Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117879
Name   oriT_pKOCBH-B in_silico
Organism   Klebsiella michiganensis strain M82255
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP035216 (69345..69394 [+], 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_pKOCBH-B
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11359 GenBank   WP_128697097
Name   traI_KOCBH_RS30815_pKOCBH-B 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: 190455.10 Da        Isoelectric Point: 5.9703

>WP_128697097.1 conjugative transfer relaxase/helicase TraI [Klebsiella michiganensis]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDGGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1554)

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

(576-628)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   13272 GenBank   WP_013214038
Name   traD_KOCBH_RS30820_pKOCBH-B insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 86010.07 Da        Isoelectric Point: 5.1787

>WP_013214038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 39892..69952

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KOCBH_RS30820 (KOCBH_B00035) 39892..42204 - 2313 WP_013214038 type IV conjugative transfer system coupling protein TraD virb4
KOCBH_RS32895 (KOCBH_B00036) 42331..43020 - 690 WP_013023831 hypothetical protein -
KOCBH_RS30830 (KOCBH_B00037) 43213..43942 - 730 Protein_36 conjugal transfer complement resistance protein TraT -
KOCBH_RS33635 44043..44261 - 219 WP_320406678 hypothetical protein -
KOCBH_RS30845 (KOCBH_B00040) 45330..45857 - 528 WP_032409657 conjugal transfer protein TraS -
KOCBH_RS30850 (KOCBH_B00041) 45863..48712 - 2850 WP_128697098 conjugal transfer mating-pair stabilization protein TraG traG
KOCBH_RS30855 (KOCBH_B00042) 48712..50091 - 1380 WP_072159474 conjugal transfer pilus assembly protein TraH traH
KOCBH_RS30860 (KOCBH_B00043) 50069..50512 - 444 WP_023287131 F-type conjugal transfer protein TrbF -
KOCBH_RS30865 (KOCBH_B00044) 50558..51115 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KOCBH_RS30870 (KOCBH_B00045) 51087..51326 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
KOCBH_RS30875 (KOCBH_B00046) 51337..52089 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
KOCBH_RS30880 (KOCBH_B00047) 52110..52436 - 327 WP_004152676 hypothetical protein -
KOCBH_RS30885 (KOCBH_B00048) 52449..52697 - 249 WP_013214029 hypothetical protein -
KOCBH_RS30890 (KOCBH_B00049) 52675..52929 - 255 WP_023287133 conjugal transfer protein TrbE -
KOCBH_RS30895 (KOCBH_B00050) 52961..54916 - 1956 WP_023287134 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KOCBH_RS30900 (KOCBH_B00051) 54975..55613 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
KOCBH_RS30905 (KOCBH_B00052) 55626..56615 - 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
KOCBH_RS30910 (KOCBH_B00053) 56612..57013 - 402 WP_004194979 hypothetical protein -
KOCBH_RS30915 (KOCBH_B00054) 57048..57683 - 636 WP_032441885 type-F conjugative transfer system protein TraW traW
KOCBH_RS30920 (KOCBH_B00055) 57683..58072 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
KOCBH_RS30925 (KOCBH_B00056) 58069..60711 - 2643 WP_128697099 type IV secretion system protein TraC virb4
KOCBH_RS30930 (KOCBH_B00057) 60783..61181 - 399 WP_023179972 hypothetical protein -
KOCBH_RS30945 (KOCBH_B00059) 61559..61963 - 405 WP_004197817 hypothetical protein -
KOCBH_RS30950 (KOCBH_B00060) 62030..62350 - 321 WP_128697101 hypothetical protein -
KOCBH_RS30955 (KOCBH_B00061) 62351..62569 - 219 WP_004195235 hypothetical protein -
KOCBH_RS30960 (KOCBH_B00062) 62675..63085 - 411 WP_004152499 hypothetical protein -
KOCBH_RS30965 (KOCBH_B00063) 63217..63801 - 585 WP_032441881 type IV conjugative transfer system lipoprotein TraV traV
KOCBH_RS30970 (KOCBH_B00064) 63915..65339 - 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
KOCBH_RS30975 (KOCBH_B00065) 65339..66079 - 741 WP_015065528 type-F conjugative transfer system secretin TraK traK
KOCBH_RS30980 (KOCBH_B00066) 66066..66632 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
KOCBH_RS30985 (KOCBH_B00067) 66652..66957 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
KOCBH_RS30990 (KOCBH_B00068) 66971..67339 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
KOCBH_RS30995 67388..67606 - 219 WP_185157841 TraY domain-containing protein -
KOCBH_RS31000 (KOCBH_B00069) 67739..68459 - 721 Protein_68 conjugal transfer protein TrbJ -
KOCBH_RS31005 (KOCBH_B00070) 68661..69077 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
KOCBH_RS31010 (KOCBH_B00071) 69467..69952 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
KOCBH_RS33420 69985..70314 - 330 Protein_71 DUF5983 family protein -
KOCBH_RS31015 (KOCBH_B00072) 70347..71168 - 822 WP_004152492 DUF932 domain-containing protein -
KOCBH_RS31030 (KOCBH_B00073) 71998..72411 - 414 WP_128697102 type II toxin-antitoxin system HigA family antitoxin -
KOCBH_RS31035 (KOCBH_B00074) 72412..72690 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
KOCBH_RS31040 (KOCBH_B00075) 72680..72913 - 234 WP_128697103 type II toxin-antitoxin system RelE/ParE family toxin -
KOCBH_RS31045 (KOCBH_B00076) 72979..73947 - 969 WP_164913933 IS5-like element IS903 family transposase -
KOCBH_RS31050 (KOCBH_B00077) 73989..74498 - 510 WP_029497411 IS3 family transposase -

Host bacterium

ID   18312 GenBank   NZ_CP035216
Plasmid name   pKOCBH-B Incompatibility group   IncFII
Plasmid size   231662 bp Coordinate of oriT [Strand]   69345..69394 [+]
Host baterium   Klebsiella michiganensis strain M82255

Cargo genes

Drug resistance gene   sul1, aph(6)-Id, aph(3'')-Ib
Virulence gene   -
Metal resistance gene   pcoE, silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -