Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119100
Name   oriT_p201908033-3 in_silico
Organism   Shigella sonnei strain 201908033
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OP038279 (34781..34866 [-], 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_p201908033-3
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12062 GenBank   WP_267191411
Name   traI_OVP35_RS00445_p201908033-3 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: 191766.38 Da        Isoelectric Point: 5.7966

>WP_267191411.1 conjugative transfer relaxase/helicase TraI [Shigella sonnei]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)

AAA domain (AAA_30)

(968-1156)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   6895 GenBank   WP_001354030
Name   WP_001354030_p201908033-3 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   6896 GenBank   WP_000089263
Name   WP_000089263_p201908033-3 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   14124 GenBank   WP_000069777
Name   traC_OVP35_RS00345_p201908033-3 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   14125 GenBank   WP_001617742
Name   traD_OVP35_RS00440_p201908033-3 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83547.19 Da        Isoelectric Point: 5.1644

>WP_001617742.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 34213..62302

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OVP35_RS00210 (p201908033-3__00037) 29383..29901 + 519 WP_001178556 hypothetical protein -
OVP35_RS00215 (p201908033-3__00038) 30019..30171 + 153 Protein_43 DUF5431 family protein -
OVP35_RS00220 30116..30238 + 123 WP_223200913 Hok/Gef family protein -
OVP35_RS00225 30331..30612 + 282 WP_001465039 hypothetical protein -
OVP35_RS00230 30532..30787 - 256 Protein_46 hypothetical protein -
OVP35_RS00235 (p201908033-3__00039) 31083..31406 + 324 WP_000533253 hypothetical protein -
OVP35_RS00240 (p201908033-3__00040) 31465..31707 + 243 WP_000540588 hypothetical protein -
OVP35_RS00505 31806..32051 + 246 WP_077870516 hypothetical protein -
OVP35_RS00245 31973..32221 + 249 WP_071606928 hypothetical protein -
OVP35_RS00250 32393..32626 - 234 WP_001591123 hypothetical protein -
OVP35_RS00255 (p201908033-3__00041) 32689..32985 + 297 WP_001272251 hypothetical protein -
OVP35_RS00260 (p201908033-3__00042) 33095..33916 + 822 WP_001234441 DUF932 domain-containing protein -
OVP35_RS00265 (p201908033-3__00043) 34213..34815 - 603 WP_072205450 transglycosylase SLT domain-containing protein virB1
OVP35_RS00270 (p201908033-3__00044) 35138..35521 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
OVP35_RS00275 (p201908033-3__00045) 35715..36386 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
OVP35_RS00280 36523..36750 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
OVP35_RS00285 (p201908033-3__00046) 36783..37142 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
OVP35_RS00290 (p201908033-3__00047) 37157..37468 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
OVP35_RS00295 (p201908033-3__00048) 37490..38056 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
OVP35_RS00300 (p201908033-3__00049) 38043..38771 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
OVP35_RS00305 (p201908033-3__00050) 38771..40222 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
OVP35_RS00310 (p201908033-3__00051) 40212..40778 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
OVP35_RS00315 (p201908033-3__00052) 40765..41085 + 321 WP_001057307 conjugal transfer protein TrbD -
OVP35_RS00320 (p201908033-3__00053) 41082..41597 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
OVP35_RS00325 41732..41953 + 222 WP_001278683 conjugal transfer protein TraR -
OVP35_RS00330 (p201908033-3__00054) 41946..42422 + 477 WP_000549587 hypothetical protein -
OVP35_RS00335 (p201908033-3__00055) 42502..42720 + 219 WP_000556745 hypothetical protein -
OVP35_RS00340 (p201908033-3__00056) 42748..43095 + 348 WP_000836682 hypothetical protein -
OVP35_RS00345 (p201908033-3__00057) 43221..45851 + 2631 WP_000069777 type IV secretion system protein TraC virb4
OVP35_RS00350 (p201908033-3__00058) 45848..46234 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
OVP35_RS00355 (p201908033-3__00059) 46231..46863 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
OVP35_RS00360 (p201908033-3__00060) 46860..47852 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
OVP35_RS00365 (p201908033-3__00061) 47882..48187 + 306 WP_000224416 hypothetical protein -
OVP35_RS00370 (p201908033-3__00062) 48196..48834 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
OVP35_RS00375 (p201908033-3__00063) 48831..50681 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
OVP35_RS00380 (p201908033-3__00064) 50708..50965 + 258 WP_000864353 conjugal transfer protein TrbE -
OVP35_RS00385 (p201908033-3__00065) 50958..51701 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
OVP35_RS00390 (p201908033-3__00066) 51715..52059 + 345 WP_000556796 conjugal transfer protein TrbA -
OVP35_RS00395 (p201908033-3__00067) 52178..52462 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
OVP35_RS00400 (p201908033-3__00068) 52449..52994 + 546 WP_060965180 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
OVP35_RS00405 52924..53271 + 348 WP_060965181 P-type conjugative transfer protein TrbJ -
OVP35_RS00410 (p201908033-3__00069) 53252..53644 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
OVP35_RS00415 (p201908033-3__00070) 53631..55004 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
OVP35_RS00420 (p201908033-3__00071) 55001..57823 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
OVP35_RS00425 (p201908033-3__00072) 57839..58324 + 486 WP_000605870 hypothetical protein -
OVP35_RS00430 (p201908033-3__00073) 58373..59104 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
OVP35_RS00435 (p201908033-3__00074) 59307..60044 + 738 WP_000199905 hypothetical protein -
OVP35_RS00440 (p201908033-3__00075) 60095..62302 + 2208 WP_001617742 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19532 GenBank   NZ_OP038279
Plasmid name   p201908033-3 Incompatibility group   IncFIC
Plasmid size   73493 bp Coordinate of oriT [Strand]   34781..34866 [-]
Host baterium   Shigella sonnei strain 201908033

Cargo genes

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