Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113030
Name   oriT_p10907_2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4[5]12:i:- strain 01_0907
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ658824 (58533..58884 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_p10907_2
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8366 GenBank   WP_054377139
Name   traI_QTM59_RS00215_p10907_2 insolico UniProt ID   A0A5W1N632
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191884.75 Da        Isoelectric Point: 6.1058

>WP_054377139.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHTVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNSYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGEILLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGRQQTRVIRPAQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETVRRADEIVRKMAENKPDLP
DSKTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   4791 GenBank   WP_001369361
Name   WP_001369361_p10907_2 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   4792 GenBank   WP_001151524
Name   WP_001151524_p10907_2 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 34196..59455

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QTM59_RS00220 (p02_00215) 34196..36376 - 2181 WP_063078088 type IV conjugative transfer system coupling protein TraD virb4
QTM59_RS00225 (p02_00220) 36629..37360 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
QTM59_RS00230 (p02_00225) 37392..37895 - 504 WP_000605510 hypothetical protein -
QTM59_RS00235 (p02_00230) 37910..40732 - 2823 WP_001007048 conjugal transfer mating-pair stabilization protein TraG traG
QTM59_RS00240 (p02_00235) 40729..42105 - 1377 WP_000982842 conjugal transfer pilus assembly protein TraH traH
QTM59_RS00245 42102..42464 - 363 WP_001443292 P-type conjugative transfer protein TrbJ -
QTM59_RS00250 (p02_00240) 42394..42939 - 546 WP_000052613 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QTM59_RS00255 (p02_00245) 42926..43207 - 282 WP_039002206 type-F conjugative transfer system pilin chaperone TraQ -
QTM59_RS00260 (p02_00250) 43323..44066 - 744 WP_039002205 type-F conjugative transfer system pilin assembly protein TraF traF
QTM59_RS00265 (p02_00255) 44059..44319 - 261 WP_000864348 conjugal transfer protein TrbE -
QTM59_RS00270 (p02_00260) 44346..46154 - 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QTM59_RS00275 (p02_00265) 46151..46789 - 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
QTM59_RS00280 (p02_00270) 46798..47790 - 993 WP_023148235 conjugal transfer pilus assembly protein TraU traU
QTM59_RS00285 (p02_00275) 47787..48419 - 633 WP_001749440 type-F conjugative transfer system protein TraW traW
QTM59_RS00290 (p02_00280) 48416..48802 - 387 WP_039002198 type-F conjugative transfer system protein TrbI -
QTM59_RS00295 (p02_00285) 48799..51426 - 2628 WP_001064265 type IV secretion system protein TraC virb4
QTM59_RS00300 (p02_00290) 51586..51807 - 222 WP_001278692 conjugal transfer protein TraR -
QTM59_RS00305 (p02_00295) 51942..52457 - 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
QTM59_RS00310 (p02_00300) 52454..52774 - 321 WP_001057285 conjugal transfer protein TrbD -
QTM59_RS00315 (p02_00305) 52761..53348 - 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
QTM59_RS00320 (p02_00310) 53338..54765 - 1428 WP_000146690 F-type conjugal transfer pilus assembly protein TraB traB
QTM59_RS00325 (p02_00315) 54765..55493 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
QTM59_RS00330 (p02_00320) 55480..56046 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
QTM59_RS00335 (p02_00325) 56068..56379 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
QTM59_RS00340 (p02_00330) 56384..56746 - 363 WP_000994784 type IV conjugative transfer system pilin TraA -
QTM59_RS00345 (p02_00335) 56779..57174 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
QTM59_RS00350 (p02_00340) 57273..57962 - 690 WP_039002187 conjugal transfer transcriptional regulator TraJ -
QTM59_RS00355 (p02_00350) 58149..58532 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
QTM59_RS00360 (p02_00355) 58853..59455 + 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
QTM59_RS00365 (p02_00360) 59752..60573 - 822 WP_001234469 DUF932 domain-containing protein -
QTM59_RS00370 (p02_00365) 60695..60982 - 288 WP_000107535 hypothetical protein -
QTM59_RS00375 61007..61213 - 207 WP_000547968 hypothetical protein -
QTM59_RS00380 61283..61456 + 174 Protein_76 hypothetical protein -
QTM59_RS00385 61454..61684 - 231 WP_001426396 hypothetical protein -
QTM59_RS00390 61904..62029 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
QTM59_RS00395 61971..62120 - 150 Protein_79 plasmid maintenance protein Mok -
QTM59_RS00400 (p02_00385) 62342..63061 - 720 WP_001276232 plasmid SOS inhibition protein A -
QTM59_RS00405 (p02_00390) 63058..63492 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   13465 GenBank   NZ_OQ658824
Plasmid name   p10907_2 Incompatibility group   IncFIB
Plasmid size   90994 bp Coordinate of oriT [Strand]   58533..58884 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4[5]12:i:- strain 01_0907

Cargo genes

Drug resistance gene   aadA2, lnu(F), qnrS1, mcr-3.1, aac(3)-IId
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -