Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101733
Name   oriT_pRHBSTW-00900_5 in_silico
Organism   Klebsiella michiganensis strain RHBSTW-00900
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABXPC010000005 (116983..117032 [+], 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-00900_5
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1468 GenBank   WP_040224080
Name   traI_HV317_RS29950_pRHBSTW-00900_5 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   1147 GenBank   WP_023329042
Name   traD_HV317_RS29955_pRHBSTW-00900_5 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: 88346..117590

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV317_RS29955 (HV317_29960) 88346..90655 - 2310 WP_023329042 type IV conjugative transfer system coupling protein TraD virb4
HV317_RS29960 (HV317_29965) 91013..91744 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
HV317_RS29965 (HV317_29970) 91934..92461 - 528 WP_029498351 conjugal transfer protein TraS -
HV317_RS29970 (HV317_29975) 92467..95316 - 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
HV317_RS29975 (HV317_29980) 95316..96695 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
HV317_RS29980 (HV317_29985) 96673..97116 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
HV317_RS29985 (HV317_29990) 97162..97719 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV317_RS29990 (HV317_29995) 97691..97930 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
HV317_RS29995 (HV317_30000) 97941..98693 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
HV317_RS30000 (HV317_30005) 98714..99040 - 327 WP_015065534 hypothetical protein -
HV317_RS30005 (HV317_30010) 99053..99301 - 249 WP_004152675 hypothetical protein -
HV317_RS30010 (HV317_30015) 99279..99533 - 255 WP_015065558 conjugal transfer protein TrbE -
HV317_RS30015 (HV317_30020) 99565..101520 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV317_RS30020 (HV317_30025) 101579..102226 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV317_RS30025 (HV317_30030) 102305..102481 - 177 WP_162866177 hypothetical protein -
HV317_RS30030 (HV317_30035) 102502..103491 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
HV317_RS30035 (HV317_30040) 103488..103889 - 402 WP_023158005 hypothetical protein -
HV317_RS30040 (HV317_30045) 103924..104559 - 636 WP_020325113 type-F conjugative transfer system protein TraW traW
HV317_RS30045 (HV317_30050) 104559..104948 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
HV317_RS30050 (HV317_30055) 104948..107587 - 2640 WP_023158007 type IV secretion system protein TraC virb4
HV317_RS30055 (HV317_30060) 107659..108057 - 399 WP_023158008 hypothetical protein -
HV317_RS30060 (HV317_30065) 108065..108454 - 390 WP_023158009 hypothetical protein -
HV317_RS30065 (HV317_30070) 108497..108901 - 405 WP_182158414 hypothetical protein -
HV317_RS30070 (HV317_30075) 108968..109279 - 312 WP_016831041 hypothetical protein -
HV317_RS30075 (HV317_30080) 109280..109498 - 219 WP_014386199 hypothetical protein -
HV317_RS30080 (HV317_30085) 109522..109811 - 290 Protein_112 hypothetical protein -
HV317_RS30085 (HV317_30090) 109816..110226 - 411 WP_016831039 hypothetical protein -
HV317_RS30090 (HV317_30095) 110358..110942 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
HV317_RS30095 (HV317_30100) 110965..111561 - 597 Protein_115 conjugal transfer pilus-stabilizing protein TraP -
HV317_RS30100 (HV317_30105) 111554..112978 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
HV317_RS30105 (HV317_30110) 112978..113718 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
HV317_RS30110 (HV317_30115) 113705..114271 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
HV317_RS30115 (HV317_30120) 114291..114596 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV317_RS30120 (HV317_30125) 114610..114978 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV317_RS30125 (HV317_30130) 115040..115246 - 207 WP_171773970 TraY domain-containing protein -
HV317_RS30130 (HV317_30135) 115379..116098 - 720 WP_016831034 conjugal transfer protein TrbJ -
HV317_RS30135 (HV317_30140) 116298..116714 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
HV317_RS30140 (HV317_30145) 117105..117590 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
HV317_RS30145 (HV317_30150) 117623..117952 - 330 WP_011977736 DUF5983 family protein -
HV317_RS30150 (HV317_30155) 117985..118806 - 822 WP_004182076 DUF932 domain-containing protein -
HV317_RS30155 (HV317_30160) 119639..120052 - 414 WP_004182074 helix-turn-helix domain-containing protein -
HV317_RS30160 (HV317_30165) 120053..120331 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HV317_RS30165 (HV317_30170) 120321..120641 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HV317_RS30170 (HV317_30175) 120722..120946 - 225 WP_020325128 hypothetical protein -
HV317_RS30175 (HV317_30180) 120957..121169 - 213 WP_004182070 hypothetical protein -
HV317_RS30180 (HV317_30185) 121230..121586 - 357 WP_004152717 hypothetical protein -
HV317_RS30185 (HV317_30190) 122222..122572 - 351 WP_182158415 hypothetical protein -

Host bacterium

ID   2177 GenBank   NZ_JABXPC010000005
Plasmid name   pRHBSTW-00900_5 Incompatibility group   IncFIB
Plasmid size   150104 bp Coordinate of oriT [Strand]   116983..117032 [+]
Host baterium   Klebsiella michiganensis strain RHBSTW-00900

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9