Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103300
Name   oriT_pUCLA3 in_silico
Organism   Klebsiella pneumoniae
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY940546 (49325..49372 [-], 48 nt)
oriT length   48 nt
IRs (inverted repeats)      5..12, 15..22  (GCAAAATT..AATTTTGC)
Location of nic site      31..32
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 48 nt

>oriT_pUCLA3
ATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2466 GenBank   WP_020315134
Name   traI_HTM92_RS00505_pUCLA3 insolico UniProt ID   A0A3P2ILZ7
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190299.85 Da        Isoelectric Point: 5.9174

>WP_020315134.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGENKHRPGYDLTFSAPKSVSMLAMLGGDKRLVDAHNQAVTEAVKQLETLTATRVMADGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQTAFGKLYREALKPLVE
KLGYETEVVGKHGMWEMKDVPVEAFSSRSREVREAAGPDASLKSRDVAALDTRRSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAEEIARAPVAPEKTDGPDITDVVTRAIAGLSDRKVQFTYADVLARTVGQLE
AKPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDASVVREAP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSREFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGKQATADIISEPDKSARYSRLAQEFAVSVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGSRD
MMVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAV
DSQWTLFRTNKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSE
QLKVRSGEADLEAAIAQQKAGLHTPAEQAIHLSVPLLESNSLTFTRPQLLATALETGGGKVPMKDIEATI
QAQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMGRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFKAVMSAISLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDISRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQ
DALKEGKEIPPGTPVSLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTL
SVLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTL
YRPEHITVSQGDRMRFSKSDPERGYVANSVWEVKTVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGVEGRRKALVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PQNTRAVKNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRDGRLEAIGGEGRIMGDETARFVALQNSRNGESLLAGNMGEGVRTARDNPDSGVIVRLAGDDR
PWNPEAITGGRIWADPLPNTPLPDTGTDIPLPPEVLAQRAAEEAQRREMEKQAEQAAREVAGEEKKAGEP
GDRIKEVIGDVIRGLERDRPGEEKTPLTDDPQTRRQEAAIQQVASESLQRERLQEMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

TrwC relaxase (TrwC)

(10-284)


  Protein structure



No available structure.




T4CP

ID   2240 GenBank   WP_020315126
Name   traD_HTM92_RS00500_pUCLA3 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: 85732.61 Da        Isoelectric Point: 4.9642

>WP_020315126.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDTRLSALLEAREAEGSLARALFTPDAPEPEQRDADSKTSPGQPVPESAP
VSPVPVKPVSTAETLSAQSSVKAQGAPQAKVATVPLTRPAPAATPAAASATASSAAATAATTGGTEQELA
QQPAEQGQEMMPAGMNEDGEIEDMQAYDAWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  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: 51823..77379

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTM92_RS00310 (PUCLA3_00161) 47110..47340 + 231 WP_020314756 hypothetical protein -
HTM92_RS00590 47425..47544 + 120 Protein_65 SAM-dependent DNA methyltransferase -
HTM92_RS00315 47830..48000 - 171 WP_020314758 hypothetical protein -
HTM92_RS00320 (PUCLA3_00160) 48193..48735 + 543 WP_020314754 antirestriction protein -
HTM92_RS00325 (PUCLA3_00159) 48758..49180 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
HTM92_RS00330 (PUCLA3_00158) 49673..50068 + 396 WP_022644714 conjugal transfer relaxosome DNA-binding protein TraM -
HTM92_RS00335 (PUCLA3_00157) 50240..50926 + 687 WP_022644713 transcriptional regulator TraJ family protein -
HTM92_RS00340 51005..51385 + 381 WP_032409797 TraY domain-containing protein -
HTM92_RS00345 (PUCLA3_00155) 51444..51809 + 366 WP_020314752 type IV conjugative transfer system pilin TraA -
HTM92_RS00350 (PUCLA3_00154) 51823..52128 + 306 WP_020323523 type IV conjugative transfer system protein TraL traL
HTM92_RS00355 (PUCLA3_00153) 52148..52714 + 567 WP_020323527 type IV conjugative transfer system protein TraE traE
HTM92_RS00360 (PUCLA3_00152) 52701..53441 + 741 WP_020315147 type-F conjugative transfer system secretin TraK traK
HTM92_RS00365 (PUCLA3_00151) 53441..54862 + 1422 WP_020315140 F-type conjugal transfer pilus assembly protein TraB traB
HTM92_RS00370 (PUCLA3_00150) 54855..55289 + 435 WP_020322358 conjugal transfer protein TraP -
HTM92_RS00375 (PUCLA3_00149) 55323..55886 + 564 WP_020315143 type IV conjugative transfer system lipoprotein TraV traV
HTM92_RS00380 (PUCLA3_00148) 56031..56219 + 189 WP_000957857 hypothetical protein -
HTM92_RS00385 (PUCLA3_00147) 56229..57428 + 1200 WP_000948429 IS91 family transposase -
HTM92_RS00390 (PUCLA3_00146) 57721..57924 + 204 WP_020315141 hypothetical protein -
HTM92_RS00395 58165..58578 + 414 WP_020315139 hypothetical protein -
HTM92_RS00400 (PUCLA3_00145) 58607..58906 + 300 WP_020315144 hypothetical protein -
HTM92_RS00405 (PUCLA3_00144) 58923..59147 + 225 WP_022644711 hypothetical protein -
HTM92_RS00410 (PUCLA3_00143) 59144..59548 + 405 WP_020323520 hypothetical protein -
HTM92_RS00415 (PUCLA3_00142) 59545..59835 + 291 WP_020323516 hypothetical protein -
HTM92_RS00420 (PUCLA3_00141) 59843..60241 + 399 WP_072156904 hypothetical protein -
HTM92_RS00425 (PUCLA3_00140) 60313..62952 + 2640 WP_020323518 type IV secretion system protein TraC virb4
HTM92_RS00430 (PUCLA3_00139) 62952..63341 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
HTM92_RS00435 (PUCLA3_00138) 63341..63967 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HTM92_RS00440 (PUCLA3_00137) 64011..64970 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HTM92_RS00445 (PUCLA3_00136) 64983..65621 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTM92_RS00450 (PUCLA3_00135) 65680..67635 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTM92_RS00455 (PUCLA3_00134) 67668..67949 + 282 WP_022644736 hypothetical protein -
HTM92_RS00460 (PUCLA3_00133) 67939..68166 + 228 WP_012540032 conjugal transfer protein TrbE -
HTM92_RS00465 (PUCLA3_00132) 68177..68503 + 327 WP_020323521 hypothetical protein -
HTM92_RS00470 (PUCLA3_00131) 68524..69276 + 753 WP_020323528 type-F conjugative transfer system pilin assembly protein TraF traF
HTM92_RS00475 (PUCLA3_00130) 69287..69526 + 240 WP_020315123 type-F conjugative transfer system pilin chaperone TraQ -
HTM92_RS00480 (PUCLA3_00129) 69498..70073 + 576 WP_020315129 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTM92_RS00485 (PUCLA3_00128) 70060..71430 + 1371 WP_020315127 conjugal transfer pilus assembly protein TraH traH
HTM92_RS00490 (PUCLA3_00127) 71430..74309 + 2880 WP_020315125 conjugal transfer mating-pair stabilization protein TraG traG
HTM92_RS00495 (PUCLA3_00126) 74315..74842 + 528 WP_020315130 hypothetical protein -
HTM92_RS00500 (PUCLA3_00125) 75079..77379 + 2301 WP_020315126 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3743 GenBank   NZ_KY940546
Plasmid name   pUCLA3 Incompatibility group   IncFII
Plasmid size   88127 bp Coordinate of oriT [Strand]   49325..49372 [-]
Host baterium   Klebsiella pneumoniae

Cargo genes

Drug resistance gene   dfrA14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -