Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107522
Name   oriT_p888048 in_silico
Organism   Shigella flexneri 3a strain 888048
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MW396860 (34817..34940 [+], 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_p888048
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5046 GenBank   WP_000948354
Name   traI_J5X05_RS00420_p888048 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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)


  Protein structure



No available structure.




Auxiliary protein

ID   2315 GenBank   WP_001151562
Name   WP_001151562_p888048 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

ID   2316 GenBank   WP_001254388
Name   WP_001254388_p888048 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   5264 GenBank   WP_000069772
Name   traC_J5X05_RS00320_p888048 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: 99344.15 Da        Isoelectric Point: 6.4096

>WP_000069772.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   5265 GenBank   WP_025985153
Name   traD_J5X05_RS00415_p888048 insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84960.70 Da        Isoelectric Point: 5.1644

>WP_025985153.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESG
EVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 34245..62758

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J5X05_RS00205 (JOIPEEHJ_00039) 30213..30647 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
J5X05_RS00210 (JOIPEEHJ_00040) 30644..31363 + 720 WP_001276217 plasmid SOS inhibition protein A -
J5X05_RS00470 (JOIPEEHJ_00041) 31585..31734 + 150 Protein_41 plasmid maintenance protein Mok -
J5X05_RS00215 (JOIPEEHJ_00041) 31676..31801 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
J5X05_RS00475 32120..32417 - 298 Protein_43 hypothetical protein -
J5X05_RS00225 (JOIPEEHJ_00042) 32720..33016 + 297 WP_001272251 hypothetical protein -
J5X05_RS00230 (JOIPEEHJ_00043) 33127..33948 + 822 WP_001234445 DUF932 domain-containing protein -
J5X05_RS00235 (JOIPEEHJ_00044) 34245..34847 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
J5X05_RS00240 (JOIPEEHJ_00045) 35178..35561 + 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
J5X05_RS00245 (JOIPEEHJ_00046) 35755..36441 + 687 WP_152061377 PAS domain-containing protein -
J5X05_RS00250 (JOIPEEHJ_00047) 36535..36762 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
J5X05_RS00255 (JOIPEEHJ_00048) 36796..37158 + 363 WP_001098993 type IV conjugative transfer system pilin TraA -
J5X05_RS00260 (JOIPEEHJ_00049) 37173..37484 + 312 WP_000012100 type IV conjugative transfer system protein TraL traL
J5X05_RS00265 (JOIPEEHJ_00050) 37506..38072 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
J5X05_RS00270 (JOIPEEHJ_00051) 38059..38787 + 729 WP_152061378 type-F conjugative transfer system secretin TraK traK
J5X05_RS00275 (JOIPEEHJ_00052) 38787..40238 + 1452 WP_000146663 F-type conjugal transfer pilus assembly protein TraB traB
J5X05_RS00280 (JOIPEEHJ_00053) 40228..40794 + 567 WP_000896598 conjugal transfer pilus-stabilizing protein TraP -
J5X05_RS00285 (JOIPEEHJ_00054) 40781..41098 + 318 WP_001057297 conjugal transfer protein TrbD -
J5X05_RS00290 (JOIPEEHJ_00055) 41098..41613 + 516 WP_000809872 type IV conjugative transfer system lipoprotein TraV traV
J5X05_RS00295 41748..41969 + 222 WP_001278695 conjugal transfer protein TraR -
J5X05_RS00300 (JOIPEEHJ_00056) 41962..42375 + 414 WP_000549574 hypothetical protein -
J5X05_RS00305 (JOIPEEHJ_00057) 42368..42841 + 474 WP_042004837 hypothetical protein -
J5X05_RS00310 (JOIPEEHJ_00058) 42922..43140 + 219 WP_000556751 hypothetical protein -
J5X05_RS00315 (JOIPEEHJ_00059) 43168..43515 + 348 WP_000836682 hypothetical protein -
J5X05_RS00320 (JOIPEEHJ_00060) 43641..46271 + 2631 WP_000069772 type IV secretion system protein TraC virb4
J5X05_RS00325 (JOIPEEHJ_00061) 46268..46654 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
J5X05_RS00330 (JOIPEEHJ_00062) 46651..47283 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
J5X05_RS00335 (JOIPEEHJ_00063) 47280..48272 + 993 WP_000830849 conjugal transfer pilus assembly protein TraU traU
J5X05_RS00340 (JOIPEEHJ_00064) 48302..48607 + 306 WP_000224418 hypothetical protein -
J5X05_RS00345 (JOIPEEHJ_00065) 48616..49254 + 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
J5X05_RS00350 (JOIPEEHJ_00066) 49251..51101 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
J5X05_RS00355 (JOIPEEHJ_00067) 51128..51385 + 258 WP_000864353 conjugal transfer protein TrbE -
J5X05_RS00360 (JOIPEEHJ_00068) 51378..52121 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
J5X05_RS00365 (JOIPEEHJ_00069) 52135..52479 + 345 WP_000556796 conjugal transfer protein TrbA -
J5X05_RS00370 (JOIPEEHJ_00070) 52598..52882 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
J5X05_RS00375 (JOIPEEHJ_00071) 52869..53414 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
J5X05_RS00380 53344..53691 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
J5X05_RS00385 (JOIPEEHJ_00072) 53672..54064 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
J5X05_RS00390 (JOIPEEHJ_00073) 54051..55424 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
J5X05_RS00395 (JOIPEEHJ_00074) 55421..58243 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
J5X05_RS00400 (JOIPEEHJ_00075) 58259..58744 + 486 WP_000605870 hypothetical protein -
J5X05_RS00405 (JOIPEEHJ_00076) 58793..59524 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
J5X05_RS00410 (JOIPEEHJ_00077) 59727..60464 + 738 WP_000199905 hypothetical protein -
J5X05_RS00415 (JOIPEEHJ_00078) 60515..62758 + 2244 WP_025985153 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7957 GenBank   NZ_MW396860
Plasmid name   p888048 Incompatibility group   IncFII
Plasmid size   73104 bp Coordinate of oriT [Strand]   34817..34940 [+]
Host baterium   Shigella flexneri 3a strain 888048

Cargo genes

Drug resistance gene   mph(A), erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -