Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102715
Name   oriT_pKPN-7c3 in_silico
Organism   Klebsiella pneumoniae strain Kpn555
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP015131 (22479..22602 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      92..99, 113..120  (ATAATGTA..TACATTAT)
 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_pKPN-7c3
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   810 GenBank   WP_001254388
Name   WP_001254388_pKPN-7c3 insolico UniProt ID   W9A0Z2
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB W9A0Z2

ID   811 GenBank   WP_001151562
Name   WP_001151562_pKPN-7c3 insolico UniProt ID   A0A7I0KNG1
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14420.36 Da        Isoelectric Point: 4.8624

>WP_001151562.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVHEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0KNG1


T4CP

ID   1639 GenBank   WP_000069778
Name   traC_WM92_RS26490_pKPN-7c3 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: 99300.06 Da        Isoelectric Point: 6.3461

>WP_000069778.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  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   1640 GenBank   WP_021526623
Name   traD_WM92_RS27185_pKPN-7c3 insolico UniProt ID   _
Length   750 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 750 a.a.        Molecular weight: 85328.11 Da        Isoelectric Point: 5.1644

>WP_021526623.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGIS
ESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2019..23174

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
WM92_RS26425 (WM92_26420) 2019..3401 - 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
WM92_RS26430 (WM92_26425) 3379..3771 - 393 WP_000660700 F-type conjugal transfer protein TrbF -
WM92_RS29735 3752..4099 - 348 WP_001309242 P-type conjugative transfer protein TrbJ -
WM92_RS26435 (WM92_26430) 4029..4574 - 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
WM92_RS26440 (WM92_26435) 4561..4845 - 285 WP_000624107 type-F conjugative transfer system pilin chaperone TraQ -
WM92_RS26445 (WM92_26440) 4926..5261 + 336 WP_000736414 hypothetical protein -
WM92_RS29740 5242..5583 - 342 WP_001298557 conjugal transfer protein TrbA -
WM92_RS26450 (WM92_26445) 5597..6346 - 750 WP_001323331 type-F conjugative transfer system pilin assembly protein TraF traF
WM92_RS26455 (WM92_26450) 6333..6590 - 258 WP_000864314 conjugal transfer protein TrbE -
WM92_RS26460 (WM92_26455) 6617..8467 - 1851 WP_000821859 type-F conjugative transfer system mating-pair stabilization protein TraN traN
WM92_RS26465 (WM92_26460) 8464..9102 - 639 WP_001080251 type-F conjugative transfer system pilin assembly protein TrbC trbC
WM92_RS26470 (WM92_26465) 9111..9416 - 306 WP_000224418 hypothetical protein -
WM92_RS26475 (WM92_26470) 9446..10438 - 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
WM92_RS26480 (WM92_26475) 10435..11067 - 633 WP_001203736 type-F conjugative transfer system protein TraW traW
WM92_RS26485 (WM92_26480) 11064..11450 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
WM92_RS26490 (WM92_26485) 11447..14077 - 2631 WP_000069778 type IV secretion system protein TraC virb4
WM92_RS32390 14203..14416 - 214 Protein_17 hypothetical protein -
WM92_RS29745 14444..14662 - 219 WP_000556746 hypothetical protein -
WM92_RS26495 (WM92_26490) 14742..15215 - 474 WP_000549566 hypothetical protein -
WM92_RS29750 15208..15429 - 222 WP_001278694 conjugal transfer protein TraR -
WM92_RS26500 (WM92_26495) 15564..16079 - 516 WP_000809888 type IV conjugative transfer system lipoprotein TraV traV
WM92_RS29755 16076..16328 - 253 Protein_22 conjugal transfer protein TrbG -
WM92_RS26505 (WM92_26500) 16321..16641 - 321 WP_001057275 conjugal transfer protein TrbD virb4
WM92_RS26510 (WM92_26505) 16628..17218 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
WM92_RS26515 (WM92_26510) 17208..18635 - 1428 WP_000146665 F-type conjugal transfer pilus assembly protein TraB traB
WM92_RS26520 (WM92_26515) 18635..19363 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
WM92_RS26525 (WM92_26520) 19350..19916 - 567 WP_000399776 type IV conjugative transfer system protein TraE traE
WM92_RS26530 (WM92_26525) 19938..20249 - 312 WP_000012100 type IV conjugative transfer system protein TraL traL
WM92_RS26535 (WM92_26530) 20264..20623 - 360 WP_001098988 type IV conjugative transfer system pilin TraA -
WM92_RS26540 (WM92_26535) 20657..20884 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
WM92_RS29760 20978..21664 - 687 WP_000332487 PAS domain-containing protein -
WM92_RS26550 (WM92_26545) 21858..22241 - 384 WP_001151562 conjugal transfer relaxosome DNA-binding protein TraM -
WM92_RS26555 (WM92_26550) 22584..23174 + 591 WP_000252681 transglycosylase SLT domain-containing protein -
WM92_RS26560 (WM92_26555) 23470..24291 - 822 WP_001234489 DUF932 domain-containing protein -
WM92_RS26565 (WM92_26560) 24410..24697 - 288 WP_000107526 hypothetical protein -
WM92_RS32205 (WM92_26565) 24998..25295 + 298 Protein_36 hypothetical protein -
WM92_RS31130 (WM92_26570) 25613..25738 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
WM92_RS32210 25680..25829 - 150 Protein_38 DUF5431 family protein -
WM92_RS26580 (WM92_26575) 26003..26766 - 764 Protein_39 plasmid SOS inhibition protein A -
WM92_RS26585 (WM92_26580) 26763..27197 - 435 WP_000845910 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   3158 GenBank   NZ_CP015131
Plasmid name   pKPN-7c3 Incompatibility group   IncFIB
Plasmid size   142858 bp Coordinate of oriT [Strand]   22479..22602 [-]
Host baterium   Klebsiella pneumoniae strain Kpn555

Cargo genes

Drug resistance gene   tet(B), mph(A)
Virulence gene   senB
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -