28515) 140206..140457 - 252 WP_001038351 conjugal transfer protein TrbG -
APECO2_RS27420 (APECO2_28520) 140469..140666 - 198 WP_001324648 conjugal transfer protein TrbD -
APECO2_RS27425 (APECO2_28525) 140653..141243 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
APECO2_RS27430 (APECO2_28530) 141233..142660 - 1428 WP_031570446 F-type conjugal transfer pilus assembly protein TraB traB
APECO2_RS27435 (APECO2_28535) 142660..143388 - 729 WP_001230796 type-F conjugative transfer system secretin TraK traK
APECO2_RS27440 (APECO2_28540) 143375..143941 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
APECO2_RS27445 (APECO2_28545) 143963..144274 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
APECO2_RS27450 (APECO2_28550) 144289..144648 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
APECO2_RS27455 (APECO2_28555) 144682..144909 - 228 WP_001254385 conjugal transfer relaxosome protein TraY -
APECO2_RS27460 (APECO2_28560) 145003..145689 - 687 WP_000332490 PAS domain-containing protein -
APECO2_RS27465 (APECO2_28565) 145879..146262 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
APECO2_RS27475 (APECO2_28575) 146584..147186 + 603 WP_023145258 transglycosylase SLT domain-containing protein -
APECO2_RS27480 (APECO2_28580) 147482..148303 - 822 WP_157917628 DUF932 domain-containing protein -
APECO2_RS28715 148422..148708 - 287 Protein_156 hypothetical protein -
APECO2_RS28720 148710..149031 + 322 Protein_157 hypothetical protein -
APECO2_RS27490 (APECO2_28590) 149332..149454 - 123 WP_223195199 Hok/Gef family protein -
APECO2_RS28725 149399..149551 - 153 Protein_159 DUF5431 family protein -
APECO2_RS27500 (APECO2_28600) 149768..150487 - 720 WP_001276275 plasmid SOS inhibition protein A -
APECO2_RS27505 (APECO2_28605) 150484..150918 - 435 WP_000845935 conjugation system SOS inhibitor PsiB -
APECO2_RS27510 (APECO2_28610) 150973..151554 - 582 Protein_162 hypothetical protein -

Host bacterium

ID   3409 GenBank   NZ_CP030791
Plasmid name   pAPEC-O2-211A-ColV Incompatibility group   IncFIB
Plasmid size   197773 bp Coordinate of oriT [Strand]   146491..146614 [-]
Host baterium   Escherichia coli APEC O2-211

Cargo genes

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