Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102506
Name   oriT_L4M4-CTX03|unnamed in_silico
Organism   Escherichia coli strain L4M4-CTX03
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQIZC010000002 (51008..51131 [+], 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)
 88..93, 105..110  (ATAAAT..ATTTAT)
 39..45, 50..56  (GCAAAAA..TTTTTGC)
 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_L4M4-CTX03|unnamed
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAATTTTTGCTGATTTGTTTTTTGAATCATTAGCTTATGTTATAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1861 GenBank   WP_047667298
Name   traI_PIA89_RS02020_L4M4-CTX03|unnamed insolico UniProt ID   A0A3Q8VPW8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191897.75 Da        Isoelectric Point: 6.0145

>WP_047667298.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREKLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPRLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(633-712)

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)


  Protein structure



No available structure.




Auxiliary protein

ID   769 GenBank   WP_000124979
Name   WP_000124979_L4M4-CTX03|unnamed insolico UniProt ID   Q5JBL6
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14456.50 Da        Isoelectric Point: 5.2973

>WP_000124979.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB Q5JBL6

ID   770 GenBank   WP_001254385
Name   WP_001254385_L4M4-CTX03|unnamed 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


T4CP

ID   1456 GenBank   WP_000069740
Name   traC_PIA89_RS01925_L4M4-CTX03|unnamed 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: 99356.04 Da        Isoelectric Point: 6.0797

>WP_000069740.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLDAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKKNKARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

  Protein structure



No available structure.



ID   1457 GenBank   WP_097416344
Name   traD_PIA89_RS02015_L4M4-CTX03|unnamed insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83583.22 Da        Isoelectric Point: 5.0504

>WP_097416344.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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   1458 GenBank   WP_001332879
Name   yjgR_PIA89_RS02110_L4M4-CTX03|unnamed insolico UniProt ID   _
Length   500 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 500 a.a.        Molecular weight: 54209.22 Da        Isoelectric Point: 6.1946

>WP_001332879.1 MULTISPECIES: helicase HerA-like C-terminal domain-containing protein [Enterobacteriaceae]
MSEPLLIARTPDTELFLLPGMANRHGLITGATGTGKTVTLQKLAESLSEIGVPVFMADVKGDLTGIAQAG
TASEKLLARLKNIGVNDWQPHANPVVVWDIFGEKGHPVRATVSDLGPLLLARLLNLNDVQSGVLNIIFRI
ADDQGLLLLDFKDLRAITQYIGDNAKSFQNQYGNISSASVGAIQRGLLSLEQQGAAHFFGEPMLDIKDLM
RTDANGKGVINILSAEKLYQMPKLYAASLLWMISELYEQLPEAGDLEKPKLVFFFDEAHLLFNDAPQVLL
DKIEQVIRLIRSKGVGVWFVSQNPSDIPDNVLGQLGNRVQHALRAFTPKDQKAVKAAAQTMRANPAFDTE
KAIQELGTGEALISFLDAKGSPSVVERAMVIAPCSRMGPVTEDERNGLINHSPVYGKYEDDVDRESAYEM
LQKGVQASIEQQNNPPAKGKEIAVDDGILGGLKDILFGTTGPRGGKKDGVVQTMAKSAARQVTNQIVRGM
LGSLLGGRRR

  Protein domains


Predicted by InterproScan.

Helicase HerA-like C-terminal (HerA_C)

(4-500)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 50436..79007

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PIA89_RS01780 (PIA89_01780) 46402..46836 + 435 WP_000845894 conjugation system SOS inhibitor PsiB -
PIA89_RS01785 (PIA89_01785) 46833..47595 + 763 Protein_67 plasmid SOS inhibition protein A -
PIA89_RS01790 (PIA89_01790) 47564..47752 - 189 WP_001299721 hypothetical protein -
PIA89_RS01795 (PIA89_01795) 47774..47923 + 150 Protein_69 plasmid maintenance protein Mok -
PIA89_RS01800 (PIA89_01800) 47865..47990 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
PIA89_RS01805 (PIA89_01805) 48210..48440 + 231 WP_001426396 hypothetical protein -
PIA89_RS01810 (PIA89_01810) 48438..48611 - 174 Protein_72 hypothetical protein -
PIA89_RS01815 (PIA89_01815) 48681..48887 + 207 WP_000547968 hypothetical protein -
PIA89_RS01820 (PIA89_01820) 48912..49199 + 288 WP_000107535 hypothetical protein -
PIA89_RS01825 (PIA89_01825) 49318..50139 + 822 WP_001234469 DUF932 domain-containing protein -
PIA89_RS01830 (PIA89_01830) 50436..51083 - 648 WP_139119334 transglycosylase SLT domain-containing protein virB1
PIA89_RS01835 (PIA89_01835) 51360..51743 + 384 WP_000124979 conjugal transfer relaxosome DNA-binding protein TraM -
PIA89_RS01840 (PIA89_01840) 51934..52620 + 687 WP_062880639 PAS domain-containing protein -
PIA89_RS01845 (PIA89_01845) 52714..52941 + 228 WP_001254385 conjugal transfer relaxosome protein TraY -
PIA89_RS01850 (PIA89_01850) 52975..53334 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
PIA89_RS01855 (PIA89_01855) 53349..53660 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
PIA89_RS01860 (PIA89_01860) 53682..54248 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
PIA89_RS01865 (PIA89_01865) 54235..54963 + 729 WP_001230786 type-F conjugative transfer system secretin TraK traK
PIA89_RS01870 (PIA89_01870) 54963..56390 + 1428 WP_000146655 F-type conjugal transfer pilus assembly protein TraB traB
PIA89_RS01875 (PIA89_01875) 56380..56964 + 585 WP_001299233 conjugal transfer pilus-stabilizing protein TraP -
PIA89_RS01880 (PIA89_01880) 56951..57271 + 321 WP_001057287 conjugal transfer protein TrbD virb4
PIA89_RS01885 (PIA89_01885) 57264..57515 + 252 WP_001038338 conjugal transfer protein TrbG -
PIA89_RS01890 (PIA89_01890) 57512..58027 + 516 WP_000809833 type IV conjugative transfer system lipoprotein TraV traV
PIA89_RS01895 (PIA89_01895) 58162..58383 + 222 WP_001278696 conjugal transfer protein TraR -
PIA89_RS01900 (PIA89_01900) 58376..58789 + 414 WP_000549581 hypothetical protein -
PIA89_RS01905 (PIA89_01905) 58782..59255 + 474 WP_000549572 hypothetical protein -
PIA89_RS01910 (PIA89_01910) 59334..59550 + 217 Protein_92 hypothetical protein -
PIA89_RS01915 (PIA89_01915) 59551..59862 + 312 WP_000141580 hypothetical protein -
PIA89_RS01920 (PIA89_01920) 59932..60294 + 363 WP_000835374 hypothetical protein -
PIA89_RS01925 (PIA89_01925) 60420..63050 + 2631 WP_000069740 type IV secretion system protein TraC virb4
PIA89_RS01930 (PIA89_01930) 63047..63433 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
PIA89_RS01935 (PIA89_01935) 63430..64062 + 633 WP_001203746 type-F conjugative transfer system protein TraW traW
PIA89_RS01940 (PIA89_01940) 64059..65051 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
PIA89_RS01945 (PIA89_01945) 65077..65538 + 462 WP_000277845 hypothetical protein -
PIA89_RS01950 (PIA89_01950) 65568..66020 + 453 WP_000069427 hypothetical protein -
PIA89_RS01955 (PIA89_01955) 66048..66686 + 639 WP_001104248 type-F conjugative transfer system pilin assembly protein TrbC trbC
PIA89_RS01960 (PIA89_01960) 66683..68491 + 1809 WP_000821823 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PIA89_RS01965 (PIA89_01965) 68518..68775 + 258 WP_000864325 conjugal transfer protein TrbE -
PIA89_RS01970 (PIA89_01970) 68768..69511 + 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
PIA89_RS01975 (PIA89_01975) 69527..69874 + 348 WP_001287893 conjugal transfer protein TrbA -
PIA89_RS01980 (PIA89_01980) 69993..70277 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
PIA89_RS01985 (PIA89_01985) 70264..70809 + 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PIA89_RS01990 (PIA89_01990) 70739..71101 + 363 WP_023181029 P-type conjugative transfer protein TrbJ -
PIA89_RS01995 (PIA89_01995) 71101..72474 + 1374 WP_021530364 conjugal transfer pilus assembly protein TraH traH
PIA89_RS02000 (PIA89_02000) 72471..75296 + 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
PIA89_RS02005 (PIA89_02005) 75293..75802 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
PIA89_RS02010 (PIA89_02010) 75816..76547 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
PIA89_RS02015 (PIA89_02015) 76800..79007 + 2208 WP_097416344 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2950 GenBank   NZ_JAQIZC010000002
Plasmid name   L4M4-CTX03|unnamed Incompatibility group   IncFII
Plasmid size   233201 bp Coordinate of oriT [Strand]   51008..51131 [+]
Host baterium   Escherichia coli strain L4M4-CTX03

Cargo genes

Drug resistance gene   sul3, ant(3'')-Ia, cmlA1, aadA2
Virulence gene   htpB
Metal resistance gene   merR, merT, merP, merA, merD, merE, mgtA, cutA
Degradation gene   bhpD
Symbiosis gene   -
Anti-CRISPR   AcrIIA9