Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113049
Name   oriT_HJL222|unnamed1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain HJL222
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098742 (76240..76325 [+], 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_HJL222|unnamed1
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8376 GenBank   WP_000948354
Name   traI_NCG87_RS23635_HJL222|unnamed1 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 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
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)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   4802 GenBank   WP_000089263
Name   WP_000089263_HJL222|unnamed1 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

ID   4803 GenBank   WP_001354030
Name   WP_001354030_HJL222|unnamed1 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


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 48329..76893

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NCG87_RS23640 48329..50608 - 2280 WP_087760849 type IV conjugative transfer system coupling protein TraD prgC
NCG87_RS23645 50659..51396 - 738 WP_000199905 hypothetical protein -
NCG87_RS23650 51599..52330 - 732 WP_000782451 conjugal transfer complement resistance protein TraT -
NCG87_RS23655 52379..52864 - 486 WP_000605870 hypothetical protein -
NCG87_RS23660 52880..55702 - 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
NCG87_RS23665 55699..57072 - 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
NCG87_RS23670 57059..57451 - 393 WP_000660699 F-type conjugal transfer protein TrbF -
NCG87_RS23675 57432..57779 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
NCG87_RS23680 57709..58254 - 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NCG87_RS23685 58241..58525 - 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
NCG87_RS23690 58644..58988 - 345 WP_000556796 conjugal transfer protein TrbA -
NCG87_RS23695 59002..59745 - 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
NCG87_RS23700 59738..59995 - 258 WP_000864353 conjugal transfer protein TrbE -
NCG87_RS23705 60022..61872 - 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NCG87_RS23710 61869..62507 - 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
NCG87_RS23715 62516..62821 - 306 WP_000224416 hypothetical protein -
NCG87_RS23720 62851..63843 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NCG87_RS23725 63840..64472 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
NCG87_RS23730 64469..64855 - 387 WP_000214084 type-F conjugative transfer system protein TrbI -
NCG87_RS23735 64852..67482 - 2631 WP_000069777 type IV secretion system protein TraC virb4
NCG87_RS23740 67608..67955 - 348 WP_000836682 hypothetical protein -
NCG87_RS23745 67983..68201 - 219 WP_000556745 hypothetical protein -
NCG87_RS23750 68281..68754 - 474 WP_000549568 hypothetical protein -
NCG87_RS23755 68747..69160 - 414 WP_000549589 hypothetical protein -
NCG87_RS23760 69153..69374 - 222 WP_001278683 conjugal transfer protein TraR -
NCG87_RS23765 69509..70024 - 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
NCG87_RS23770 70021..70341 - 321 WP_001057307 conjugal transfer protein TrbD -
NCG87_RS23775 70328..70894 - 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
NCG87_RS23780 70884..72335 - 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
NCG87_RS23785 72335..73063 - 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
NCG87_RS23790 73050..73616 - 567 WP_000399780 type IV conjugative transfer system protein TraE traE
NCG87_RS23795 73638..73949 - 312 WP_000012113 type IV conjugative transfer system protein TraL traL
NCG87_RS23800 73964..74323 - 360 WP_001098992 type IV conjugative transfer system pilin TraA -
NCG87_RS23805 74356..74583 - 228 WP_000089263 conjugal transfer relaxosome protein TraY -
NCG87_RS23810 74720..75391 - 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
NCG87_RS23815 75585..75968 - 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
NCG87_RS23820 76303..76893 + 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
NCG87_RS23825 77190..78011 - 822 WP_001234445 DUF932 domain-containing protein -
NCG87_RS23830 78122..78418 - 297 WP_001272251 hypothetical protein -
NCG87_RS23835 78718..79014 + 297 Protein_93 hypothetical protein -
NCG87_RS23840 79333..79458 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NCG87_RS23845 79400..79549 - 150 Protein_95 plasmid maintenance protein Mok -
NCG87_RS23850 79771..80490 - 720 WP_001276217 plasmid SOS inhibition protein A -
NCG87_RS23855 80487..80921 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   13484 GenBank   NZ_CP098742
Plasmid name   HJL222|unnamed1 Incompatibility group   IncFIB
Plasmid size   109442 bp Coordinate of oriT [Strand]   76240..76325 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain HJL222

Cargo genes

Drug resistance gene   sitABCD, tet(B)
Virulence gene   iutA, iucC, iucB, iucA
Metal resistance gene   yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -