Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107520
Name   oriT_pSH282 in_silico
Organism   Shigella flexneri strain SH282
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ291179 (29539..29624 [-], 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_pSH282
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5044 GenBank   WP_281041327
Name   traI_SH282_RS00385_pSH282 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: 191704.42 Da        Isoelectric Point: 5.6468

>WP_281041327.1 conjugative transfer relaxase/helicase TraI [Shigella flexneri]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTFGIHMLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTLLNEDRRVLNSMIHDAREKAGELGKEQVM
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)

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

(575-626)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   2311 GenBank   WP_001354030
Name   WP_001354030_pSH282 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   2312 GenBank   WP_000089263
Name   WP_000089263_pSH282 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   5260 GenBank   WP_000069777
Name   traC_SH282_RS00285_pSH282 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   5261 GenBank   WP_281041326
Name   traD_SH282_RS00380_pSH282 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85595.40 Da        Isoelectric Point: 5.2308

>WP_281041326.1 type IV conjugative transfer system coupling protein TraD [Shigella flexneri]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQGLKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 28971..57114

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SH282_RS00170 (SH282_00033) 24943..25377 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
SH282_RS00175 (SH282_00034) 25374..26093 + 720 WP_001276217 plasmid SOS inhibition protein A -
SH282_RS00180 (SH282_00035) 26315..26464 + 150 Protein_36 plasmid maintenance protein Mok -
SH282_RS00185 26406..26531 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
SH282_RS00190 26850..27146 - 297 Protein_38 hypothetical protein -
SH282_RS00195 (SH282_00036) 27446..27742 + 297 WP_001272251 hypothetical protein -
SH282_RS00200 (SH282_00037) 27853..28674 + 822 WP_001234445 DUF932 domain-containing protein -
SH282_RS00205 (SH282_00038) 28971..29573 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
SH282_RS00210 (SH282_00039) 29896..30279 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
SH282_RS00215 (SH282_00040) 30473..31144 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
SH282_RS00220 31281..31508 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
SH282_RS00225 (SH282_00041) 31541..31900 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
SH282_RS00230 (SH282_00042) 31915..32226 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
SH282_RS00235 (SH282_00043) 32248..32814 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
SH282_RS00240 (SH282_00044) 32801..33529 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
SH282_RS00245 (SH282_00045) 33529..34980 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
SH282_RS00250 (SH282_00046) 34970..35536 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
SH282_RS00255 (SH282_00047) 35523..35843 + 321 WP_001057307 conjugal transfer protein TrbD -
SH282_RS00260 (SH282_00048) 35840..36355 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
SH282_RS00265 36490..36711 + 222 WP_001278683 conjugal transfer protein TraR -
SH282_RS00270 (SH282_00049) 36704..37180 + 477 WP_000549587 hypothetical protein -
SH282_RS00275 (SH282_00050) 37260..37478 + 219 WP_000556745 hypothetical protein -
SH282_RS00280 (SH282_00051) 37506..37853 + 348 WP_000836682 hypothetical protein -
SH282_RS00285 (SH282_00052) 37979..40609 + 2631 WP_000069777 type IV secretion system protein TraC virb4
SH282_RS00290 (SH282_00053) 40606..40992 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
SH282_RS00295 (SH282_00054) 40989..41621 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
SH282_RS00300 (SH282_00055) 41618..42610 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
SH282_RS00305 (SH282_00056) 42640..42945 + 306 WP_000224416 hypothetical protein -
SH282_RS00310 (SH282_00057) 42954..43592 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
SH282_RS00315 (SH282_00058) 43589..45439 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SH282_RS00320 (SH282_00059) 45466..45723 + 258 WP_000864353 conjugal transfer protein TrbE -
SH282_RS00325 (SH282_00060) 45716..46459 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
SH282_RS00330 (SH282_00061) 46473..46817 + 345 WP_000556796 conjugal transfer protein TrbA -
SH282_RS00335 (SH282_00062) 46936..47220 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
SH282_RS00340 (SH282_00063) 47207..47752 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SH282_RS00345 47682..48029 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
SH282_RS00350 (SH282_00064) 48010..48402 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
SH282_RS00355 (SH282_00065) 48389..49762 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
SH282_RS00360 (SH282_00066) 49759..52581 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
SH282_RS00365 (SH282_00067) 52597..53082 + 486 WP_000605870 hypothetical protein -
SH282_RS00370 (SH282_00068) 53131..53862 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
SH282_RS00375 (SH282_00069) 54065..54802 + 738 WP_000199905 hypothetical protein -
SH282_RS00380 (SH282_00070) 54853..57114 + 2262 WP_281041326 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7955 GenBank   NZ_OQ291179
Plasmid name   pSH282 Incompatibility group   IncFII
Plasmid size   67461 bp Coordinate of oriT [Strand]   29539..29624 [-]
Host baterium   Shigella flexneri strain SH282

Cargo genes

Drug resistance gene   blaCTX-M-27
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -