Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100435
Name   oriT_pYT2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019001 (96724..96982 [-], 259 nt)
oriT length   259 nt
IRs (inverted repeats)      115..128, 134..147  (ATAGCGGTGCCGGC..GCCTGCACCGCTAT)
Location of nic site      241..242
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 259 nt

>oriT_pYT2
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   506 GenBank   YP_006955649
Name   Nickase/helicase_pYT2 insolico UniProt ID   H9L4G8
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191683.72 Da        Isoelectric Point: 5.9311

>YP_006955649.1 conjugal transfer nickase/helicase (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

TrwC relaxase (TrwC)

(11-282)

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

(632-711)

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

(574-626)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 96180..122536

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXC66_RS00545 (D645_p1146) 91340..93337 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
HXC66_RS00550 (D645_p1133) 93377..93811 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
HXC66_RS00555 (D645_p1134) 93808..94545 + 738 WP_000581933 plasmid SOS inhibition protein A -
HXC66_RS00560 (D645_p1148) 94782..94952 + 171 WP_000229547 hypothetical protein -
HXC66_RS00565 95055..95873 + 819 Protein_112 DUF945 domain-containing protein -
HXC66_RS00570 (D645_p1151) 96180..96650 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
HXC66_RS00575 (D645_p1098) 97065..97445 + 381 WP_013307857 conjugal transfer relaxosome DNA-binding protein TraM -
HXC66_RS00580 (D645_p1104) 97638..98324 + 687 WP_000336297 PAS domain-containing protein -
HXC66_RS00585 (D645_p1090) 98418..98645 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
HXC66_RS00590 (D645_p1111) 98687..99049 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
HXC66_RS00595 (D645_p1102) 99064..99375 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
HXC66_RS00600 (D645_p1107) 99397..99963 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
HXC66_RS00605 (D645_p1103) 99950..100690 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
HXC66_RS00610 (D645_p1109) 100690..102111 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
HXC66_RS00615 (D645_p1094) 102101..102697 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
HXC66_RS00620 (D645_p1089) 102675..102920 + 246 WP_010999944 DUF2689 domain-containing protein virb4
HXC66_RS00625 (D645_p1091) 102917..103432 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
HXC66_RS00630 (D645_p1093) 103567..103788 + 222 WP_001278699 conjugal transfer protein TraR -
HXC66_RS00635 (D645_p1152) 103781..104248 + 468 WP_000549562 hypothetical protein -
HXC66_RS00640 (D645_p1154) 104365..104628 + 264 WP_001239255 hypothetical protein -
HXC66_RS00645 (D645_p1113) 104644..107292 + 2649 WP_000793310 type IV secretion system protein TraC virb4
HXC66_RS00650 (D645_p1092) 107267..107653 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
HXC66_RS00655 (D645_p1095) 107650..108282 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
HXC66_RS00660 (D645_p1100) 108279..109271 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
HXC66_RS00665 (D645_p1156) 109290..109598 + 309 WP_010999945 hypothetical protein -
HXC66_RS00670 (D645_p1157) 109583..110221 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
HXC66_RS00675 (D645_p1158) 110258..110677 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
HXC66_RS00680 (D645_p1110) 110674..112500 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HXC66_RS00685 (D645_p1097) 112511..112726 + 216 WP_000700023 conjugal transfer protein TrbE -
HXC66_RS00690 (D645_p1118) 112738..113487 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
HXC66_RS00695 (D645_p1108) 113701..113994 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
HXC66_RS00700 (D645_p1099) 113981..114529 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HXC66_RS00705 (D645_p1116) 114519..115901 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
HXC66_RS00710 (D645_p1117) 115898..118720 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
HXC66_RS00715 (D645_p1106) 118736..119230 + 495 WP_010999946 entry exclusion protein -
HXC66_RS00720 (D645_p1105) 119266..119997 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
HXC66_RS00725 (D645_p1120) 120374..122536 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
HXC66_RS00730 122545..122943 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
HXC66_RS00735 122943..123170 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   896 GenBank   NC_019001
Plasmid name   pYT2 Incompatibility group   IncFIB
Plasmid size   132842 bp Coordinate of oriT [Strand]   96724..96982 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

Drug resistance gene   tetracycline resistance; aminoglycoside resistance
Virulence gene   Salmonella plasmid virulence protein
Metal resistance gene   mercury resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -