Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101239
Name   oriT_pKPt4 in_silico
Organism   Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 strain DSM 30104
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AJJI01000026 (45990..46113 [-], 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)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pKPt4
GGTTGGTGGTTCTCACCACAAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1212 GenBank   WP_004150637
Name   traI_UUU_RS00240_pKPt4 insolico UniProt ID   A0A378P204
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191792.51 Da        Isoelectric Point: 6.0128

>WP_004150637.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEGASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQPILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPNALALVDNVYHRIAGISRDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAVQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDVINNAVQKGTAHDVF
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQEGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERDRAAITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   426 GenBank   WP_001254388
Name   WP_001254388_pKPt4 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   427 GenBank   WP_001151564
Name   WP_001151564_pKPt4 insolico UniProt ID   A0AA36PD43
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14446.39 Da        Isoelectric Point: 4.7197

>WP_001151564.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   823 GenBank   WP_004150638
Name   traD_UUU_RS00235_pKPt4 insolico UniProt ID   _
Length   762 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 762 a.a.        Molecular weight: 86779.77 Da        Isoelectric Point: 5.4094

>WP_004150638.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDKKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPE
EEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 17674..43757

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
UUU_RS00235 (UUU_26200) 17674..19962 - 2289 WP_004150638 type IV conjugative transfer system coupling protein TraD prgC
UUU_RS0126745 (UUU_26230) 20244..20723 - 480 WP_025861836 hypothetical protein -
UUU_RS0126750 20927..21658 - 732 WP_025861835 conjugal transfer complement resistance protein TraT -
UUU_RS28785 21707..22192 - 486 WP_077513832 surface exclusion protein -
UUU_RS00230 (UUU_26270) 22208..25051 - 2844 WP_004150645 conjugal transfer mating-pair stabilization protein TraG traG
UUU_RS00225 (UUU_26280) 25048..26421 - 1374 WP_001673176 conjugal transfer pilus assembly protein TraH traH
UUU_RS0126755 26408..26800 - 393 WP_001763765 F-type conjugal transfer protein TrbF -
UUU_RS28790 26781..27128 - 348 WP_011666494 P-type conjugative transfer protein TrbJ -
UUU_RS0126760 27058..27603 - 546 WP_000059830 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
UUU_RS0126765 27590..27874 - 285 WP_000623730 type-F conjugative transfer system pilin chaperone TraQ -
UUU_RS0126770 27993..28340 - 348 WP_025861831 conjugal transfer protein TrbA -
UUU_RS00220 (UUU_26330) 28356..29105 - 750 WP_073980596 type-F conjugative transfer system pilin assembly protein TraF traF
UUU_RS0126775 29092..29349 - 258 WP_025861828 conjugal transfer protein TrbE -
UUU_RS00215 (UUU_26340) 29376..31328 - 1953 WP_032444065 type-F conjugative transfer system mating-pair stabilization protein TraN traN
UUU_RS0126780 31376..32023 - 648 WP_025861826 type-F conjugative transfer system pilin assembly protein TrbC trbC
UUU_RS31465 (UUU_26350) 32167..32661 - 495 WP_004150653 hypothetical protein -
UUU_RS28795 (UUU_26370) 32718..33392 + 675 WP_071531401 hypothetical protein -
UUU_RS30005 33404..33955 - 552 WP_025861824 hypothetical protein -
UUU_RS00210 (UUU_26400) 33973..34152 - 180 WP_004150658 hypothetical protein -
UUU_RS00205 (UUU_26410) 34173..35165 - 993 WP_004150659 conjugal transfer pilus assembly protein TraU traU
UUU_RS0126795 35162..35794 - 633 WP_001203728 type-F conjugative transfer system protein TraW traW
UUU_RS0126800 35791..36177 - 387 WP_025861823 type-F conjugative transfer system protein TrbI -
UUU_RS00200 (UUU_26430) 36174..38801 - 2628 WP_004150661 type IV secretion system protein TraC virb4
UUU_RS28800 38961..39182 - 222 WP_025861821 conjugal transfer protein TraR -
UUU_RS0126810 39317..39832 - 516 WP_001403433 type IV conjugative transfer system lipoprotein TraV traV
UUU_RS28805 39838..40149 - 312 WP_230871211 conjugal transfer protein TrbD -
UUU_RS0126815 40136..40702 - 567 WP_032444064 conjugal transfer pilus-stabilizing protein TraP -
UUU_RS00195 (UUU_26500) 40692..42143 - 1452 WP_004150666 F-type conjugal transfer pilus assembly protein TraB traB
UUU_RS0126820 42143..42871 - 729 WP_025861819 type-F conjugative transfer system secretin TraK traK
UUU_RS00190 (UUU_26510) 42858..43424 - 567 WP_000399776 type IV conjugative transfer system protein TraE traE
UUU_RS0126825 43446..43757 - 312 WP_025861817 type IV conjugative transfer system protein TraL traL
UUU_RS0126830 43772..44134 - 363 WP_001098993 type IV conjugative transfer system pilin TraA -
UUU_RS0126835 (UUU_26550) 44168..44395 - 228 WP_001254388 conjugal transfer relaxosome protein TraY -
UUU_RS28810 44490..45176 - 687 WP_071531404 PAS domain-containing protein -
UUU_RS00180 (UUU_26590) 45369..45752 - 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
UUU_RS0126840 46095..46685 + 591 WP_280518244 transglycosylase SLT domain-containing protein -
UUU_RS0126845 46981..47802 - 822 WP_032447228 DUF932 domain-containing protein -
UUU_RS0126850 47921..48208 - 288 WP_000107526 hypothetical protein -
UUU_RS31720 48509..48682 + 174 Protein_59 hypothetical protein -

Host bacterium

ID   1683 GenBank   NZ_AJJI01000026
Plasmid name   pKPt4 Incompatibility group   IncFII
Plasmid size   88770 bp Coordinate of oriT [Strand]   45990..46113 [-]
Host baterium   Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 strain DSM 30104

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -