Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101594
Name   oriT_pIncFII in_silico
Organism   Escherichia coli strain C1S1_DTRP20
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAJPGL010000091 (2260..2383 [+], 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_pIncFII
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1415 GenBank   WP_000986934
Name   traI_LT671_RS02340_pIncFII insolico UniProt ID   A0A291R9S5
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191764.68 Da        Isoelectric Point: 5.9593

>WP_000986934.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(968-1156)

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   551 GenBank   WP_001151564
Name   WP_001151564_pIncFII insolico UniProt ID   A0AA36PD43
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14446.39 Da        Isoelectric Point: 4.7197

>WP_001151564.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   552 GenBank   WP_001254388
Name   WP_001254388_pIncFII 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


T4CP

ID   1070 GenBank   WP_001064239
Name   traC_LT671_RS02245_pIncFII 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: 99485.47 Da        Isoelectric Point: 6.6265

>WP_001064239.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGM
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1071 GenBank   WP_049077307
Name   traD_LT671_RS02335_pIncFII insolico UniProt ID   _
Length   723 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 723 a.a.        Molecular weight: 82233.92 Da        Isoelectric Point: 5.1048

>WP_049077307.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PVSPAINDKKSDSGVNIPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQ
RREEVNINVHRERGEDVEPGDDF

  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: 1688..24352

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LT671_RS02160 (LT671_02155) 18..137 + 120 WP_001426400 hypothetical protein -
LT671_RS02165 (LT671_02160) 162..449 + 288 WP_000107537 hypothetical protein -
LT671_RS02170 (LT671_02165) 570..1391 + 822 WP_001234469 DUF932 domain-containing protein -
LT671_RS02175 (LT671_02170) 1688..2335 - 648 WP_000614282 transglycosylase SLT domain-containing protein virB1
LT671_RS02180 (LT671_02175) 2621..3004 + 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
LT671_RS02185 (LT671_02180) 3198..3884 + 687 WP_000332487 PAS domain-containing protein -
LT671_RS02190 (LT671_02185) 3978..4205 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
LT671_RS02195 (LT671_02190) 4239..4601 + 363 WP_001098998 type IV conjugative transfer system pilin TraA -
LT671_RS02200 (LT671_02195) 4606..4917 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
LT671_RS02205 (LT671_02200) 4939..5505 + 567 WP_000399804 type IV conjugative transfer system protein TraE traE
LT671_RS02210 (LT671_02205) 5492..6220 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
LT671_RS02215 (LT671_02210) 6220..7647 + 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
LT671_RS02220 (LT671_02215) 7637..8221 + 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
LT671_RS02225 (LT671_02220) 8208..8528 + 321 WP_001057302 conjugal transfer protein TrbD virb4
LT671_RS02230 (LT671_02225) 8521..8772 + 252 WP_001038341 conjugal transfer protein TrbG -
LT671_RS02235 (LT671_02230) 8769..9284 + 516 WP_000809893 type IV conjugative transfer system lipoprotein TraV traV
LT671_RS02240 (LT671_02235) 9419..9640 + 222 WP_001278978 conjugal transfer protein TraR -
LT671_RS02245 (LT671_02240) 9800..12427 + 2628 WP_001064239 type IV secretion system protein TraC virb4
LT671_RS02250 (LT671_02245) 12424..12810 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
LT671_RS02255 (LT671_02250) 12807..13439 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
LT671_RS02260 (LT671_02255) 13436..14428 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
LT671_RS02265 (LT671_02260) 14458..14763 + 306 WP_000224411 hypothetical protein -
LT671_RS02270 (LT671_02265) 14772..15410 + 639 WP_001080257 type-F conjugative transfer system pilin assembly protein TrbC trbC
LT671_RS02275 (LT671_02270) 15407..17215 + 1809 WP_000821863 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LT671_RS02280 (LT671_02275) 17242..17499 + 258 WP_000864320 conjugal transfer protein TrbE -
LT671_RS02285 (LT671_02280) 17492..18235 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
LT671_RS02290 (LT671_02285) 18251..18589 + 339 WP_001287905 conjugal transfer protein TrbA -
LT671_RS02295 (LT671_02290) 18716..19000 + 285 WP_001448202 type-F conjugative transfer system pilin chaperone TraQ -
LT671_RS02300 (LT671_02295) 18987..19532 + 546 WP_000059824 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LT671_RS02305 (LT671_02300) 19462..19803 + 342 WP_001448115 P-type conjugative transfer protein TrbJ -
LT671_RS02310 (LT671_02305) 19784..20176 + 393 WP_000660703 F-type conjugal transfer protein TrbF -
LT671_RS02315 (LT671_02310) 20163..21536 + 1374 WP_001137364 conjugal transfer pilus assembly protein TraH traH
LT671_RS02320 (LT671_02315) 21533..24352 + 2820 WP_001007057 conjugal transfer mating-pair stabilization protein TraG traG
LT671_RS02325 (LT671_02320) 24371..24868 + 498 WP_000605861 hypothetical protein -
LT671_RS02330 (LT671_02325) 24900..25631 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
LT671_RS02335 (LT671_02330) 25884..28055 + 2172 WP_049077307 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   2038 GenBank   NZ_JAJPGL010000091
Plasmid name   pIncFII Incompatibility group   IncFII
Plasmid size   41912 bp Coordinate of oriT [Strand]   2260..2383 [+]
Host baterium   Escherichia coli strain C1S1_DTRP20

Cargo genes

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