Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101575
Name   oriT_pMFDS1012367 in_silico
Organism   Escherichia coli strain MFDS1012367
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMUR010000003 (112647..112770 [-], 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_pMFDS1012367
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTCTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1397 GenBank   WP_000986971
Name   traI_V6M18_RS27025_pMFDS1012367 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: 192129.86 Da        Isoelectric Point: 5.8508

>WP_000986971.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Escherichia]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMPGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIRAAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAESRMQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTTGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLISDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKIPVAEGERLRVTGKIPGLRISGGDRLQVASVSEDAMTVVVPGRAEPASLPVGYSPFTALKL
ESGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFTDLGREINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETIDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDAIVLVDNVYHRIAGISRDDGLITLQDTDGNSRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVMAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIALGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSEDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAEEKPDQP
DDKTEQAVRDIAGQERDRAVTSEREAVLPESVLREPQRVQDAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

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

(575-626)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   529 GenBank   WP_001254381
Name   WP_001254381_pMFDS1012367 insolico UniProt ID   _
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9037.10 Da        Isoelectric Point: 9.9851

>WP_001254381.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Escherichia]
MRRRNAKAGTSRTISVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRYPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure



No available structure.



ID   530 GenBank   WP_001151555
Name   WP_001151555_pMFDS1012367 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14461.36 Da        Isoelectric Point: 4.5221

>WP_001151555.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Escherichia]
MAKVQAYVSDEIVYKINEIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAIKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   1040 GenBank   WP_000009375
Name   traD_V6M18_RS27040_pMFDS1012367 insolico UniProt ID   _
Length   714 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 714 a.a.        Molecular weight: 81137.72 Da        Isoelectric Point: 5.1669

>WP_000009375.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Escherichia]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATIVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDLNPEMENRLSAVLAAREAEGRQMASLFEPEVVSGEDVTQAEQPQQPVSSVINDK
KSDAGVSVPAGGIAQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQQMQRREEVNINV
HRERGEDVEPGDDF

  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   1041 GenBank   WP_001064271
Name   traC_V6M18_RS27155_pMFDS1012367 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: 99434.22 Da        Isoelectric Point: 5.9665

>WP_001064271.1 MULTISPECIES: type IV secretion system protein TraC [Escherichia]
MNNPLEAVTQAVNSLVTALKLPDESSKANEILGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANETIVEALDHMLRTKLPRGIPLCIHLMSSQLVGERIKYGLREFSWSGEQAERFNAITRAYYMKAAE
TLFPLPEGLNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGAYITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLVKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRQEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(468-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 84316..113342

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M18_RS27030 83682..83909 + 228 WP_000450526 toxin-antitoxin system antitoxin VapB -
V6M18_RS27035 83909..84307 + 399 WP_000911316 type II toxin-antitoxin system VapC family toxin -
V6M18_RS27040 84316..86460 - 2145 WP_000009375 type IV conjugative transfer system coupling protein TraD virb4
V6M18_RS27045 86516..87246 - 731 Protein_99 hypothetical protein -
V6M18_RS27050 87481..87960 - 480 WP_001355324 hypothetical protein -
V6M18_RS27055 88164..88895 - 732 WP_001364068 conjugal transfer complement resistance protein TraT -
V6M18_RS27060 88927..89430 - 504 WP_000605506 hypothetical protein -
V6M18_RS27065 89446..92289 - 2844 WP_001006995 conjugal transfer mating-pair stabilization protein TraG traG
V6M18_RS27070 92286..93659 - 1374 WP_001137366 conjugal transfer pilus assembly protein TraH traH
V6M18_RS27075 93646..94038 - 393 WP_000138366 F-type conjugal transfer protein TrbF -
V6M18_RS27080 93992..94306 - 315 WP_001244895 P-type conjugative transfer protein TrbJ -
V6M18_RS27085 94296..94832 - 537 WP_000059854 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6M18_RS27090 94819..95103 - 285 WP_000624195 type-F conjugative transfer system pilin chaperone TraQ -
V6M18_RS27095 95184..95519 + 336 WP_000415768 hypothetical protein -
V6M18_RS27100 95500..95805 - 306 WP_236922840 conjugal transfer protein TrbA -
V6M18_RS27105 95850..96593 - 744 WP_001030399 type-F conjugative transfer system pilin assembly protein TraF traF
V6M18_RS27110 96586..96843 - 258 WP_000864356 conjugal transfer protein TrbE -
V6M18_RS27115 96857..98761 - 1905 WP_000662057 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6M18_RS27120 98789..99007 + 219 WP_001364024 hypothetical protein -
V6M18_RS27125 98996..99376 - 381 WP_000009645 hypothetical protein -
V6M18_RS27130 99373..100011 - 639 WP_000087541 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M18_RS27135 100038..100557 - 520 Protein_117 hypothetical protein -
V6M18_RS27140 100833..101825 - 993 WP_001355328 conjugal transfer pilus assembly protein TraU traU
V6M18_RS27145 101822..102454 - 633 WP_000650119 type-F conjugative transfer system protein TraW traW
V6M18_RS27150 102451..102837 - 387 WP_000214089 type-F conjugative transfer system protein TrbI -
V6M18_RS27155 102834..105461 - 2628 WP_001064271 type IV secretion system protein TraC virb4
V6M18_RS27160 105621..105842 - 222 WP_001278688 conjugal transfer protein TraR -
V6M18_RS27165 105977..106492 - 516 WP_000802746 type IV conjugative transfer system lipoprotein TraV traV
V6M18_RS27170 106489..106809 - 321 WP_001057269 DUF2689 domain-containing protein -
V6M18_RS27175 106796..107383 - 588 WP_000002892 conjugal transfer pilus-stabilizing protein TraP -
V6M18_RS27180 107373..108803 - 1431 WP_000146619 F-type conjugal transfer pilus assembly protein TraB traB
V6M18_RS27185 108803..109531 - 729 WP_001355329 type-F conjugative transfer system secretin TraK traK
V6M18_RS27190 109518..110084 - 567 WP_000399757 type IV conjugative transfer system protein TraE traE
V6M18_RS27195 110106..110417 - 312 WP_000012121 type IV conjugative transfer system protein TraL traL
V6M18_RS27200 110432..110791 - 360 WP_000340277 type IV conjugative transfer system pilin TraA -
V6M18_RS27205 110825..111052 - 228 WP_001254381 conjugal transfer relaxosome protein TraY -
V6M18_RS27210 111146..111832 - 687 WP_000332479 PAS domain-containing protein -
V6M18_RS27215 112026..112409 - 384 WP_001151555 conjugal transfer relaxosome DNA-binding protein TraM -
V6M18_RS27220 112695..113342 + 648 WP_000614283 transglycosylase SLT domain-containing protein virB1
V6M18_RS27225 113639..114460 - 822 WP_001234470 DUF932 domain-containing protein -
V6M18_RS27230 114579..114866 - 288 WP_000107542 hypothetical protein -
V6M18_RS27235 115117..116121 + 1005 WP_024166184 IS110 family transposase -
V6M18_RS27240 116215..116475 - 261 WP_000547943 hypothetical protein -
V6M18_RS27245 117170..117295 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6M18_RS27250 117237..117386 - 150 Protein_140 plasmid maintenance protein Mok -
V6M18_RS27255 117408..117596 + 189 WP_001355331 hypothetical protein -
V6M18_RS27260 117541..118327 - 787 Protein_142 plasmid SOS inhibition protein A -

Host bacterium

ID   2019 GenBank   NZ_JAQMUR010000003
Plasmid name   pMFDS1012367 Incompatibility group   IncFIB
Plasmid size   238325 bp Coordinate of oriT [Strand]   112647..112770 [-]
Host baterium   Escherichia coli strain MFDS1012367

Cargo genes

Drug resistance gene   -
Virulence gene   estIa, hlyD, hlyB, hlyA, hlyC, faeC, faeD, faeE, faeF, faeH, faeI, faeJ
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11