Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101574
Name   oriT_pMFDS1009772_1 in_silico
Organism   Escherichia coli strain MFDS1009772
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMUN010000004 (9644..9729 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pMFDS1009772_1
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1396 GenBank   WP_332832535
Name   traI_V6M09_RS26950_pMFDS1009772_1 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: 191719.27 Da        Isoelectric Point: 5.7960

>WP_332832535.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTATSERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   527 GenBank   WP_001354030
Name   WP_001354030_pMFDS1009772_1 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   528 GenBank   WP_000089263
Name   WP_000089263_pMFDS1009772_1 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   1038 GenBank   WP_000069777
Name   traC_V6M09_RS26850_pMFDS1009772_1 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: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   1039 GenBank   WP_125097878
Name   traD_V6M09_RS26945_pMFDS1009772_1 insolico UniProt ID   _
Length   762 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 762 a.a.        Molecular weight: 86727.59 Da        Isoelectric Point: 5.1644

>WP_125097878.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPE
EEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 9076..37649

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M09_RS26725 5048..5482 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
V6M09_RS26730 5479..6241 + 763 Protein_8 plasmid SOS inhibition protein A -
V6M09_RS26735 6219..6398 - 180 WP_001309233 hypothetical protein -
V6M09_RS26740 6420..6569 + 150 Protein_10 plasmid maintenance protein Mok -
V6M09_RS26745 6511..6636 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6M09_RS26750 6955..7251 - 297 Protein_12 hypothetical protein -
V6M09_RS26755 7551..7847 + 297 WP_001272251 hypothetical protein -
V6M09_RS26760 7958..8779 + 822 WP_001234445 DUF932 domain-containing protein -
V6M09_RS26765 9076..9678 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
V6M09_RS26770 10001..10384 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
V6M09_RS26775 10578..11249 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
V6M09_RS26780 11386..11613 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
V6M09_RS26785 11646..12005 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
V6M09_RS26790 12020..12331 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
V6M09_RS26795 12353..12919 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
V6M09_RS26800 12906..13634 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
V6M09_RS26805 13634..15085 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
V6M09_RS26810 15075..15641 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
V6M09_RS26815 15628..15948 + 321 WP_001057307 conjugal transfer protein TrbD -
V6M09_RS26820 15945..16460 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
V6M09_RS26825 16595..16816 + 222 WP_001278683 conjugal transfer protein TraR -
V6M09_RS26830 16809..17222 + 414 WP_000549589 hypothetical protein -
V6M09_RS26835 17215..17688 + 474 WP_000549568 hypothetical protein -
V6M09_RS26840 17768..17986 + 219 WP_000556745 hypothetical protein -
V6M09_RS26845 18014..18361 + 348 WP_000836682 hypothetical protein -
V6M09_RS26850 18487..21117 + 2631 WP_000069777 type IV secretion system protein TraC virb4
V6M09_RS26855 21114..21500 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
V6M09_RS26860 21497..22129 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
V6M09_RS26865 22126..23118 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
V6M09_RS26870 23148..23453 + 306 WP_000224416 hypothetical protein -
V6M09_RS26875 23462..24100 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M09_RS26880 24097..25947 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6M09_RS26885 25974..26231 + 258 WP_016235952 conjugal transfer protein TrbE -
V6M09_RS26890 26224..26967 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
V6M09_RS26895 26981..27325 + 345 WP_000556796 conjugal transfer protein TrbA -
V6M09_RS26900 27444..27728 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
V6M09_RS26905 27715..28260 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6M09_RS26910 28190..28537 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
V6M09_RS26915 28518..28910 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
V6M09_RS26920 28897..30270 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
V6M09_RS26925 30267..33089 + 2823 WP_094307824 conjugal transfer mating-pair stabilization protein TraG traG
V6M09_RS26930 33105..33590 + 486 WP_000605870 hypothetical protein -
V6M09_RS26935 33639..34370 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
V6M09_RS26940 34573..35310 + 738 WP_000199905 hypothetical protein -
V6M09_RS26945 35361..37649 + 2289 WP_125097878 type IV conjugative transfer system coupling protein TraD prgC

Host bacterium

ID   2018 GenBank   NZ_JAQMUN010000004
Plasmid name   pMFDS1009772_1 Incompatibility group   IncFII
Plasmid size   88879 bp Coordinate of oriT [Strand]   9644..9729 [-]
Host baterium   Escherichia coli strain MFDS1009772

Cargo genes

Drug resistance gene   floR, aac(3)-VIa, ant(3'')-Ia, qnrS1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -