Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101729
Name   oriT_pRHBSTW-00069_3 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00069
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXRQ010000003 (80423..80472 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pRHBSTW-00069_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1466 GenBank   WP_181575849
Name   traI_HV053_RS26260_pRHBSTW-00069_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: 190454.16 Da        Isoelectric Point: 6.1897

>WP_181575849.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGINAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALAPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGRLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRASTRM
ILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSQIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVTSERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1144)


  Protein structure



No available structure.




Auxiliary protein

ID   587 GenBank   WP_182207456
Name   WP_182207456_pRHBSTW-00069_3 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14381.22 Da        Isoelectric Point: 4.6159

>WP_182207456.1 conjugal transfer relaxosome DNA-binding protein TraM [Klebsiella pneumoniae]
MARVQAYASDEVAEKINAIVEKRRAEGAKEKDVSFSSVASMLLELGLRVYEAQMESKDSGFNQTEFNKIL
LENVMKTQFTVSKLLAIGSLSPHVTGDERFEFRSMVSNIREDAKDVISHFFPEQEEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.




T4CP

ID   1145 GenBank   WP_228725417
Name   traD_HV053_RS26255_pRHBSTW-00069_3 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84917.00 Da        Isoelectric Point: 5.1110

>WP_228725417.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADDQTQRDMQRREEVNINHSHRHDKQDDVEIGGNI

  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: 79865..108439

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV053_RS26040 (HV053_26040) 74891..75241 + 351 WP_182207454 hypothetical protein -
HV053_RS26045 (HV053_26045) 75873..76229 + 357 WP_019706019 hypothetical protein -
HV053_RS26050 (HV053_26050) 76290..76502 + 213 WP_019706020 hypothetical protein -
HV053_RS26055 (HV053_26055) 76513..76737 + 225 WP_014343499 hypothetical protein -
HV053_RS26060 (HV053_26060) 76818..77138 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HV053_RS26065 (HV053_26065) 77128..77406 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
HV053_RS26070 (HV053_26070) 77407..77820 + 414 WP_004182074 helix-turn-helix domain-containing protein -
HV053_RS26075 (HV053_26075) 78649..79470 + 822 WP_004152492 DUF932 domain-containing protein -
HV053_RS26080 (HV053_26080) 79503..79832 + 330 WP_015065524 DUF5983 family protein -
HV053_RS26085 (HV053_26085) 79865..80350 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
HV053_RS26090 (HV053_26090) 80764..81147 + 384 WP_182207456 conjugal transfer relaxosome DNA-binding protein TraM -
HV053_RS26095 (HV053_26095) 81347..82084 + 738 WP_182207458 conjugal transfer protein TrbJ -
HV053_RS26100 (HV053_26100) 82199..82405 + 207 WP_171773970 TraY domain-containing protein -
HV053_RS26105 (HV053_26105) 82467..82835 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV053_RS26110 (HV053_26110) 82849..83154 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV053_RS26115 (HV053_26115) 83174..83740 + 567 WP_182207460 type IV conjugative transfer system protein TraE traE
HV053_RS26120 (HV053_26120) 83727..84467 + 741 WP_182207462 type-F conjugative transfer system secretin TraK traK
HV053_RS26125 (HV053_26125) 84467..85891 + 1425 WP_016529134 F-type conjugal transfer pilus assembly protein TraB traB
HV053_RS26130 (HV053_26130) 85964..86548 + 585 WP_032440547 type IV conjugative transfer system lipoprotein TraV traV
HV053_RS26135 (HV053_26135) 86871..87089 + 219 WP_004195468 hypothetical protein -
HV053_RS26140 (HV053_26140) 87090..87401 + 312 WP_181575857 hypothetical protein -
HV053_RS26145 (HV053_26145) 87468..87872 + 405 WP_181575856 hypothetical protein -
HV053_RS26150 (HV053_26150) 87997..88242 + 246 WP_228725418 hypothetical protein -
HV053_RS26155 (HV053_26155) 88250..88648 + 399 WP_074188112 hypothetical protein -
HV053_RS26160 (HV053_26160) 88720..91359 + 2640 WP_032431388 type IV secretion system protein TraC virb4
HV053_RS26165 (HV053_26165) 91359..91748 + 390 WP_117046014 type-F conjugative transfer system protein TrbI -
HV053_RS26170 (HV053_26170) 91748..92383 + 636 WP_181575855 type-F conjugative transfer system protein TraW traW
HV053_RS26175 (HV053_26175) 92418..92819 + 402 WP_004194979 hypothetical protein -
HV053_RS26180 (HV053_26180) 92816..93805 + 990 WP_032408909 conjugal transfer pilus assembly protein TraU traU
HV053_RS26185 (HV053_26185) 93818..94456 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV053_RS26190 (HV053_26190) 94515..96470 + 1956 WP_181575854 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV053_RS26195 (HV053_26195) 96502..96756 + 255 WP_004152674 conjugal transfer protein TrbE -
HV053_RS26200 (HV053_26200) 96734..96982 + 249 WP_004152675 hypothetical protein -
HV053_RS26205 (HV053_26205) 96995..97321 + 327 WP_004152676 hypothetical protein -
HV053_RS26210 (HV053_26210) 97342..98094 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HV053_RS26215 (HV053_26215) 98105..98344 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HV053_RS26220 (HV053_26220) 98316..98873 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV053_RS26225 (HV053_26225) 98919..99362 + 444 WP_014343488 F-type conjugal transfer protein TrbF -
HV053_RS26230 (HV053_26230) 99340..100719 + 1380 WP_181575853 conjugal transfer pilus assembly protein TraH traH
HV053_RS26235 (HV053_26235) 100719..103541 + 2823 WP_101455613 conjugal transfer mating-pair stabilization protein TraG traG
HV053_RS26240 (HV053_26240) 103564..104166 + 603 WP_181575852 hypothetical protein -
HV053_RS26245 (HV053_26245) 104417..105148 + 732 WP_181575851 conjugal transfer complement resistance protein TraT -
HV053_RS26250 (HV053_26250) 105341..106030 + 690 WP_181575850 hypothetical protein -
HV053_RS26255 (HV053_26255) 106157..108439 + 2283 WP_228725417 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2173 GenBank   NZ_JABXRQ010000003
Plasmid name   pRHBSTW-00069_3 Incompatibility group   IncFIA
Plasmid size   120084 bp Coordinate of oriT [Strand]   80423..80472 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00069

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsH, arsR, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9