Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   112714
Name   oriT_pN38232-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Kentucky strain CVM N38232
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP123661 (46464..46816 [+], 353 nt)
oriT length   353 nt
IRs (inverted repeats)      256..263, 272..279  (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: 353 nt

>oriT_pN38232-1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8205 GenBank   WP_000986988
Name   traI_DE22_RS23295_pN38232-1 insolico UniProt ID   A0A5V2AWD5
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  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.




Auxiliary protein

ID   4678 GenBank   WP_001151524
Name   WP_001151524_pN38232-1 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

ID   4679 GenBank   WP_001369361
Name   WP_001369361_pN38232-1 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


T4CP

ID   9501 GenBank   WP_001064251
Name   traC_DE22_RS23210_pN38232-1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99173.85 Da        Isoelectric Point: 5.9407

>WP_001064251.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRESGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLHVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   9502 GenBank   WP_000009364
Name   traD_DE22_RS23290_pN38232-1 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83567.22 Da        Isoelectric Point: 5.0524

>WP_000009364.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 45893..71701

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DE22_RS23105 (DE22_23110) 41884..42318 + 435 WP_000845922 conjugation system SOS inhibitor PsiB -
DE22_RS23110 (DE22_23115) 42315..43101 + 787 Protein_45 plasmid SOS inhibition protein A -
DE22_RS23115 (DE22_23120) 43291..43404 + 114 Protein_46 DUF5431 family protein -
DE22_RS23120 (DE22_23125) 43349..43471 + 123 WP_223195199 Hok/Gef family protein -
DE22_RS23125 (DE22_23130) 43772..44069 - 298 Protein_48 hypothetical protein -
DE22_RS23130 (DE22_23135) 44370..44657 + 288 WP_000107520 hypothetical protein -
DE22_RS23135 (DE22_23140) 44776..45597 + 822 WP_001234468 DUF932 domain-containing protein -
DE22_RS23140 (DE22_23145) 45893..46402 - 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
DE22_RS23145 (DE22_23150) 46817..47200 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
DE22_RS23150 (DE22_23155) 47387..48076 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
DE22_RS23155 (DE22_23160) 48175..48570 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
DE22_RS23160 (DE22_23165) 48603..48968 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
DE22_RS23165 (DE22_23170) 48983..49294 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
DE22_RS23170 (DE22_23175) 49316..49882 + 567 WP_000399785 type IV conjugative transfer system protein TraE traE
DE22_RS23175 (DE22_23180) 49869..50597 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
DE22_RS23180 (DE22_23185) 50597..52024 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
DE22_RS23185 (DE22_23190) 52014..52604 + 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
DE22_RS23190 (DE22_23195) 52591..52788 + 198 WP_001324648 conjugal transfer protein TrbD -
DE22_RS23195 (DE22_23200) 52800..53051 + 252 WP_001038342 conjugal transfer protein TrbG -
DE22_RS23200 (DE22_23205) 53048..53563 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
DE22_RS23205 (DE22_23210) 53698..53919 + 222 WP_001278689 conjugal transfer protein TraR -
DE22_RS23210 (DE22_23215) 54079..56706 + 2628 WP_001064251 type IV secretion system protein TraC virb4
DE22_RS23215 (DE22_23220) 56703..57089 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
DE22_RS23220 (DE22_23225) 57086..57718 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
DE22_RS23225 (DE22_23230) 57715..58707 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
DE22_RS23230 (DE22_23235) 58716..59354 + 639 WP_022630459 type-F conjugative transfer system pilin assembly protein TrbC trbC
DE22_RS23235 (DE22_23240) 59351..61159 + 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DE22_RS23240 (DE22_23245) 61186..61443 + 258 WP_000864325 conjugal transfer protein TrbE -
DE22_RS23245 (DE22_23250) 61436..62179 + 744 WP_001030389 type-F conjugative transfer system pilin assembly protein TraF traF
DE22_RS23250 (DE22_23255) 62195..62542 + 348 WP_001287676 conjugal transfer protein TrbA -
DE22_RS23255 (DE22_23260) 62661..62945 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
DE22_RS23260 (DE22_23265) 62932..63477 + 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DE22_RS23265 (DE22_23270) 63407..63769 + 363 WP_071779407 P-type conjugative transfer protein TrbJ -
DE22_RS23270 (DE22_23275) 63766..65142 + 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
DE22_RS23275 (DE22_23280) 65139..67961 + 2823 WP_001007012 conjugal transfer mating-pair stabilization protein TraG traG
DE22_RS23280 (DE22_23285) 67976..68479 + 504 WP_000605510 hypothetical protein -
DE22_RS23285 (DE22_23290) 68511..69242 + 732 WP_001447147 conjugal transfer complement resistance protein TraT -
DE22_RS23290 (DE22_23295) 69494..71701 + 2208 WP_000009364 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   13149 GenBank   NZ_CP123661
Plasmid name   pN38232-1 Incompatibility group   IncFIB
Plasmid size   146005 bp Coordinate of oriT [Strand]   46464..46816 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Kentucky strain CVM N38232

Cargo genes

Drug resistance gene   sitABCD, tet(B), aph(3'')-Ib, aph(6)-Id
Virulence gene   iucA, iucB, iucC, iutA, iroN, iroE, iroD, iroC, iroB
Metal resistance gene   yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -