Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100429
Name   oriT_pCS0010A in_silico
Organism   Salmonella enterica subsp. enterica serovar Kentucky
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_018954 (51468..51758 [+], 291 nt)
oriT length   291 nt
IRs (inverted repeats)      226..233, 236..243 n  (GCAAAAAC..GTTTTTGC)
Location of nic site      252..253
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 291 nt

>oriT_pCS0010A
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCCCCCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   500 GenBank   YP_006970897
Name   TraI_pCS0010A insolico UniProt ID   E1QML0
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191867.46 Da        Isoelectric Point: 5.6862

>YP_006970897.1 IncF conjugal transfer nickase/helicase TraI (plasmid) [Salmonella enterica subsp. enterica serovar Kentucky]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRIMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFVASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLESAISHQKSALHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISRDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 26512..52320

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS350_RS00135 (pCS0010A_24) 26512..28719 - 2208 WP_000009364 type IV conjugative transfer system coupling protein TraD virb4
HS350_RS00140 (pCS0010A_25) 28971..29702 - 732 WP_001447147 conjugal transfer complement resistance protein TraT -
HS350_RS00145 (pCS0010A_26) 29734..30237 - 504 WP_000605510 hypothetical protein -
HS350_RS00150 (pCS0010A_27) 30252..33074 - 2823 WP_052970644 conjugal transfer mating-pair stabilization protein TraG traG
HS350_RS00155 (pCS0010A_28) 33071..34447 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
HS350_RS00160 34444..34806 - 363 WP_071779407 P-type conjugative transfer protein TrbJ -
HS350_RS00165 (pCS0010A_29) 34736..35281 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS350_RS00170 (pCS0010A_30) 35268..35552 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HS350_RS00175 (pCS0010A_31) 35671..36018 - 348 WP_001287676 conjugal transfer protein TrbA -
HS350_RS00180 (pCS0010A_32) 36034..36777 - 744 WP_001030389 type-F conjugative transfer system pilin assembly protein TraF traF
HS350_RS00185 36770..37027 - 258 WP_000864325 conjugal transfer protein TrbE -
HS350_RS00190 (pCS0010A_33) 37054..38862 - 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS350_RS00195 (pCS0010A_34) 38859..39497 - 639 WP_022630459 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS350_RS00200 (pCS0010A_35) 39506..40498 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HS350_RS00205 (pCS0010A_36) 40495..41127 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HS350_RS00210 41124..41510 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
HS350_RS00215 (pCS0010A_37) 41507..44134 - 2628 WP_001064251 type IV secretion system protein TraC virb4
HS350_RS00220 44294..44515 - 222 WP_001278689 conjugal transfer protein TraR -
HS350_RS00225 (pCS0010A_38) 44650..45165 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HS350_RS00230 45162..45413 - 252 WP_001038342 conjugal transfer protein TrbG -
HS350_RS00235 45425..45622 - 198 WP_001324648 conjugal transfer protein TrbD -
HS350_RS00240 (pCS0010A_39) 45609..46199 - 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
HS350_RS00245 (pCS0010A_40) 46189..47616 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HS350_RS00250 (pCS0010A_41) 47616..48344 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HS350_RS00255 (pCS0010A_42) 48331..48897 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
HS350_RS00260 (pCS0010A_43) 48919..49230 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS350_RS00265 (pCS0010A_44) 49245..49610 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HS350_RS00270 (pCS0010A_45) 49643..50038 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HS350_RS00275 (pCS0010A_46) 50137..50826 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HS350_RS00280 (pCS0010A_47) 51013..51396 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HS350_RS00285 (pCS0010A_48) 51811..52320 + 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
HS350_RS00290 (pCS0010A_49) 52616..53437 - 822 WP_001234468 DUF932 domain-containing protein -
HS350_RS00295 (pCS0010A_50) 53556..53843 - 288 WP_000107520 hypothetical protein -
HS350_RS00300 53868..53987 - 120 WP_001127499 hypothetical protein -
HS350_RS00305 54144..54441 + 298 Protein_60 hypothetical protein -
HS350_RS00310 54742..54864 - 123 WP_223195199 Hok/Gef family protein -
HS350_RS00790 54809..54961 - 153 Protein_62 DUF5431 family protein -
HS350_RS00315 (pCS0010A_51) 55112..55898 - 787 Protein_63 plasmid SOS inhibition protein A -
HS350_RS00320 (pCS0010A_52) 55895..56329 - 435 WP_000845922 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   890 GenBank   NC_018954
Plasmid name   pCS0010A Incompatibility group   IncFIB
Plasmid size   146811 bp Coordinate of oriT [Strand]   51468..51758 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Kentucky

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, tet(B), sitABCD
Virulence gene   iutA, iucC, iucB, iucA, iroB, iroC, iroD, iroE, iroN
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -