Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105032
Name   oriT_p50595_ERM in_silico
Organism   Klebsiella pneumoniae strain 50595
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP050372 (69493..69578 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_p50595_ERM
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   1569 GenBank   WP_001354030
Name   WP_001354030_p50595_ERM insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   1570 GenBank   WP_000089263
Name   WP_000089263_p50595_ERM insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   3484 GenBank   WP_000069777
Name   traC_HB637_RS26910_p50595_ERM 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: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   3485 GenBank   WP_025985153
Name   traD_HB637_RS27010_p50595_ERM insolico UniProt ID   _
Length   747 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 747 a.a.        Molecular weight: 84960.70 Da        Isoelectric Point: 5.1644

>WP_025985153.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESG
EVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 1546..21440

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HB637_RS26890 (HB637_26900) 57..278 + 222 WP_001278683 conjugal transfer protein TraR -
HB637_RS26895 (HB637_26905) 271..747 + 477 WP_000549587 hypothetical protein -
HB637_RS26900 (HB637_26910) 827..1045 + 219 WP_000556745 hypothetical protein -
HB637_RS26905 (HB637_26915) 1073..1420 + 348 WP_000836682 hypothetical protein -
HB637_RS26910 (HB637_26920) 1546..4176 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HB637_RS26915 (HB637_26925) 4173..4559 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HB637_RS26920 (HB637_26930) 4556..5188 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HB637_RS26925 (HB637_26935) 5185..6177 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HB637_RS26930 (HB637_26940) 6207..6512 + 306 WP_000224416 hypothetical protein -
HB637_RS26935 (HB637_26945) 6521..7159 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HB637_RS26940 (HB637_26950) 7156..9006 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HB637_RS26945 (HB637_26955) 9033..9290 + 258 WP_000864353 conjugal transfer protein TrbE -
HB637_RS26950 (HB637_26960) 9277..10026 + 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
HB637_RS26955 (HB637_26965) 10040..10384 + 345 WP_000556796 conjugal transfer protein TrbA -
HB637_RS26960 (HB637_26970) 10503..10787 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HB637_RS26965 (HB637_26975) 10774..11319 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HB637_RS26970 (HB637_26980) 11249..11596 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HB637_RS30370 11577..11654 + 78 Protein_17 conjugal transfer protein TrbF -
HB637_RS26980 (HB637_26990) 12423..12746 + 324 Protein_19 F-type conjugal transfer protein TrbF -
HB637_RS26985 (HB637_26995) 12724..14106 + 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
HB637_RS26990 (HB637_27000) 14103..16925 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HB637_RS26995 (HB637_27005) 16941..17426 + 486 WP_000605870 hypothetical protein -
HB637_RS27000 (HB637_27010) 17475..18206 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HB637_RS27005 (HB637_27015) 18409..19146 + 738 WP_000199905 hypothetical protein -
HB637_RS27010 (HB637_27020) 19197..21440 + 2244 WP_025985153 type IV conjugative transfer system coupling protein TraD virb4

Region 2: 68925..76309

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HB637_RS27270 (HB637_27280) 64897..65331 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HB637_RS27275 (HB637_27285) 65328..66047 + 720 WP_001276217 plasmid SOS inhibition protein A -
HB637_RS30145 66269..66418 + 150 Protein_79 plasmid maintenance protein Mok -
HB637_RS27280 (HB637_27290) 66360..66485 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HB637_RS29915 66804..67100 - 297 Protein_81 hypothetical protein -
HB637_RS27295 (HB637_27305) 67400..67696 + 297 WP_001272251 hypothetical protein -
HB637_RS27300 (HB637_27310) 67807..68628 + 822 WP_001234445 DUF932 domain-containing protein -
HB637_RS27305 (HB637_27315) 68925..69515 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
HB637_RS27310 (HB637_27320) 69850..70233 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HB637_RS27315 (HB637_27325) 70427..71098 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HB637_RS27320 (HB637_27330) 71235..71462 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HB637_RS27325 (HB637_27335) 71495..71854 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HB637_RS27330 (HB637_27340) 71869..72180 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HB637_RS27335 (HB637_27345) 72202..72768 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HB637_RS27340 (HB637_27350) 72755..73483 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HB637_RS27345 (HB637_27355) 73483..74934 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HB637_RS27350 (HB637_27360) 74924..75490 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HB637_RS27355 (HB637_27365) 75477..75797 + 321 WP_001057307 conjugal transfer protein TrbD -
HB637_RS27360 (HB637_27370) 75794..76309 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV

Host bacterium

ID   5470 GenBank   NZ_CP050372
Plasmid name   p50595_ERM Incompatibility group   IncFII
Plasmid size   76387 bp Coordinate of oriT [Strand]   69493..69578 [-]
Host baterium   Klebsiella pneumoniae strain 50595

Cargo genes

Drug resistance gene   erm(B), mph(A)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -