Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100857
Name   oriT_pSARB26_03 in_silico
Organism   Salmonella enterica subsp. enterica serovar Stanleyville str. CFSAN000624 strain SGSC 2518 isolate SARB61
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP017726 (1509..1970 [-], 462 nt)
oriT length   462 nt
IRs (inverted repeats)      142..151, 154..163  (ATAGTGTCGT..ACGACCCTAT)
 231..238, 241..248  (GCAAAAAC..GTTTTTGC)
Location of nic site      257..258
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 462 nt

>oriT_pSARB26_03
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGTCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATAAAATTTGTCAGTACTGACCCTAACAAGGGTCGCCATAGGGTCGCCATAGTGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGCTAATGATTCAAAAAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCATGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   929 GenBank   WP_023181027
Name   TraI_pSARB26_03 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192134.70 Da        Isoelectric Point: 5.8254

>WP_023181027.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETLSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSVLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFTELGGEIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEMLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDTINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(575-627)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1113..27369

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CFSAN000624_RS24640 (CFSAN000624_024640) 1113..1622 - 510 WP_001595287 transglycosylase SLT domain-containing protein virB1
CFSAN000624_RS24645 (CFSAN000624_024645) 2037..2420 + 384 WP_000124982 conjugal transfer relaxosome DNA-binding protein TraM -
CFSAN000624_RS24650 (CFSAN000624_024650) 2614..3300 + 687 WP_000332484 PAS domain-containing protein -
CFSAN000624_RS26595 3394..3621 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
CFSAN000624_RS24660 (CFSAN000624_024660) 3655..4014 + 360 WP_021532670 type IV conjugative transfer system pilin TraA -
CFSAN000624_RS24665 (CFSAN000624_024665) 4029..4340 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
CFSAN000624_RS24670 (CFSAN000624_024670) 4362..4928 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
CFSAN000624_RS24675 (CFSAN000624_024675) 4915..5643 + 729 WP_023181042 type-F conjugative transfer system secretin TraK traK
CFSAN000624_RS24680 (CFSAN000624_024680) 5643..7070 + 1428 WP_021545202 F-type conjugal transfer pilus assembly protein TraB traB
CFSAN000624_RS24685 (CFSAN000624_024685) 7060..7644 + 585 WP_023181041 conjugal transfer pilus-stabilizing protein TraP -
CFSAN000624_RS24690 (CFSAN000624_024690) 7631..7951 + 321 WP_023181040 conjugal transfer protein TrbD virb4
CFSAN000624_RS24695 (CFSAN000624_024695) 7944..8195 + 252 WP_023181039 conjugal transfer protein TrbG -
CFSAN000624_RS24700 (CFSAN000624_024700) 8192..8707 + 516 WP_023181038 type IV conjugative transfer system lipoprotein TraV traV
CFSAN000624_RS24705 (CFSAN000624_024705) 8842..9063 + 222 WP_023181037 conjugal transfer protein TraR -
CFSAN000624_RS24710 (CFSAN000624_024710) 9456..12086 + 2631 WP_023181036 type IV secretion system protein TraC virb4
CFSAN000624_RS24715 (CFSAN000624_024715) 12083..12469 + 387 WP_000214096 type-F conjugative transfer system protein TrbI -
CFSAN000624_RS24720 (CFSAN000624_024720) 12466..13098 + 633 WP_023181035 type-F conjugative transfer system protein TraW traW
CFSAN000624_RS24725 (CFSAN000624_024725) 13095..14087 + 993 WP_023181034 conjugal transfer pilus assembly protein TraU traU
CFSAN000624_RS24730 (CFSAN000624_024730) 14096..14734 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
CFSAN000624_RS24735 (CFSAN000624_024735) 14731..16539 + 1809 WP_023181033 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CFSAN000624_RS24740 (CFSAN000624_024740) 16565..16822 + 258 WP_000864328 conjugal transfer protein TrbE -
CFSAN000624_RS24745 (CFSAN000624_024745) 16815..17558 + 744 WP_023181032 type-F conjugative transfer system pilin assembly protein TraF traF
CFSAN000624_RS24750 (CFSAN000624_024750) 17572..17913 + 342 WP_023181031 conjugal transfer protein TrbA -
CFSAN000624_RS24755 (CFSAN000624_024755) 18315..18596 + 282 WP_077990627 type-F conjugative transfer system pilin chaperone TraQ -
CFSAN000624_RS24760 (CFSAN000624_024760) 18583..19128 + 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CFSAN000624_RS24765 (CFSAN000624_024765) 19058..19420 + 363 WP_023181029 P-type conjugative transfer protein TrbJ -
CFSAN000624_RS24770 (CFSAN000624_024770) 19417..20793 + 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
CFSAN000624_RS24775 (CFSAN000624_024775) 20790..23615 + 2826 WP_001554363 conjugal transfer mating-pair stabilization protein TraG traG
CFSAN000624_RS24780 (CFSAN000624_024780) 23612..24121 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
CFSAN000624_RS24785 (CFSAN000624_024785) 24135..24866 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
CFSAN000624_RS24790 (CFSAN000624_024790) 25117..27369 + 2253 WP_023181028 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1317 GenBank   NZ_CP017726
Plasmid name   pSARB26_03 Incompatibility group   IncFII
Plasmid size   58302 bp Coordinate of oriT [Strand]   1509..1970 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Stanleyville str. CFSAN000624 strain SGSC 2518 isolate SARB61

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -