Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121994
Name   oriT_981|981p2 in_silico
Organism   Shigella flexneri 2a strain 981
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP012139 (47207..47292 [-], 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_981|981p2
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13875 GenBank   WP_061460723
Name   traI_AD867_RS26405_981|981p2 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: 191935.59 Da        Isoelectric Point: 5.7963

>WP_061460723.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
IALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLIIDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISKDDRLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLSGGDSPARFIAPGRKYPQPYVVLPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERDRAAITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   7700 GenBank   WP_001354030
Name   WP_001354030_981|981p2 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   7701 GenBank   WP_000089263
Name   WP_000089263_981|981p2 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   16251 GenBank   WP_000069777
Name   traC_AD867_RS26300_981|981p2 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   16252 GenBank   WP_061460721
Name   traD_AD867_RS26400_981|981p2 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83842.53 Da        Isoelectric Point: 5.2327

>WP_061460721.1 type IV conjugative transfer system coupling protein TraD [Shigella flexneri]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 46639..76073

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AD867_RS26190 (AD867_26380) 42611..43045 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
AD867_RS26195 (AD867_26385) 43042..43761 + 720 WP_001276217 plasmid SOS inhibition protein A -
AD867_RS31005 (AD867_26390) 43782..43961 - 180 WP_001309233 hypothetical protein -
AD867_RS31675 43983..44132 + 150 Protein_56 plasmid maintenance protein Mok -
AD867_RS26205 (AD867_26395) 44074..44199 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
AD867_RS31680 (AD867_26400) 44518..44814 - 297 Protein_58 hypothetical protein -
AD867_RS26215 (AD867_26405) 45114..45410 + 297 WP_001272251 hypothetical protein -
AD867_RS26220 (AD867_26410) 45521..46342 + 822 WP_001234445 DUF932 domain-containing protein -
AD867_RS26225 (AD867_26415) 46639..47229 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
AD867_RS26230 (AD867_26420) 47564..47947 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
AD867_RS26235 (AD867_26425) 48141..48812 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
AD867_RS26240 (AD867_26430) 48949..49176 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
AD867_RS26245 (AD867_26435) 49209..49568 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
AD867_RS26250 (AD867_26440) 49583..49894 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
AD867_RS26255 (AD867_26445) 49916..50482 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
AD867_RS26260 (AD867_26450) 50469..51197 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
AD867_RS26265 (AD867_26455) 51197..52648 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
AD867_RS26270 (AD867_26460) 52638..53204 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
AD867_RS26275 (AD867_26465) 53191..53511 + 321 WP_001057307 conjugal transfer protein TrbD -
AD867_RS26280 (AD867_26470) 53508..54023 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
AD867_RS29785 (AD867_26475) 54158..54379 + 222 WP_001278683 conjugal transfer protein TraR -
AD867_RS26285 (AD867_26480) 54372..54848 + 477 WP_000549587 hypothetical protein -
AD867_RS26290 (AD867_26485) 54928..55146 + 219 WP_000556745 hypothetical protein -
AD867_RS30650 (AD867_26490) 55174..55521 + 348 WP_000836682 hypothetical protein -
AD867_RS26300 (AD867_26495) 55647..58277 + 2631 WP_000069777 type IV secretion system protein TraC virb4
AD867_RS26305 (AD867_26500) 58274..58660 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
AD867_RS26310 (AD867_26505) 58657..59289 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
AD867_RS26315 (AD867_26510) 59286..60278 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
AD867_RS26320 (AD867_26515) 60308..60613 + 306 WP_000224416 hypothetical protein -
AD867_RS26325 (AD867_26520) 60622..61260 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
AD867_RS26330 (AD867_26525) 61257..63107 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AD867_RS26335 (AD867_26530) 63134..63391 + 258 WP_000864353 conjugal transfer protein TrbE -
AD867_RS26340 (AD867_26535) 63384..64127 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
AD867_RS26350 (AD867_26545) 64430..65658 + 1229 WP_088895425 IS3-like element IS2 family transposase -
AD867_RS31920 65666..65821 + 156 Protein_87 conjugal transfer protein TrbA -
AD867_RS26355 (AD867_26550) 65940..66224 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
AD867_RS26360 (AD867_26555) 66211..66756 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AD867_RS26365 (AD867_26560) 66686..67033 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
AD867_RS26370 (AD867_26565) 67014..67406 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
AD867_RS26375 (AD867_26570) 67393..68766 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
AD867_RS26380 (AD867_26575) 68763..71585 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
AD867_RS26385 (AD867_26580) 71601..72086 + 486 WP_000605870 hypothetical protein -
AD867_RS26390 (AD867_26585) 72135..72866 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
AD867_RS26395 (AD867_26590) 73069..73806 + 738 WP_000199905 hypothetical protein -
AD867_RS26400 (AD867_26595) 73857..76073 + 2217 WP_061460721 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   22421 GenBank   NZ_CP012139
Plasmid name   981|981p2 Incompatibility group   IncFII
Plasmid size   86407 bp Coordinate of oriT [Strand]   47207..47292 [-]
Host baterium   Shigella flexneri 2a strain 981

Cargo genes

Drug resistance gene   erm(B), sul1, qacE, ARR-3, catB3, blaOXA-1, aac(6')-Ib-cr, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -