Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101566
Name   oriT_pMFDS1016235 in_silico
Organism   Escherichia coli strain MFDS1016235
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMVJ010000004 (20868..20991 [+], 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)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 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_pMFDS1016235
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1388 GenBank   WP_096124000
Name   traI_V6L95_RS25530_pMFDS1016235 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: 192290.18 Da        Isoelectric Point: 5.9188

>WP_096124000.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGRNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIEAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGVVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERVRAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYETEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVELPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   512 GenBank   WP_032083503
Name   WP_032083503_pMFDS1016235 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: 14584.63 Da        Isoelectric Point: 5.0278

>WP_032083503.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVERRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSIEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   513 GenBank   WP_001254386
Name   WP_001254386_pMFDS1016235 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   1024 GenBank   WP_001064245
Name   traC_V6L95_RS25425_pMFDS1016235 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: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   1025 GenBank   WP_062873762
Name   traD_V6L95_RS25515_pMFDS1016235 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81434.90 Da        Isoelectric Point: 5.0485

>WP_062873762.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPDMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 20296..46434

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6L95_RS25305 16262..16696 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
V6L95_RS25310 16693..17455 + 763 Protein_25 plasmid SOS inhibition protein A -
V6L95_RS25315 17424..17612 - 189 WP_032084246 hypothetical protein -
V6L95_RS25320 17634..17783 + 150 Protein_27 plasmid maintenance protein Mok -
V6L95_RS25325 17725..17850 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6L95_RS25330 18070..18300 + 231 WP_074014914 hypothetical protein -
V6L95_RS25335 18298..18471 - 174 Protein_30 hypothetical protein -
V6L95_RS25340 18541..18738 + 198 WP_332829938 single-stranded DNA-binding protein -
V6L95_RS25345 18773..19059 + 287 Protein_32 hypothetical protein -
V6L95_RS25350 19178..19999 + 822 WP_074014913 DUF932 domain-containing protein -
V6L95_RS25355 20296..20943 - 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6L95_RS25360 21220..21603 + 384 WP_032083503 conjugal transfer relaxosome DNA-binding protein TraM -
V6L95_RS25365 21793..22479 + 687 WP_000332492 PAS domain-containing protein -
V6L95_RS25370 22573..22800 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6L95_RS25375 22834..23199 + 366 WP_332829939 type IV conjugative transfer system pilin TraA -
V6L95_RS25380 23214..23525 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6L95_RS25385 23547..24113 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6L95_RS25390 24100..24828 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
V6L95_RS25395 24828..26255 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6L95_RS25400 26245..26835 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6L95_RS25405 26822..27019 + 198 WP_001324648 conjugal transfer protein TrbD -
V6L95_RS25410 27031..27281 + 251 Protein_45 conjugal transfer protein TrbG -
V6L95_RS25415 27278..27793 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
V6L95_RS25420 27928..28149 + 222 WP_001278689 conjugal transfer protein TraR -
V6L95_RS25425 28309..30936 + 2628 WP_001064245 type IV secretion system protein TraC virb4
V6L95_RS25430 30933..31319 + 387 WP_000214096 type-F conjugative transfer system protein TrbI -
V6L95_RS25435 31316..31948 + 633 WP_062873969 type-F conjugative transfer system protein TraW traW
V6L95_RS25440 31945..32937 + 993 WP_021559016 conjugal transfer pilus assembly protein TraU traU
V6L95_RS25445 32946..33584 + 639 WP_282868777 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6L95_RS25450 33581..35389 + 1809 WP_096111975 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6L95_RS25455 35416..35673 + 258 WP_000864318 conjugal transfer protein TrbE -
V6L95_RS25460 35666..36409 + 744 WP_123010632 type-F conjugative transfer system pilin assembly protein TraF traF
V6L95_RS25465 36425..36772 + 348 WP_032082949 conjugal transfer protein TrbA -
V6L95_RS25470 36774..37049 - 276 WP_001513501 hypothetical protein -
V6L95_RS25475 37130..37414 + 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6L95_RS25480 37401..37946 + 546 WP_000059818 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6L95_RS25485 37876..38217 + 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6L95_RS25490 38204..38596 + 393 WP_282868770 F-type conjugal transfer protein TrbF -
V6L95_RS25495 38583..39956 + 1374 WP_021532658 conjugal transfer pilus assembly protein TraH traH
V6L95_RS25500 39953..42778 + 2826 WP_032082912 conjugal transfer mating-pair stabilization protein TraG traG
V6L95_RS25505 42775..43284 + 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6L95_RS25510 43298..44029 + 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6L95_RS25515 44281..46434 + 2154 WP_062873762 type IV conjugative transfer system coupling protein TraD virb4
V6L95_RS25520 46443..46841 - 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6L95_RS25525 46841..47068 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2010 GenBank   NZ_JAQMVJ010000004
Plasmid name   pMFDS1016235 Incompatibility group   IncFII
Plasmid size   84772 bp Coordinate of oriT [Strand]   20868..20991 [+]
Host baterium   Escherichia coli strain MFDS1016235

Cargo genes

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