Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100430
Name   oriT_pSSAP03302A in_silico
Organism   Salmonella enterica subsp. enterica serovar Kentucky
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_018966 (51466..51756 [+], 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_pSSAP03302A
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCCCCCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   501 GenBank   YP_006971025
Name   TraI_pSSAP03302A 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_006971025.1 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: 26511..52318

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS381_RS00135 (pSSAP3002A_24) 26511..28718 - 2208 WP_000009364 type IV conjugative transfer system coupling protein TraD virb4
HS381_RS00140 (pSSAP3002A_25) 28970..29683 - 714 WP_015056170 conjugal transfer complement resistance protein TraT -
HS381_RS00145 (pSSAP3002A_26) 29732..30235 - 504 WP_000605510 hypothetical protein -
HS381_RS00150 (pSSAP3002A_27) 30250..33072 - 2823 WP_001007012 conjugal transfer mating-pair stabilization protein TraG traG
HS381_RS00155 (pSSAP3002A_28) 33069..34445 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
HS381_RS00160 34442..34804 - 363 WP_071779407 P-type conjugative transfer protein TrbJ -
HS381_RS00165 (pSSAP3002A_29) 34734..35279 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS381_RS00170 (pSSAP3002A_30) 35266..35550 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HS381_RS00175 (pSSAP3002A_31) 35669..36016 - 348 WP_001287676 conjugal transfer protein TrbA -
HS381_RS00180 (pSSAP3002A_32) 36032..36775 - 744 WP_001030389 type-F conjugative transfer system pilin assembly protein TraF traF
HS381_RS00185 36768..37025 - 258 WP_000864325 conjugal transfer protein TrbE -
HS381_RS00190 (pSSAP3002A_33) 37052..38860 - 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS381_RS00195 (pSSAP3002A_34) 38857..39495 - 639 WP_022630459 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS381_RS00200 (pSSAP3002A_35) 39504..40496 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HS381_RS00205 (pSSAP3002A_36) 40493..41125 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HS381_RS00210 41122..41508 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
HS381_RS00215 (pSSAP3002A_37) 41505..44132 - 2628 WP_001064251 type IV secretion system protein TraC virb4
HS381_RS00220 44292..44513 - 222 WP_001278689 conjugal transfer protein TraR -
HS381_RS00225 (pSSAP3002A_38) 44648..45163 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HS381_RS00230 45160..45411 - 252 WP_001038342 conjugal transfer protein TrbG -
HS381_RS00235 45423..45620 - 198 WP_001324648 conjugal transfer protein TrbD -
HS381_RS00240 (pSSAP3002A_39) 45607..46197 - 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
HS381_RS00245 (pSSAP3002A_40) 46187..47614 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HS381_RS00250 (pSSAP3002A_41) 47614..48342 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HS381_RS00255 (pSSAP3002A_42) 48329..48895 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
HS381_RS00260 (pSSAP3002A_43) 48917..49228 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS381_RS00265 (pSSAP3002A_44) 49243..49608 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HS381_RS00270 (pSSAP3002A_45) 49641..50036 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HS381_RS00275 (pSSAP3002A_46) 50135..50824 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HS381_RS00280 (pSSAP3002A_47) 51011..51394 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HS381_RS00285 (pSSAP3002A_48) 51809..52318 + 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
HS381_RS00290 (pSSAP3002A_49) 52614..53435 - 822 WP_001234468 DUF932 domain-containing protein -
HS381_RS00295 (pSSAP3002A_50) 53554..53841 - 288 WP_000107520 hypothetical protein -
HS381_RS00300 53866..53985 - 120 WP_001127499 hypothetical protein -
HS381_RS00305 54142..54439 + 298 Protein_60 hypothetical protein -
HS381_RS00310 54740..54862 - 123 WP_223195199 Hok/Gef family protein -
HS381_RS00790 54807..54959 - 153 Protein_62 DUF5431 family protein -
HS381_RS00315 (pSSAP3002A_51) 55110..55896 - 787 Protein_63 plasmid SOS inhibition protein A -
HS381_RS00320 (pSSAP3002A_52) 55893..56327 - 435 WP_000845922 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   891 GenBank   NC_018966
Plasmid name   pSSAP03302A Incompatibility group   IncFIB
Plasmid size   146002 bp Coordinate of oriT [Strand]   51466..51756 [+]
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   -