Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103010
Name   oriT_p42-2 in_silico
Organism   Escherichia coli strain 42-2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT990220 (69650..69773 [+], 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)
 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_p42-2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2259 GenBank   WP_072648275
Name   traI_HTG57_RS00620_p42-2 insolico UniProt ID   A0A647AQ34
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192066.85 Da        Isoelectric Point: 6.0285

>WP_072648275.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLACSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   921 GenBank   WP_000124981
Name   WP_000124981_p42-2 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

ID   922 GenBank   WP_001254386
Name   WP_001254386_p42-2 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1948 GenBank   WP_015059012
Name   traC_HTG57_RS00510_p42-2 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: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1949 GenBank   WP_011402783
Name   traD_HTG57_RS00615_p42-2 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83199.81 Da        Isoelectric Point: 5.0504

>WP_011402783.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 69078..97239

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG57_RS00690 64140..64229 + 90 WP_032200426 hypothetical protein -
HTG57_RS00410 (DK80_076) 64453..64683 + 231 WP_000218642 hypothetical protein -
HTG57_RS00415 (DK80_077) 64735..66096 + 1362 WP_000170695 DUF3560 domain-containing protein -
HTG57_RS00420 (DK80_078) 66143..66706 + 564 WP_015059007 class I SAM-dependent methyltransferase -
HTG57_RS00680 (DK80_079) 66792..67241 - 450 Protein_84 hypothetical protein -
HTG57_RS00430 (DK80_081) 67553..67849 + 297 WP_001272251 hypothetical protein -
HTG57_RS00435 (DK80_082) 67960..68781 + 822 WP_001234445 DUF932 domain-containing protein -
HTG57_RS00440 (DK80_084) 69078..69725 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HTG57_RS00445 70002..70385 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTG57_RS00450 70576..71262 + 687 WP_015059009 PAS domain-containing protein -
HTG57_RS00455 71356..71583 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTG57_RS00460 71617..71982 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HTG57_RS00465 71997..72308 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTG57_RS00470 72330..72896 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HTG57_RS00475 (DK80_091) 72883..73611 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTG57_RS00480 73611..75038 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HTG57_RS00485 75028..75618 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HTG57_RS00490 75605..75802 + 198 WP_001324648 conjugal transfer protein TrbD -
HTG57_RS00495 (DK80_095) 75814..76065 + 252 WP_001038341 conjugal transfer protein TrbG -
HTG57_RS00500 76062..76577 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HTG57_RS00505 76712..76933 + 222 WP_001278692 conjugal transfer protein TraR -
HTG57_RS00510 77093..79720 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HTG57_RS00515 79717..80103 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HTG57_RS00520 80100..80732 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HTG57_RS00525 (DK80_102) 80729..81721 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTG57_RS00530 (DK80_103) 81850..82056 + 207 WP_204902719 hypothetical protein -
HTG57_RS00535 (DK80_104) 82119..82640 + 522 WP_015059014 hypothetical protein -
HTG57_RS00540 82667..83305 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTG57_RS00545 (DK80_106) 83302..83673 + 372 WP_000056336 hypothetical protein -
HTG57_RS00550 (DK80_107) 83699..84121 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HTG57_RS00555 (DK80_108) 84118..85968 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTG57_RS00560 85995..86252 + 258 WP_053913405 conjugal transfer protein TrbE -
HTG57_RS00565 86245..86988 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HTG57_RS00570 87149..87385 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HTG57_RS00575 87372..87917 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTG57_RS00580 87907..88221 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HTG57_RS00585 88175..88567 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HTG57_RS00590 88554..89927 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HTG57_RS00595 89924..92740 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HTG57_RS00600 92773..93294 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HTG57_RS00605 93319..94050 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HTG57_RS00610 (DK80_119) 94253..94990 + 738 WP_015059020 hypothetical protein -
HTG57_RS00615 95041..97239 + 2199 WP_011402783 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3453 GenBank   NZ_KT990220
Plasmid name   p42-2 Incompatibility group   IncX1
Plasmid size   106886 bp Coordinate of oriT [Strand]   69650..69773 [+]
Host baterium   Escherichia coli strain 42-2

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, aph(3')-IIa, oqxB, oqxA, fosA3, blaTEM-1B, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -