Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101760
Name   oriT_pRHBSTW-00215_2 in_silico
Organism   Klebsiella sp. RHBSTW-00215
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXQS010000002 (177157..177206 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pRHBSTW-00215_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1483 GenBank   WP_040224080
Name   traI_HV127_RS30075_pRHBSTW-00215_2 insolico UniProt ID   A0A7W3BA55
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190352.82 Da        Isoelectric Point: 5.9133

>WP_040224080.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMNVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   1158 GenBank   WP_023329042
Name   traD_HV127_RS30080_pRHBSTW-00215_2 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: 85943.90 Da        Isoelectric Point: 5.0577

>WP_023329042.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 147320..177764

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV127_RS30080 (HV127_30075) 147320..149629 - 2310 WP_023329042 type IV conjugative transfer system coupling protein TraD virb4
HV127_RS30085 (HV127_30080) 149987..150718 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
HV127_RS30090 (HV127_30085) 150908..151264 - 357 WP_228727545 hypothetical protein -
HV127_RS32125 151167..151376 - 210 WP_345944685 hypothetical protein -
HV127_RS30095 (HV127_30090) 151358..152338 - 981 WP_016156491 IS5-like element ISKpn26 family transposase -
HV127_RS31920 152405..152635 - 231 Protein_159 conjugal transfer protein TraS -
HV127_RS30100 (HV127_30095) 152641..155490 - 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
HV127_RS30105 (HV127_30100) 155490..156869 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
HV127_RS30110 (HV127_30105) 156847..157290 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
HV127_RS30115 (HV127_30110) 157336..157893 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV127_RS30120 (HV127_30115) 157865..158104 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
HV127_RS30125 (HV127_30120) 158115..158867 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
HV127_RS30130 (HV127_30125) 158888..159214 - 327 WP_015065534 hypothetical protein -
HV127_RS30135 (HV127_30130) 159227..159475 - 249 WP_004152675 hypothetical protein -
HV127_RS30140 (HV127_30135) 159453..159707 - 255 WP_015065558 conjugal transfer protein TrbE -
HV127_RS30145 (HV127_30140) 159739..161694 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV127_RS30150 (HV127_30145) 161753..162400 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV127_RS30155 (HV127_30150) 162479..162655 - 177 WP_162866177 hypothetical protein -
HV127_RS30160 (HV127_30155) 162676..163665 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
HV127_RS30165 (HV127_30160) 163662..164063 - 402 WP_023158005 hypothetical protein -
HV127_RS30170 (HV127_30165) 164098..164733 - 636 WP_020325113 type-F conjugative transfer system protein TraW traW
HV127_RS30175 (HV127_30170) 164733..165122 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
HV127_RS30180 (HV127_30175) 165122..167761 - 2640 WP_023158007 type IV secretion system protein TraC virb4
HV127_RS30185 (HV127_30180) 167833..168231 - 399 WP_023158008 hypothetical protein -
HV127_RS30190 (HV127_30185) 168239..168628 - 390 WP_023158009 hypothetical protein -
HV127_RS30195 (HV127_30190) 168671..169075 - 405 WP_016831042 hypothetical protein -
HV127_RS30200 (HV127_30195) 169142..169453 - 312 WP_016831041 hypothetical protein -
HV127_RS30205 (HV127_30200) 169454..169672 - 219 WP_014386199 hypothetical protein -
HV127_RS30210 (HV127_30205) 169696..169985 - 290 Protein_182 hypothetical protein -
HV127_RS30215 (HV127_30210) 169990..170400 - 411 WP_016831039 hypothetical protein -
HV127_RS30220 (HV127_30215) 170532..171116 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
HV127_RS30225 (HV127_30220) 171139..171735 - 597 Protein_185 conjugal transfer pilus-stabilizing protein TraP -
HV127_RS30230 (HV127_30225) 171728..173152 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
HV127_RS30235 (HV127_30230) 173152..173892 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
HV127_RS30240 (HV127_30235) 173879..174445 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
HV127_RS30245 (HV127_30240) 174465..174770 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV127_RS30250 (HV127_30245) 174784..175152 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV127_RS30255 (HV127_30250) 175214..175420 - 207 WP_171773970 TraY domain-containing protein -
HV127_RS30260 (HV127_30255) 175553..176272 - 720 WP_016831034 conjugal transfer protein TrbJ -
HV127_RS30265 (HV127_30260) 176472..176888 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
HV127_RS30270 (HV127_30265) 177279..177764 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
HV127_RS30275 (HV127_30270) 177797..178126 - 330 WP_011977736 DUF5983 family protein -
HV127_RS30280 (HV127_30275) 178159..178980 - 822 WP_004182076 DUF932 domain-containing protein -
HV127_RS30285 (HV127_30280) 179813..180226 - 414 WP_004182074 helix-turn-helix domain-containing protein -
HV127_RS30290 (HV127_30285) 180227..180505 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HV127_RS30295 (HV127_30290) 180495..180815 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HV127_RS30300 (HV127_30295) 180896..181120 - 225 WP_020325128 hypothetical protein -
HV127_RS30305 (HV127_30300) 181131..181343 - 213 WP_004182070 hypothetical protein -
HV127_RS30310 (HV127_30305) 181404..181760 - 357 WP_004152717 hypothetical protein -
HV127_RS30315 (HV127_30310) 182396..182746 - 351 WP_004182068 hypothetical protein -

Host bacterium

ID   2204 GenBank   NZ_JABXQS010000002
Plasmid name   pRHBSTW-00215_2 Incompatibility group   IncFIB
Plasmid size   218228 bp Coordinate of oriT [Strand]   177157..177206 [+]
Host baterium   Klebsiella sp. RHBSTW-00215

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9