Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105115
Name   oriT_pRHBSTW-00184_3 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00184
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055555 (81356..81404 [-], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pRHBSTW-00184_3
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGATGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3551 GenBank   WP_181468472
Name   traI_HV113_RS27380_pRHBSTW-00184_3 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190236.93 Da        Isoelectric Point: 6.1891

>WP_181468472.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINTTQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNTLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPAQEKAIQK
ALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1584 GenBank   WP_004197733
Name   WP_004197733_pRHBSTW-00184_3 insolico UniProt ID   A0A0E3KB00
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14835.90 Da        Isoelectric Point: 4.6012

>WP_004197733.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0E3KB00


T4CP

ID   3518 GenBank   WP_023313941
Name   traD_HV113_RS27375_pRHBSTW-00184_3 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85666.78 Da        Isoelectric Point: 5.2499

>WP_023313941.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 83818..110433

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV113_RS27185 (HV113_27190) 79309..79611 + 303 Protein_76 SAM-dependent DNA methyltransferase -
HV113_RS27190 (HV113_27195) 80236..80766 + 531 WP_042938443 antirestriction protein -
HV113_RS27195 (HV113_27200) 80804..81211 - 408 WP_023292159 transglycosylase SLT domain-containing protein -
HV113_RS27200 (HV113_27205) 81716..82105 + 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
HV113_RS27205 (HV113_27210) 82344..83018 + 675 WP_004197737 hypothetical protein -
HV113_RS27210 (HV113_27215) 83210..83374 + 165 WP_032444506 TraY domain-containing protein -
HV113_RS27215 (HV113_27220) 83436..83804 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
HV113_RS27220 (HV113_27225) 83818..84123 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV113_RS27225 (HV113_27230) 84143..84709 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
HV113_RS27230 (HV113_27235) 84696..85436 + 741 WP_064174024 type-F conjugative transfer system secretin TraK traK
HV113_RS27235 (HV113_27240) 85436..86860 + 1425 WP_042946342 F-type conjugal transfer pilus assembly protein TraB traB
HV113_RS27240 (HV113_27245) 86853..87449 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
HV113_RS27245 (HV113_27250) 87472..88041 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
HV113_RS27250 (HV113_27255) 88173..88583 + 411 WP_023316400 hypothetical protein -
HV113_RS27255 (HV113_27260) 88588..88872 + 285 WP_023316401 hypothetical protein -
HV113_RS27260 (HV113_27265) 88896..89114 + 219 WP_023316402 hypothetical protein -
HV113_RS27265 (HV113_27270) 89115..89426 + 312 WP_023316403 hypothetical protein -
HV113_RS27270 (HV113_27275) 89493..89897 + 405 WP_023316404 hypothetical protein -
HV113_RS27275 (HV113_27280) 89894..90184 + 291 WP_020323516 hypothetical protein -
HV113_RS27280 (HV113_27285) 90192..90590 + 399 WP_072156904 hypothetical protein -
HV113_RS27285 (HV113_27290) 90662..93301 + 2640 WP_020323518 type IV secretion system protein TraC virb4
HV113_RS27290 (HV113_27295) 93301..93690 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
HV113_RS27295 (HV113_27300) 93690..94316 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV113_RS27300 (HV113_27305) 94360..95319 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HV113_RS27305 (HV113_27310) 95332..95970 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV113_RS27310 (HV113_27315) 96029..97984 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV113_RS27315 (HV113_27320) 98017..98298 + 282 WP_022644736 hypothetical protein -
HV113_RS27320 (HV113_27325) 98288..98515 + 228 WP_012540032 conjugal transfer protein TrbE -
HV113_RS27325 (HV113_27330) 98526..98852 + 327 WP_020323521 hypothetical protein -
HV113_RS27330 (HV113_27335) 98873..99625 + 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
HV113_RS27335 (HV113_27340) 100080..100319 + 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
HV113_RS27340 (HV113_27345) 100291..100848 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV113_RS27345 (HV113_27350) 100894..101337 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
HV113_RS27350 (HV113_27355) 101315..102694 + 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
HV113_RS27355 (HV113_27360) 102694..105537 + 2844 WP_181468470 conjugal transfer mating-pair stabilization protein TraG traG
HV113_RS27360 (HV113_27365) 105548..106072 + 525 WP_023316410 hypothetical protein -
HV113_RS27365 (HV113_27370) 106382..107113 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
HV113_RS27370 (HV113_27375) 107306..107995 + 690 WP_181468471 hypothetical protein -
HV113_RS27375 (HV113_27380) 108124..110433 + 2310 WP_023313941 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5553 GenBank   NZ_CP055555
Plasmid name   pRHBSTW-00184_3 Incompatibility group   IncFIA
Plasmid size   121090 bp Coordinate of oriT [Strand]   81356..81404 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00184

Cargo genes

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