Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103402
Name   oriT_p2GS3-tetX4 in_silico
Organism   Escherichia sp. strain 2GS3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MW940614 (54862..55213 [+], 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_p2GS3-tetX4
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2539 GenBank   WP_015059123
Name   traI_KSF47_RS00475_p2GS3-tetX4 insolico UniProt ID   I1WZQ7
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191914.74 Da        Isoelectric Point: 6.1060

>WP_015059123.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

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

(575-627)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   1099 GenBank   WP_001151524
Name   WP_001151524_p2GS3-tetX4 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   1100 GenBank   WP_001369361
Name   WP_001369361_p2GS3-tetX4 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   2320 GenBank   WP_001064265
Name   traC_KSF47_RS00395_p2GS3-tetX4 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: 99296.07 Da        Isoelectric Point: 6.3032

>WP_001064265.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.



ID   2321 GenBank   WP_015059124
Name   traD_KSF47_RS00470_p2GS3-tetX4 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84273.98 Da        Isoelectric Point: 5.0524

>WP_015059124.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 54291..79595

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KSF47_RS00300 (ENAODHDH_00058) 49307..50069 + 763 Protein_60 plasmid SOS inhibition protein A -
KSF47_RS00535 (ENAODHDH_00059) 50248..50397 + 150 Protein_61 plasmid maintenance protein Mok -
KSF47_RS00305 (ENAODHDH_00059) 50339..50464 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
KSF47_RS00540 50684..50914 + 231 WP_001426396 hypothetical protein -
KSF47_RS00545 50912..51085 - 174 Protein_64 hypothetical protein -
KSF47_RS00310 51155..51415 + 261 WP_042046747 hypothetical protein -
KSF47_RS00315 (ENAODHDH_00060) 51509..52513 - 1005 WP_024257664 IS110 family transposase -
KSF47_RS00320 (ENAODHDH_00061) 52764..53051 + 288 WP_000107535 hypothetical protein -
KSF47_RS00325 (ENAODHDH_00062) 53173..53994 + 822 WP_001234469 DUF932 domain-containing protein -
KSF47_RS00330 (ENAODHDH_00063) 54291..54893 - 603 WP_000243712 transglycosylase SLT domain-containing protein virB1
KSF47_RS00335 (ENAODHDH_00064) 55214..55597 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
KSF47_RS00340 (ENAODHDH_00065) 55784..56473 + 690 WP_039002187 conjugal transfer transcriptional regulator TraJ -
KSF47_RS00345 (ENAODHDH_00066) 56572..56967 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
KSF47_RS00350 (ENAODHDH_00067) 57000..57362 + 363 WP_000994784 type IV conjugative transfer system pilin TraA -
KSF47_RS00355 (ENAODHDH_00068) 57367..57678 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
KSF47_RS00360 (ENAODHDH_00069) 57700..58266 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
KSF47_RS00365 (ENAODHDH_00070) 58253..58981 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
KSF47_RS00370 (ENAODHDH_00071) 58981..60408 + 1428 WP_000146690 F-type conjugal transfer pilus assembly protein TraB traB
KSF47_RS00375 (ENAODHDH_00072) 60398..60985 + 588 WP_000002772 conjugal transfer pilus-stabilizing protein TraP -
KSF47_RS00380 (ENAODHDH_00073) 60972..61292 + 321 WP_001057285 conjugal transfer protein TrbD -
KSF47_RS00385 (ENAODHDH_00074) 61289..61804 + 516 WP_000724019 type IV conjugative transfer system lipoprotein TraV traV
KSF47_RS00390 61939..62160 + 222 WP_001278692 conjugal transfer protein TraR -
KSF47_RS00395 (ENAODHDH_00075) 62320..64947 + 2628 WP_001064265 type IV secretion system protein TraC virb4
KSF47_RS00400 (ENAODHDH_00076) 64944..65330 + 387 WP_039002198 type-F conjugative transfer system protein TrbI -
KSF47_RS00405 (ENAODHDH_00077) 65327..65959 + 633 WP_001749440 type-F conjugative transfer system protein TraW traW
KSF47_RS00410 (ENAODHDH_00078) 65956..66948 + 993 WP_023148235 conjugal transfer pilus assembly protein TraU traU
KSF47_RS00415 (ENAODHDH_00079) 66957..67595 + 639 WP_000777691 type-F conjugative transfer system pilin assembly protein TrbC trbC
KSF47_RS00420 (ENAODHDH_00080) 67592..69400 + 1809 WP_000821844 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KSF47_RS00425 (ENAODHDH_00081) 69427..69687 + 261 WP_000864348 conjugal transfer protein TrbE -
KSF47_RS00430 (ENAODHDH_00082) 69680..70423 + 744 WP_039002205 type-F conjugative transfer system pilin assembly protein TraF traF
KSF47_RS00435 (ENAODHDH_00083) 70584..70820 + 237 WP_054377141 type-F conjugative transfer system pilin chaperone TraQ -
KSF47_RS00440 (ENAODHDH_00084) 70807..71352 + 546 WP_000052613 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KSF47_RS00445 (ENAODHDH_00085) 71282..71644 + 363 WP_001443292 P-type conjugative transfer protein TrbJ -
KSF47_RS00450 (ENAODHDH_00086) 71644..73017 + 1374 WP_170926237 conjugal transfer pilus assembly protein TraH traH
KSF47_RS00455 (ENAODHDH_00087) 73014..75836 + 2823 WP_001007048 conjugal transfer mating-pair stabilization protein TraG traG
KSF47_RS00460 (ENAODHDH_00088) 75851..76354 + 504 WP_000605510 hypothetical protein -
KSF47_RS00465 (ENAODHDH_00089) 76386..77117 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
KSF47_RS00470 (ENAODHDH_00090) 77370..79595 + 2226 WP_015059124 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3845 GenBank   NZ_MW940614
Plasmid name   p2GS3-tetX4 Incompatibility group   IncFII
Plasmid size   91582 bp Coordinate of oriT [Strand]   54862..55213 [+]
Host baterium   Escherichia sp. strain 2GS3

Cargo genes

Drug resistance gene   qnrS1, blaLAP-2, tet(X4), sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -