Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101355
Name   oriT_pIncFII in_silico
Organism   Klebsiella pneumoniae strain SP4187
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACXCE010000029 (42096..42444 [-], 349 nt)
oriT length   349 nt
IRs (inverted repeats)      252..259, 268..275  (ACCGCTAG..CTAGCGGT)
 189..195, 203..209  (TATAAAA..TTTTATA)
 38..45, 48..55  (GCAAAAAC..GTTTTTGC)
 2..9, 14..21  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 349 nt

>oriT_pIncFII
GTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAGCGATGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1254 GenBank   WP_052994572
Name   traI_IEE95_RS24940_pIncFII insolico UniProt ID   A0A809SYV1
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191972.77 Da        Isoelectric Point: 6.0539

>WP_052994572.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

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

(575-627)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   440 GenBank   WP_001309237
Name   WP_001309237_pIncFII insolico UniProt ID   A0A5W1N5T0
Length   131 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15183.38 Da        Isoelectric Point: 9.9240

>WP_001309237.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-59)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W1N5T0

ID   441 GenBank   WP_001151524
Name   WP_001151524_pIncFII insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   863 GenBank   WP_136503695
Name   traD_IEE95_RS24945_pIncFII insolico UniProt ID   _
Length   756 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 756 a.a.        Molecular weight: 86040.87 Da        Isoelectric Point: 5.0524

>WP_136503695.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQ
LPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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.



ID   864 GenBank   WP_042065521
Name   traC_IEE95_RS25025_pIncFII insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99297.06 Da        Isoelectric Point: 6.1932

>WP_042065521.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNKARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Family of unknown function (DUF5934) (DUF5934)

(289-446)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17174..43017

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IEE95_RS24945 (IEE95_24835) 17174..19444 - 2271 WP_136503695 type IV conjugative transfer system coupling protein TraD prgC
IEE95_RS24950 (IEE95_24840) 19697..20428 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
IEE95_RS24955 (IEE95_24845) 20442..20951 - 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
IEE95_RS24960 (IEE95_24850) 20948..23773 - 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
IEE95_RS24965 (IEE95_24855) 23770..25146 - 1377 WP_000982833 conjugal transfer pilus assembly protein TraH traH
IEE95_RS24970 (IEE95_24860) 25143..25505 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
IEE95_RS24975 (IEE95_24865) 25435..25980 - 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IEE95_RS24980 (IEE95_24870) 25967..26251 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
IEE95_RS24985 (IEE95_24875) 26370..26717 - 348 WP_001287891 conjugal transfer protein TrbA -
IEE95_RS24990 (IEE95_24880) 26733..27476 - 744 WP_001430248 type-F conjugative transfer system pilin assembly protein TraF traF
IEE95_RS24995 (IEE95_24885) 27469..27726 - 258 WP_000864352 conjugal transfer protein TrbE -
IEE95_RS25000 (IEE95_24890) 27753..29561 - 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IEE95_RS25005 (IEE95_24895) 29558..30196 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
IEE95_RS25010 (IEE95_24900) 30205..31197 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
IEE95_RS25015 (IEE95_24905) 31194..31826 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
IEE95_RS25020 (IEE95_24910) 31823..32209 - 387 WP_000214092 type-F conjugative transfer system protein TrbI -
IEE95_RS25025 (IEE95_24915) 32206..34833 - 2628 WP_042065521 type IV secretion system protein TraC virb4
IEE95_RS25030 (IEE95_24920) 34993..35214 - 222 WP_001278689 conjugal transfer protein TraR -
IEE95_RS25035 (IEE95_24925) 35349..35864 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
IEE95_RS25040 (IEE95_24930) 35861..36112 - 252 WP_001038342 conjugal transfer protein TrbG -
IEE95_RS25045 (IEE95_24935) 36124..36321 - 198 WP_001324648 conjugal transfer protein TrbD -
IEE95_RS25050 (IEE95_24940) 36308..36898 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
IEE95_RS25055 (IEE95_24945) 36888..38315 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
IEE95_RS25060 (IEE95_24950) 38315..39043 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
IEE95_RS25065 (IEE95_24955) 39030..39596 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
IEE95_RS25070 (IEE95_24960) 39618..39929 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
IEE95_RS25075 (IEE95_24965) 39944..40309 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
IEE95_RS25080 (IEE95_24970) 40342..40737 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
IEE95_RS25085 (IEE95_24975) 40836..41525 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
IEE95_RS25090 (IEE95_24980) 41712..42095 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
IEE95_RS25095 (IEE95_24985) 42445..43017 + 573 WP_000949660 transglycosylase SLT domain-containing protein virB1
IEE95_RS25100 (IEE95_24990) 43313..44134 - 822 WP_001234465 DUF932 domain-containing protein -
IEE95_RS25105 (IEE95_24995) 44253..44540 - 288 WP_000107242 hypothetical protein -
IEE95_RS25110 (IEE95_25000) 44565..44771 - 207 WP_000275854 hypothetical protein -
IEE95_RS25115 44841..45138 + 298 Protein_52 hypothetical protein -
IEE95_RS25120 (IEE95_25005) 45439..45564 - 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
IEE95_RS25125 45506..45655 - 150 Protein_54 DUF5431 family protein -
IEE95_RS25130 (IEE95_25010) 46089..46406 + 318 Protein_55 IS110 family transposase -
IEE95_RS25135 (IEE95_25015) 46695..46946 - 252 Protein_56 iron-containing alcohol dehydrogenase -
IEE95_RS25140 (IEE95_25020) 47031..47654 - 624 WP_000912556 ion channel -
IEE95_RS25145 (IEE95_25025) 47670..47777 - 108 WP_214096126 IS1 family transposase -

Host bacterium

ID   1799 GenBank   NZ_JACXCE010000029
Plasmid name   pIncFII Incompatibility group   IncFII
Plasmid size   47777 bp Coordinate of oriT [Strand]   42096..42444 [-]
Host baterium   Klebsiella pneumoniae strain SP4187

Cargo genes

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