Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107511
Name   oriT_pSH242 in_silico
Organism   Shigella flexneri strain SH242
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ291177 (39705..39790 [-], 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_pSH242
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5034 GenBank   WP_281041266
Name   traI_SH242_RS00440_pSH242 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: 191630.38 Da        Isoelectric Point: 5.7956

>WP_281041266.1 conjugative transfer relaxase/helicase TraI [Shigella flexneri]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLERVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKVQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(633-712)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   2308 GenBank   WP_001354030
Name   WP_001354030_pSH242 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   2309 GenBank   WP_000089263
Name   WP_000089263_pSH242 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   5245 GenBank   WP_000069777
Name   traC_SH242_RS00340_pSH242 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   5246 GenBank   WP_096002736
Name   traD_SH242_RS00435_pSH242 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84181.88 Da        Isoelectric Point: 5.2308

>WP_096002736.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQGLKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 39137..67244

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SH242_RS00225 (SH242_00045) 35109..35543 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
SH242_RS00230 (SH242_00046) 35540..36259 + 720 WP_001276217 plasmid SOS inhibition protein A -
SH242_RS00235 (SH242_00047) 36481..36630 + 150 Protein_47 plasmid maintenance protein Mok -
SH242_RS00240 36572..36697 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
SH242_RS00245 37016..37312 - 297 Protein_49 hypothetical protein -
SH242_RS00250 (SH242_00048) 37612..37908 + 297 WP_001272251 hypothetical protein -
SH242_RS00255 (SH242_00049) 38019..38840 + 822 WP_001234445 DUF932 domain-containing protein -
SH242_RS00260 (SH242_00050) 39137..39739 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
SH242_RS00265 (SH242_00051) 40062..40445 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
SH242_RS00270 (SH242_00052) 40639..41310 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
SH242_RS00275 41447..41674 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
SH242_RS00280 (SH242_00053) 41707..42066 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
SH242_RS00285 (SH242_00054) 42081..42392 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
SH242_RS00290 (SH242_00055) 42414..42980 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
SH242_RS00295 (SH242_00056) 42967..43695 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
SH242_RS00300 (SH242_00057) 43695..45146 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
SH242_RS00305 (SH242_00058) 45136..45702 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
SH242_RS00310 (SH242_00059) 45689..46009 + 321 WP_001057307 conjugal transfer protein TrbD -
SH242_RS00315 (SH242_00060) 46006..46521 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
SH242_RS00320 46656..46877 + 222 WP_001278683 conjugal transfer protein TraR -
SH242_RS00325 (SH242_00061) 46870..47346 + 477 WP_000549587 hypothetical protein -
SH242_RS00330 (SH242_00062) 47426..47644 + 219 WP_000556745 hypothetical protein -
SH242_RS00335 (SH242_00063) 47672..48019 + 348 WP_000836682 hypothetical protein -
SH242_RS00340 (SH242_00064) 48145..50775 + 2631 WP_000069777 type IV secretion system protein TraC virb4
SH242_RS00345 (SH242_00065) 50772..51158 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
SH242_RS00350 (SH242_00066) 51155..51787 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
SH242_RS00355 (SH242_00067) 51784..52776 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
SH242_RS00360 (SH242_00068) 52806..53111 + 306 WP_000224416 hypothetical protein -
SH242_RS00365 (SH242_00069) 53120..53758 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
SH242_RS00370 (SH242_00070) 53755..55605 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SH242_RS00375 (SH242_00071) 55632..55889 + 258 WP_000864353 conjugal transfer protein TrbE -
SH242_RS00380 (SH242_00072) 55882..56625 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
SH242_RS00385 (SH242_00073) 56639..56983 + 345 WP_000556796 conjugal transfer protein TrbA -
SH242_RS00390 (SH242_00074) 57102..57386 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
SH242_RS00395 (SH242_00075) 57373..57918 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SH242_RS00400 57848..58195 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
SH242_RS00405 (SH242_00076) 58176..58568 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
SH242_RS00410 (SH242_00077) 58555..59928 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
SH242_RS00415 (SH242_00078) 59925..62747 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
SH242_RS00420 (SH242_00079) 62763..63248 + 486 WP_000605870 hypothetical protein -
SH242_RS00425 (SH242_00080) 63297..64028 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
SH242_RS00430 (SH242_00081) 64231..64968 + 738 WP_000199905 hypothetical protein -
SH242_RS00435 (SH242_00082) 65019..67244 + 2226 WP_096002736 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7946 GenBank   NZ_OQ291177
Plasmid name   pSH242 Incompatibility group   IncFII
Plasmid size   77591 bp Coordinate of oriT [Strand]   39705..39790 [-]
Host baterium   Shigella flexneri strain SH242

Cargo genes

Drug resistance gene   mph(A), erm(B), blaCTX-M-27
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -