Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114987
Name   oriT_pKM41_2 in_silico
Organism   Enterobacter hormaechei strain 22KM0641
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP126822 (25388..25511 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pKM41_2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9597 GenBank   WP_306676110
Name   traI_QPR84_RS25015_pKM41_2 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191905.58 Da        Isoelectric Point: 5.6449

>WP_306676110.1 conjugative transfer relaxase/helicase TraI [Enterobacter hormaechei]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALVSTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWVDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRSAISEREAALPESVLRESQREQEAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(968-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

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   5641 GenBank   WP_000124981
Name   WP_000124981_pKM41_2 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   5642 GenBank   WP_001254386
Name   WP_001254386_pKM41_2 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   11195 GenBank   WP_000069764
Name   traC_QPR84_RS24930_pKM41_2 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.



ID   11196 GenBank   WP_021573169
Name   traD_QPR84_RS25010_pKM41_2 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: 83553.19 Da        Isoelectric Point: 5.0504

>WP_021573169.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
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: 24816..51432

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QPR84_RS24810 (QPR84_24800) 20612..21046 + 435 WP_306676112 conjugation system SOS inhibitor PsiB -
QPR84_RS24815 (QPR84_24805) 21043..21762 + 720 WP_033803547 plasmid SOS inhibition protein A -
QPR84_RS24820 (QPR84_24810) 21759..22073 + 315 WP_000870669 hypothetical protein -
QPR84_RS24825 (QPR84_24815) 22263..22376 + 114 Protein_33 DUF5431 family protein -
QPR84_RS24830 (QPR84_24820) 22321..22443 + 123 WP_223163518 Hok/Gef family protein -
QPR84_RS24835 (QPR84_24825) 22744..22993 - 250 Protein_35 hypothetical protein -
QPR84_RS24840 (QPR84_24830) 23293..23589 + 297 WP_001272251 hypothetical protein -
QPR84_RS24845 (QPR84_24835) 23699..24520 + 822 WP_001234437 DUF932 domain-containing protein -
QPR84_RS24850 (QPR84_24840) 24816..25463 - 648 WP_306676113 transglycosylase SLT domain-containing protein virB1
QPR84_RS24855 (QPR84_24845) 25740..26123 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
QPR84_RS24860 (QPR84_24850) 26314..27000 + 687 WP_000332484 PAS domain-containing protein -
QPR84_RS24865 (QPR84_24855) 27094..27321 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
QPR84_RS24870 (QPR84_24860) 27355..27714 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
QPR84_RS24875 (QPR84_24865) 27729..28040 + 312 WP_000012103 type IV conjugative transfer system protein TraL traL
QPR84_RS24880 (QPR84_24870) 28062..28628 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
QPR84_RS24885 (QPR84_24875) 28615..29343 + 729 WP_001230798 type-F conjugative transfer system secretin TraK traK
QPR84_RS24890 (QPR84_24880) 29343..30770 + 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
QPR84_RS24895 (QPR84_24885) 30760..31350 + 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
QPR84_RS24900 (QPR84_24890) 31337..31657 + 321 WP_001057307 conjugal transfer protein TrbD -
QPR84_RS24905 (QPR84_24895) 31654..32169 + 516 WP_000809874 type IV conjugative transfer system lipoprotein TraV traV
QPR84_RS24910 (QPR84_24900) 32304..32525 + 222 WP_001278695 conjugal transfer protein TraR -
QPR84_RS24915 (QPR84_24905) 32518..32994 + 477 WP_000549579 hypothetical protein -
QPR84_RS24920 (QPR84_24910) 33074..33291 + 218 Protein_52 hypothetical protein -
QPR84_RS24925 (QPR84_24915) 33319..33666 + 348 WP_000802783 hypothetical protein -
QPR84_RS24930 (QPR84_24920) 33793..36423 + 2631 WP_000069764 type IV secretion system protein TraC virb4
QPR84_RS24935 (QPR84_24925) 36420..36806 + 387 WP_000214097 type-F conjugative transfer system protein TrbI -
QPR84_RS24940 (QPR84_24930) 36803..37435 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
QPR84_RS24945 (QPR84_24935) 37432..38424 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
QPR84_RS24950 (QPR84_24940) 38433..39071 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
QPR84_RS24955 (QPR84_24945) 39068..40918 + 1851 WP_306676107 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QPR84_RS24960 (QPR84_24950) 40944..41201 + 258 WP_000864328 conjugal transfer protein TrbE -
QPR84_RS24965 (QPR84_24955) 41194..41937 + 744 WP_001030390 type-F conjugative transfer system pilin assembly protein TraF traF
QPR84_RS24970 (QPR84_24960) 41953..42300 + 348 WP_001287679 conjugal transfer protein TrbA -
QPR84_RS24975 (QPR84_24965) 42419..42703 + 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
QPR84_RS24980 (QPR84_24970) 42690..43235 + 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QPR84_RS24985 (QPR84_24975) 43165..43527 + 363 WP_010379880 P-type conjugative transfer protein TrbJ -
QPR84_RS24990 (QPR84_24980) 43527..44900 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
QPR84_RS24995 (QPR84_24985) 44897..47722 + 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
QPR84_RS25000 (QPR84_24990) 47719..48228 + 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
QPR84_RS25005 (QPR84_24995) 48242..48973 + 732 WP_000850424 conjugal transfer complement resistance protein TraT -
QPR84_RS25010 (QPR84_25000) 49225..51432 + 2208 WP_021573169 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   15422 GenBank   NZ_CP126822
Plasmid name   pKM41_2 Incompatibility group   IncFII
Plasmid size   61092 bp Coordinate of oriT [Strand]   25388..25511 [+]
Host baterium   Enterobacter hormaechei strain 22KM0641

Cargo genes

Drug resistance gene   tet(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -