Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113582
Name   oriT_pSF07201 in_silico
Organism   Shigella flexneri 4c strain 072
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KJ201887 (29809..29894 [-], 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_pSF07201
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8700 GenBank   WP_015059148
Name   traI_HPF05_RS00400_pSF07201 insolico UniProt ID   I1YB51
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191713.24 Da        Isoelectric Point: 5.6912

>WP_015059148.1 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
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVTLSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

AAA domain (AAA_30)

(968-1156)

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

(575-626)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   5083 GenBank   WP_001354030
Name   WP_001354030_pSF07201 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   5084 GenBank   WP_000089263
Name   WP_000089263_pSF07201 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


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29241..52849

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF05_RS00185 (pSF07201_041) 25213..25647 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HPF05_RS00190 (pSF07201_042) 25644..26363 + 720 WP_001276217 plasmid SOS inhibition protein A -
HPF05_RS00510 26585..26734 + 150 Protein_37 plasmid maintenance protein Mok -
HPF05_RS00195 26676..26801 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HPF05_RS00500 (pSF07201_044) 27120..27416 - 297 Protein_39 hypothetical protein -
HPF05_RS00210 (pSF07201_046) 27716..28012 + 297 WP_001272251 hypothetical protein -
HPF05_RS00215 (pSF07201_047) 28123..28944 + 822 WP_001234445 DUF932 domain-containing protein -
HPF05_RS00220 (pSF07201_048) 29241..29843 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HPF05_RS00225 (pSF07201_049) 30166..30549 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HPF05_RS00230 (pSF07201_050) 30743..31414 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HPF05_RS00235 31551..31778 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HPF05_RS00240 (pSF07201_051) 31811..32169 + 359 Protein_46 type IV conjugative transfer system pilin TraA -
HPF05_RS00245 (pSF07201_052) 32184..32495 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HPF05_RS00250 (pSF07201_053) 32517..33083 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HPF05_RS00255 (pSF07201_054) 33070..33798 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HPF05_RS00260 (pSF07201_055) 33798..35249 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HPF05_RS00265 (pSF07201_056) 35239..35805 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HPF05_RS00270 (pSF07201_057) 35792..36112 + 321 WP_001057307 conjugal transfer protein TrbD -
HPF05_RS00275 (pSF07201_058) 36109..36624 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HPF05_RS00280 (pSF07201_059) 36759..36980 + 222 WP_001278683 conjugal transfer protein TraR -
HPF05_RS00285 (pSF07201_060) 36973..37449 + 477 WP_000549587 hypothetical protein -
HPF05_RS00290 (pSF07201_061) 37529..37747 + 219 WP_000556745 hypothetical protein -
HPF05_RS00295 (pSF07201_062) 37775..38122 + 348 WP_000836682 hypothetical protein -
HPF05_RS00300 (pSF07201_063) 38248..40877 + 2630 Protein_58 type IV secretion system protein TraC -
HPF05_RS00305 (pSF07201_065) 40874..41260 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HPF05_RS00310 (pSF07201_066) 41257..41889 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HPF05_RS00315 (pSF07201_067) 41886..42878 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HPF05_RS00320 (pSF07201_068) 42908..43213 + 306 WP_000224416 hypothetical protein -
HPF05_RS00325 (pSF07201_069) 43222..43860 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HPF05_RS00330 (pSF07201_070) 43857..45707 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HPF05_RS00335 (pSF07201_071) 45734..45991 + 258 WP_000864353 conjugal transfer protein TrbE -
HPF05_RS00340 (pSF07201_072) 45984..46727 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HPF05_RS00345 46741..47085 + 345 WP_000556796 conjugal transfer protein TrbA -
HPF05_RS00350 (pSF07201_073) 47204..47488 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HPF05_RS00355 (pSF07201_074) 47475..48020 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HPF05_RS00360 (pSF07201_075) 47950..48297 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HPF05_RS00365 (pSF07201_076) 48278..48670 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HPF05_RS00370 (pSF07201_077) 48657..50030 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HPF05_RS00375 (pSF07201_078) 50027..52849 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HPF05_RS00380 52865..53350 + 486 WP_000605870 hypothetical protein -
HPF05_RS00385 (pSF07201_080) 53399..54130 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HPF05_RS00390 (pSF07201_081) 54333..55070 + 738 WP_000199905 hypothetical protein -
HPF05_RS00395 (pSF07201_082) 55121..57401 + 2281 Protein_77 type IV conjugative transfer system coupling protein TraD -

Host bacterium

ID   14017 GenBank   NZ_KJ201887
Plasmid name   pSF07201 Incompatibility group   IncFII
Plasmid size   75335 bp Coordinate of oriT [Strand]   29809..29894 [-]
Host baterium   Shigella flexneri 4c strain 072

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, fosA3, blaTEM-1B, blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -