Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100299
Name   oriT_pCVM29188_146 in_silico
Organism   Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_011076 (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_pCVM29188_146
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCCCCCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   370 GenBank   WP_000986988
Name   TraI_pCVM29188_146 insolico UniProt ID   B4TLB7
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

>WP_000986988.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
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
SEKA_RS29630 (SeKA_D0034) 26512..28719 - 2208 WP_000009364 type IV conjugative transfer system coupling protein TraD virb4
SEKA_RS29635 (SeKA_D0035) 28971..29702 - 732 WP_001447147 conjugal transfer complement resistance protein TraT -
SEKA_RS29640 (SeKA_D0036) 29734..30237 - 504 WP_000605510 hypothetical protein -
SEKA_RS29645 (SeKA_D0037) 30252..33074 - 2823 WP_001007012 conjugal transfer mating-pair stabilization protein TraG traG
SEKA_RS29650 (SeKA_D0038) 33071..34447 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
SEKA_RS29655 (SeKA_D0039) 34444..34806 - 363 WP_071779407 P-type conjugative transfer protein TrbJ -
SEKA_RS29660 (SeKA_D0040) 34736..35281 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SEKA_RS29665 (SeKA_D0041) 35268..35552 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
SEKA_RS29670 (SeKA_D0042) 35671..36018 - 348 WP_001287676 conjugal transfer protein TrbA -
SEKA_RS29675 (SeKA_D0043) 36034..36777 - 744 WP_001030389 type-F conjugative transfer system pilin assembly protein TraF traF
SEKA_RS29680 (SeKA_D0044) 36770..37027 - 258 WP_000864325 conjugal transfer protein TrbE -
SEKA_RS29685 (SeKA_D0045) 37054..38862 - 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SEKA_RS29690 (SeKA_D0046) 38859..39497 - 639 WP_022630459 type-F conjugative transfer system pilin assembly protein TrbC trbC
SEKA_RS29695 (SeKA_D0047) 39506..40498 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
SEKA_RS29700 (SeKA_D0048) 40495..41127 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
SEKA_RS29705 (SeKA_D0049) 41124..41510 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
SEKA_RS29710 (SeKA_D0050) 41507..44134 - 2628 WP_001064251 type IV secretion system protein TraC virb4
SEKA_RS29715 (SeKA_D0053) 44294..44515 - 222 WP_001278689 conjugal transfer protein TraR -
SEKA_RS29720 (SeKA_D0054) 44650..45165 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
SEKA_RS29725 (SeKA_D0055) 45162..45413 - 252 WP_001038342 conjugal transfer protein TrbG -
SEKA_RS07295 (SeKA_D0056) 45425..45622 - 198 WP_001324648 conjugal transfer protein TrbD -
SEKA_RS29730 (SeKA_D0057) 45609..46199 - 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
SEKA_RS29735 (SeKA_D0058) 46189..47616 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
SEKA_RS29740 (SeKA_D0059) 47616..48344 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
SEKA_RS29745 (SeKA_D0060) 48331..48897 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
SEKA_RS29750 (SeKA_D0061) 48919..49230 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
SEKA_RS29755 (SeKA_D0062) 49245..49610 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
SEKA_RS29760 (SeKA_D0063) 49643..50038 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
SEKA_RS07300 (SeKA_D0065) 50137..50826 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
SEKA_RS29765 (SeKA_D0067) 51013..51396 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
SEKA_RS29770 (SeKA_D0068) 51811..52320 + 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
SEKA_RS29775 (SeKA_D0070) 52616..53437 - 822 WP_001234468 DUF932 domain-containing protein -
SEKA_RS29780 (SeKA_D0071) 53556..53843 - 288 WP_000107520 hypothetical protein -
SEKA_RS07305 54144..54441 + 298 Protein_59 hypothetical protein -
SEKA_RS29785 (SeKA_D0076) 54742..54864 - 123 WP_223195199 Hok/Gef family protein -
SEKA_RS33900 54809..54961 - 153 Protein_61 DUF5431 family protein -
SEKA_RS29790 (SeKA_D0077) 55112..55898 - 787 Protein_62 plasmid SOS inhibition protein A -
SEKA_RS29795 (SeKA_D0078) 55895..56329 - 435 WP_000845922 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   761 GenBank   NC_011076
Plasmid name   pCVM29188_146 Incompatibility group   IncFIB
Plasmid size   146811 bp Coordinate of oriT [Strand]   51468..51758 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188

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   -