Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103168
Name   oriT_pABC143C-NDM in_silico
Organism   Klebsiella pneumoniae
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY130431 (49413..49498 [-], 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_pABC143C-NDM
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2371 GenBank   WP_000948354
Name   traI_HTL22_RS00460_pABC143C-NDM insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
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   1001 GenBank   WP_001354030
Name   WP_001354030_pABC143C-NDM 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   1002 GenBank   WP_000089263
Name   WP_000089263_pABC143C-NDM 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   2114 GenBank   WP_000069777
Name   traC_HTL22_RS00360_pABC143C-NDM 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   2115 GenBank   WP_000009332
Name   traD_HTL22_RS00455_pABC143C-NDM insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83193.81 Da        Isoelectric Point: 5.1644

>WP_000009332.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 48845..76925

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTL22_RS00250 44817..45251 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTL22_RS00255 45248..45967 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTL22_RS00595 46189..46338 + 150 Protein_53 plasmid maintenance protein Mok -
HTL22_RS00260 46280..46405 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTL22_RS00265 46724..47020 - 297 Protein_55 hypothetical protein -
HTL22_RS00270 47320..47616 + 297 WP_001272251 hypothetical protein -
HTL22_RS00275 47727..48548 + 822 WP_001234445 DUF932 domain-containing protein -
HTL22_RS00280 48845..49447 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HTL22_RS00285 49770..50153 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTL22_RS00290 50347..51018 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTL22_RS00295 51155..51382 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTL22_RS00300 51415..51774 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTL22_RS00305 51789..52100 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTL22_RS00310 52122..52688 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTL22_RS00315 52675..53403 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTL22_RS00320 53403..54854 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTL22_RS00325 54844..55410 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTL22_RS00330 55397..55717 + 321 WP_001057307 conjugal transfer protein TrbD -
HTL22_RS00335 55714..56229 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTL22_RS00340 56364..56585 + 222 WP_001278683 conjugal transfer protein TraR -
HTL22_RS00345 56578..57054 + 477 WP_000549587 hypothetical protein -
HTL22_RS00350 57134..57352 + 219 WP_000556745 hypothetical protein -
HTL22_RS00355 57380..57727 + 348 WP_000836682 hypothetical protein -
HTL22_RS00360 57853..60483 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HTL22_RS00365 60480..60866 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTL22_RS00370 60863..61495 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTL22_RS00375 61492..62484 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTL22_RS00380 62514..62819 + 306 WP_000224416 hypothetical protein -
HTL22_RS00385 62828..63466 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTL22_RS00390 63463..65313 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTL22_RS00395 65340..65597 + 258 WP_000864353 conjugal transfer protein TrbE -
HTL22_RS00400 65584..66333 + 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
HTL22_RS00405 66347..66691 + 345 WP_000556796 conjugal transfer protein TrbA -
HTL22_RS00410 66810..67094 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTL22_RS00415 67081..67626 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTL22_RS00420 67556..67903 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTL22_RS00425 67884..68276 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTL22_RS00430 68254..69636 + 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
HTL22_RS00435 69633..72455 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTL22_RS00440 72471..72956 + 486 WP_000605870 hypothetical protein -
HTL22_RS00445 73005..73736 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTL22_RS00450 73939..74676 + 738 WP_000199905 hypothetical protein -
HTL22_RS00455 74727..76925 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3611 GenBank   NZ_KY130431
Plasmid name   pABC143C-NDM Incompatibility group   IncFII
Plasmid size   96549 bp Coordinate of oriT [Strand]   49413..49498 [-]
Host baterium   Klebsiella pneumoniae

Cargo genes

Drug resistance gene   mph(A), blaTEM-1B, rmtB, blaNDM-5, sul1, qacE, aadA2, dfrA12, erm(B)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11