Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100470
Name   oriT_pSH163_120 in_silico
Organism   Salmonella enterica subsp. enterica serovar Heidelberg
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019122 (38442..38731 [+], 290 nt)
oriT length   290 nt
IRs (inverted repeats)      225..232, 235..242 n  (GCAAAAAC..GTTTTTGC)
Location of nic site      251..252
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 290 nt

>oriT_pSH163_120
CGCACCGCTAGCAGCGCCCCTGGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAGCGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACTCTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   541 GenBank   YP_006957039
Name   TraI_pSH163_120 insolico UniProt ID   H9TJ05
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191917.73 Da        Isoelectric Point: 5.9718

>YP_006957039.1 IncF plasmid conjugative transfer DNA-nicking and unwinding protein TraI (plasmid) [Salmonella enterica subsp. enterica serovar Heidelberg]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
APVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVQIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12834..39293

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS879_RS00055 12200..12427 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HS879_RS00060 (pSH163_120_17) 12427..12825 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HS879_RS00065 (pSH163_120_18) 12834..14987 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HS879_RS00070 (pSH163_120_19) 15240..15953 - 714 WP_029593828 conjugal transfer complement resistance protein TraT -
HS879_RS00075 (pSH163_120_21) 16004..16501 - 498 WP_000605859 entry exclusion protein -
HS879_RS00080 (pSH163_120_22) 16517..19339 - 2823 WP_001007016 conjugal transfer mating-pair stabilization protein TraG traG
HS879_RS00085 (pSH163_120_23) 19336..20712 - 1377 WP_000982840 conjugal transfer pilus assembly protein TraH traH
HS879_RS00090 (pSH163_120_24) 20709..21089 - 381 WP_001366201 F-type conjugal transfer protein TrbF -
HS879_RS00095 (pSH163_120_25) 21076..21417 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HS879_RS00100 (pSH163_120_26) 21347..21892 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS879_RS00105 (pSH163_120_27) 21879..22163 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HS879_RS00110 (pSH163_120_28) 22244..22558 + 315 WP_000415566 protein ArtA -
HS879_RS00115 (pSH163_120_29) 22560..22907 - 348 WP_001287910 conjugal transfer protein TrbA -
HS879_RS00120 (pSH163_120_30) 22923..23666 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
HS879_RS00125 (pSH163_120_31) 23659..23916 - 258 WP_000864318 conjugal transfer protein TrbE -
HS879_RS00130 (pSH163_120_32) 23943..25751 - 1809 WP_000821840 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS879_RS00135 (pSH163_120_33) 25748..26386 - 639 WP_000777690 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS879_RS00140 (pSH163_120_34) 26395..27387 - 993 WP_000830835 conjugal transfer pilus assembly protein TraU traU
HS879_RS00145 (pSH163_120_35) 27384..28016 - 633 WP_001203750 type-F conjugative transfer system protein TraW traW
HS879_RS00150 (pSH163_120_36) 28013..28399 - 387 WP_000099693 type-F conjugative transfer system protein TrbI -
HS879_RS00155 (pSH163_120_37) 28396..31023 - 2628 WP_001064265 type IV secretion system protein TraC virb4
HS879_RS00160 (pSH163_120_39) 31183..31404 - 222 WP_001278686 conjugal transfer protein TraR -
HS879_RS00165 (pSH163_120_40) 31539..32054 - 516 WP_000809885 type IV conjugative transfer system lipoprotein TraV traV
HS879_RS00170 (pSH163_120_41) 32051..32302 - 252 WP_001038331 conjugal transfer protein TrbG -
HS879_RS00175 (pSH163_120_42) 32295..32615 - 321 WP_001057304 conjugal transfer protein TrbD virb4
HS879_RS00180 (pSH163_120_43) 32602..33162 - 561 WP_000896605 conjugal transfer pilus-stabilizing protein TraP -
HS879_RS00185 (pSH163_120_44) 33152..34603 - 1452 WP_000146659 F-type conjugal transfer pilus assembly protein TraB traB
HS879_RS00190 (pSH163_120_45) 34603..35331 - 729 WP_001230805 type-F conjugative transfer system secretin TraK traK
HS879_RS00195 (pSH163_120_46) 35318..35884 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HS879_RS00200 (pSH163_120_47) 35906..36217 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS879_RS00205 (pSH163_120_48) 36222..36584 - 363 WP_000994784 type IV conjugative transfer system pilin TraA -
HS879_RS00210 (pSH163_120_49) 36617..37012 - 396 WP_001366159 conjugal transfer relaxosome DNA-bindin protein TraY -
HS879_RS00215 (pSH163_120_50) 37111..37800 - 690 WP_000283383 conjugal transfer transcriptional regulator TraJ -
HS879_RS00220 (pSH163_120_51) 37987..38370 - 384 WP_001151528 conjugal transfer relaxosome DNA-binding protein TraM -
HS879_RS00225 (pSH163_120_52) 38691..39293 + 603 WP_000243710 transglycosylase SLT domain-containing protein virB1
HS879_RS00230 (pSH163_120_54) 39590..40411 - 822 WP_001234423 DUF932 domain-containing protein -
HS879_RS00235 (pSH163_120_55) 40531..40817 - 287 Protein_47 hypothetical protein -
HS879_RS00680 (pSH163_120_57) 40842..41048 - 207 WP_015059635 hypothetical protein -
HS879_RS00685 41118..41291 + 174 Protein_49 hypothetical protein -
HS879_RS00710 41289..41518 - 230 Protein_50 hypothetical protein -
HS879_RS00240 (pSH163_120_61) 41738..41863 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HS879_RS00690 41805..41954 - 150 Protein_52 plasmid maintenance protein Mok -

Host bacterium

ID   931 GenBank   NC_019122
Plasmid name   pSH163_120 Incompatibility group   IncFIA
Plasmid size   120524 bp Coordinate of oriT [Strand]   38442..38731 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Heidelberg

Cargo genes

Drug resistance gene   sitABCD, aph(3')-Ia, aph(6)-Id, aph(3'')-Ib, tet(B), sul2
Virulence gene   iucA, iucB, iucC, iutA
Metal resistance gene   yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -