Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120562
Name   oriT_p53828CZ_IncFII in_silico
Organism   Klebsiella michiganensis strain 53828CZ
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP085765 (88446..88494 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_p53828CZ_IncFII
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12952 GenBank   WP_064392532
Name   traI_LJU40_RS28620_p53828CZ_IncFII insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190457.39 Da        Isoelectric Point: 6.1208

>WP_064392532.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTVAVKQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQIAFGKLYREALKPLVE
KLGYETEVVGKHGMWEMKDVPVEPFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADTRAEKIARAPAAPVQTDGLDIADVVTKAIAGLSDRKVQFTYADVLARTVGQLE
AKPAVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDAGVVREKP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSREFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGKQATADIISEPDKSARYALLAQEFAASVREGQESVAQISGTREQNVLNNVIRDTLKNEGVLGKRD
MTVTTLTPVWLDSKSRGVRDYYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAV
DSQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQSLSVGSSPFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDTARTTEKLARHTAFSVVSE
QLKARSGETDLEAAIAQQKAGLHTPAEQAIHLSIPLLESNSLTFTRPQLLAMALETGDGKVPMKDIEATI
QAQIKAGSLLNVPVSPGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMDRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVTGLGPTHRAVGEMQSAGVDAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDVSRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIK
EALKEGKEIPPGTPVSLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTL
PVLVTSNIRDGELRKLSTWSEHLGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTL
YRPEHITVSQGDRMRFSKSDPERGYVANSVWEVKAFSGDSVTLADGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGVEGRRKAMVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PQNARAVKNAGQLYDRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRDGRLEAIGGEGRIMGDETARFVALQNSRNGESLLAGNMGEGVRAARNHPDSGVIVRLAGDDR
PWNPEAITGGRIWADPLPNLPLPDTGADIPLPPDVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEP
GDRIKEVIGDVIRGLERDRPGEEKTPLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

TrwC relaxase (TrwC)

(10-284)

DNA helicase TraI (TraI_C)

(1433-1555)

AAA domain (AAA_30)

(971-1158)

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

(577-629)


  Protein structure



No available structure.




Auxiliary protein

ID   7275 GenBank   WP_032426796
Name   WP_032426796_p53828CZ_IncFII insolico UniProt ID   _
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15036.10 Da        Isoelectric Point: 4.5326

>WP_032426796.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKEKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMRTFFPDEQEEADE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   15207 GenBank   WP_064392534
Name   traD_LJU40_RS28625_p53828CZ_IncFII insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85667.39 Da        Isoelectric Point: 4.8126

>WP_064392534.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMFRLSWQTFVNGCVYWWCTTLGPMR
EIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKDVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLSLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDNDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGSLARALFTPDAPEPEQSDADSRTSPGQPEPESAP
VSPAPVKSASTAETLAAPPSVKASEVPQAKVTTVPLTRPVPAATITAAASATGSSAAATATTGGTEQELT
QQSAEQGQEVMPAGMNEDGEIEDMQAYDAWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  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)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 62076..86027

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LJU40_RS28625 (LJU40_28625) 62076..64376 - 2301 WP_064392534 type IV conjugative transfer system coupling protein TraD virb4
LJU40_RS28630 (LJU40_28630) 64614..65141 - 528 WP_064392535 hypothetical protein -
LJU40_RS28635 (LJU40_28635) 65147..67996 - 2850 WP_064381395 conjugal transfer mating-pair stabilization protein TraG traG
LJU40_RS28640 (LJU40_28640) 67996..69411 - 1416 WP_177342648 conjugal transfer pilus assembly protein TraH traH
LJU40_RS28645 (LJU40_28645) 69799..70329 - 531 WP_077268548 hypothetical protein -
LJU40_RS28650 (LJU40_28650) 70354..70908 - 555 WP_064381391 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LJU40_RS28655 (LJU40_28655) 70880..71119 - 240 WP_064381389 type-F conjugative transfer system pilin chaperone TraQ -
LJU40_RS28660 (LJU40_28660) 71130..71882 - 753 WP_064381388 type-F conjugative transfer system pilin assembly protein TraF traF
LJU40_RS28665 (LJU40_28665) 71901..72227 - 327 WP_064381386 hypothetical protein -
LJU40_RS28670 (LJU40_28670) 72238..72465 - 228 WP_064392539 conjugal transfer protein TrbE -
LJU40_RS28675 (LJU40_28675) 72455..72736 - 282 WP_064392542 hypothetical protein -
LJU40_RS28680 (LJU40_28680) 72773..74647 - 1875 WP_064392546 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LJU40_RS28685 (LJU40_28685) 74644..75261 - 618 WP_064392548 type-F conjugative transfer system pilin assembly protein TrbC trbC
LJU40_RS28690 (LJU40_28690) 75274..76257 - 984 WP_177342650 conjugal transfer pilus assembly protein TraU traU
LJU40_RS28695 (LJU40_28695) 76277..76903 - 627 WP_064392552 type-F conjugative transfer system protein TraW traW
LJU40_RS28700 (LJU40_28700) 76900..77301 - 402 WP_227807615 type-F conjugative transfer system protein TrbI -
LJU40_RS28705 (LJU40_28705) 77334..79973 - 2640 WP_227807613 type IV secretion system protein TraC virb4
LJU40_RS28710 (LJU40_28710) 80104..80508 - 405 WP_064174410 hypothetical protein -
LJU40_RS28715 (LJU40_28715) 80505..80729 - 225 WP_064381372 hypothetical protein -
LJU40_RS28720 (LJU40_28720) 80753..81046 - 294 WP_049071697 hypothetical protein -
LJU40_RS28725 (LJU40_28725) 81075..81479 - 405 WP_064381370 hypothetical protein -
LJU40_RS28730 (LJU40_28730) 81596..82177 - 582 WP_064381368 type IV conjugative transfer system lipoprotein TraV traV
LJU40_RS30925 82200..82337 - 138 Protein_90 conjugal transfer protein TraP -
LJU40_RS28740 (LJU40_28740) 82405..83001 - 597 WP_136404571 conjugal transfer protein TraP -
LJU40_RS28745 (LJU40_28745) 82994..84409 - 1416 WP_064381364 F-type conjugal transfer pilus assembly protein TraB traB
LJU40_RS28750 (LJU40_28750) 84409..85149 - 741 WP_064381362 type-F conjugative transfer system secretin TraK traK
LJU40_RS28755 (LJU40_28755) 85136..85702 - 567 WP_020323527 type IV conjugative transfer system protein TraE traE
LJU40_RS28760 (LJU40_28760) 85722..86027 - 306 WP_020323523 type IV conjugative transfer system protein TraL traL
LJU40_RS28765 (LJU40_28765) 86041..86406 - 366 WP_064381359 type IV conjugative transfer system pilin TraA -
LJU40_RS28770 (LJU40_28770) 86470..86634 - 165 WP_032426810 TraY domain-containing protein -
LJU40_RS28775 (LJU40_28775) 86810..87502 - 693 WP_064381358 hypothetical protein -
LJU40_RS28780 (LJU40_28780) 87740..88132 - 393 WP_032426796 conjugal transfer relaxosome DNA-binding protein TraM -
LJU40_RS28785 (LJU40_28785) 88639..89061 + 423 WP_077268549 transglycosylase SLT domain-containing protein -
LJU40_RS28790 (LJU40_28790) 89084..89626 - 543 WP_064392555 antirestriction protein -

Host bacterium

ID   20991 GenBank   NZ_CP085765
Plasmid name   p53828CZ_IncFII Incompatibility group   IncFII
Plasmid size   100320 bp Coordinate of oriT [Strand]   88446..88494 [+]
Host baterium   Klebsiella michiganensis strain 53828CZ

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   nirD, ncrC, nirB, ncrA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -