Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102421
Name   oriT_SMG004F8|unnamed2 in_silico
Organism   Escherichia coli strain SMG004F8
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVSX010000023 (41612..41735 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 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_SMG004F8|unnamed2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1813 GenBank   WP_000948348
Name   traI_ML391_RS19955_SMG004F8|unnamed2 insolico UniProt ID   A0A7I0KNL8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191759.33 Da        Isoelectric Point: 5.7433

>WP_000948348.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
EPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

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   733 GenBank   WP_001254388
Name   WP_001254388_SMG004F8|unnamed2 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2

ID   734 GenBank   WP_001151562
Name   WP_001151562_SMG004F8|unnamed2 insolico UniProt ID   A0A7I0KNG1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14420.36 Da        Isoelectric Point: 4.8624

>WP_001151562.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVHEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0KNG1


T4CP

ID   1398 GenBank   WP_032164615
Name   traD_ML391_RS19960_SMG004F8|unnamed2 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85681.49 Da        Isoelectric Point: 5.1644

>WP_032164615.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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.



ID   1399 GenBank   WP_000069778
Name   traC_ML391_RS20060_SMG004F8|unnamed2 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: 99300.06 Da        Isoelectric Point: 6.3461

>WP_000069778.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 13800..42307

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML391_RS19960 (ML391_19960) 13800..16061 - 2262 WP_032164615 type IV conjugative transfer system coupling protein TraD virb4
ML391_RS19965 (ML391_19965) 16112..16849 - 738 WP_000199901 hypothetical protein -
ML391_RS19970 (ML391_19970) 17052..17783 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
ML391_RS19975 (ML391_19975) 17832..18317 - 486 WP_000605869 hypothetical protein -
ML391_RS19980 (ML391_19980) 18333..21155 - 2823 WP_001007080 conjugal transfer mating-pair stabilization protein TraG traG
ML391_RS19985 (ML391_19985) 21152..22525 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
ML391_RS19990 (ML391_19990) 22512..22904 - 393 WP_000660700 F-type conjugal transfer protein TrbF -
ML391_RS19995 (ML391_19995) 22885..23232 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
ML391_RS20000 (ML391_20000) 23162..23707 - 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ML391_RS20005 (ML391_20005) 23694..23978 - 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
ML391_RS20010 (ML391_20010) 24059..24394 + 336 WP_000736414 hypothetical protein -
ML391_RS20015 (ML391_20015) 24375..24716 - 342 WP_001298557 conjugal transfer protein TrbA -
ML391_RS20020 (ML391_20020) 24730..25473 - 744 WP_001030385 type-F conjugative transfer system pilin assembly protein TraF traF
ML391_RS20025 (ML391_20025) 25466..25723 - 258 WP_000864314 conjugal transfer protein TrbE -
ML391_RS20030 (ML391_20030) 25750..27600 - 1851 WP_000821859 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ML391_RS20035 (ML391_20035) 27597..28235 - 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
ML391_RS20040 (ML391_20040) 28244..28549 - 306 WP_000224418 hypothetical protein -
ML391_RS20045 (ML391_20045) 28579..29571 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
ML391_RS20050 (ML391_20050) 29568..30200 - 633 WP_001203736 type-F conjugative transfer system protein TraW traW
ML391_RS20055 (ML391_20055) 30197..30583 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
ML391_RS20060 (ML391_20060) 30580..33210 - 2631 WP_000069778 type IV secretion system protein TraC virb4
ML391_RS27810 33336..33549 - 214 Protein_37 hypothetical protein -
ML391_RS20065 (ML391_20065) 33577..33795 - 219 WP_000556746 hypothetical protein -
ML391_RS20070 (ML391_20070) 33875..34348 - 474 WP_000549566 hypothetical protein -
ML391_RS20075 (ML391_20075) 34341..34562 - 222 WP_001278694 conjugal transfer protein TraR -
ML391_RS20080 (ML391_20080) 34697..35212 - 516 WP_000809888 type IV conjugative transfer system lipoprotein TraV traV
ML391_RS20085 (ML391_20085) 35209..35461 - 253 Protein_42 conjugal transfer protein TrbG -
ML391_RS20090 (ML391_20090) 35454..35774 - 321 WP_001057275 conjugal transfer protein TrbD virb4
ML391_RS20095 (ML391_20095) 35761..36351 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
ML391_RS20100 (ML391_20100) 36341..37768 - 1428 WP_000146665 F-type conjugal transfer pilus assembly protein TraB traB
ML391_RS20105 (ML391_20105) 37768..38496 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ML391_RS20110 (ML391_20110) 38483..39049 - 567 WP_000399776 type IV conjugative transfer system protein TraE traE
ML391_RS20115 (ML391_20115) 39071..39382 - 312 WP_000012100 type IV conjugative transfer system protein TraL traL
ML391_RS20120 (ML391_20120) 39397..39756 - 360 WP_001098988 type IV conjugative transfer system pilin TraA -
ML391_RS20125 (ML391_20125) 39790..40017 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
ML391_RS20130 (ML391_20130) 40111..40797 - 687 WP_000332487 PAS domain-containing protein -
ML391_RS20135 (ML391_20135) 40991..41374 - 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
ML391_RS20140 (ML391_20140) 41705..42307 + 603 WP_001323326 transglycosylase SLT domain-containing protein virB1
ML391_RS20145 (ML391_20145) 42603..43424 - 822 WP_001234489 DUF932 domain-containing protein -
ML391_RS20150 (ML391_20150) 43543..43830 - 288 WP_000107526 hypothetical protein -
ML391_RS20155 (ML391_20155) 44131..44428 + 298 Protein_56 hypothetical protein -
ML391_RS20160 (ML391_20160) 44746..44871 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
ML391_RS20165 (ML391_20165) 44813..44962 - 150 Protein_58 DUF5431 family protein -
ML391_RS20170 (ML391_20170) 45136..45899 - 764 Protein_59 plasmid SOS inhibition protein A -
ML391_RS20175 (ML391_20175) 45896..46330 - 435 WP_000845910 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   2865 GenBank   NZ_JAKVSX010000023
Plasmid name   SMG004F8|unnamed2 Incompatibility group   IncFII
Plasmid size   82485 bp Coordinate of oriT [Strand]   41612..41735 [-]
Host baterium   Escherichia coli strain SMG004F8

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -