Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105368
Name   oriT_p5512.56-1 in_silico
Organism   Klebsiella grimontii strain 5512.56
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP067390 (194624..194673 [+], 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_p5512.56-1
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3663 GenBank   WP_064353420
Name   traI_JJJ11_RS01965_p5512.56-1 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190811.84 Da        Isoelectric Point: 6.1732

>WP_064353420.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANRHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRLVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAV
DSQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGSWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

DNA helicase TraI (TraI_C)

(1433-1555)

AAA domain (AAA_30)

(971-1157)

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

(577-629)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   3636 GenBank   WP_048235023
Name   traD_JJJ11_RS01970_p5512.56-1 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: 85941.02 Da        Isoelectric Point: 5.1149

>WP_048235023.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRSTEPSALRLTTVPLIKPKAAAAAAAAATVSSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDNVEIGGNF

  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: 166620..195231

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JJJ11_RS01970 (JJJ11_01970) 166620..168932 - 2313 WP_048235023 type IV conjugative transfer system coupling protein TraD virb4
JJJ11_RS29565 168988..169101 - 114 Protein_169 hypothetical protein -
JJJ11_RS01975 (JJJ11_01975) 169292..170023 - 732 WP_032415736 conjugal transfer complement resistance protein TraT -
JJJ11_RS01980 (JJJ11_01980) 170275..170877 - 603 WP_023280878 hypothetical protein -
JJJ11_RS01985 (JJJ11_01985) 170901..173723 - 2823 WP_023320108 conjugal transfer mating-pair stabilization protein TraG traG
JJJ11_RS01990 (JJJ11_01990) 173723..175102 - 1380 WP_011977731 conjugal transfer pilus assembly protein TraH traH
JJJ11_RS01995 (JJJ11_01995) 175080..175523 - 444 WP_032436741 F-type conjugal transfer protein TrbF -
JJJ11_RS02000 (JJJ11_02000) 175568..176125 - 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JJJ11_RS02005 (JJJ11_02005) 176097..176336 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
JJJ11_RS02010 (JJJ11_02010) 176347..177099 - 753 WP_015065637 type-F conjugative transfer system pilin assembly protein TraF traF
JJJ11_RS02015 (JJJ11_02015) 177120..177446 - 327 WP_032436744 hypothetical protein -
JJJ11_RS29775 177492..177677 - 186 WP_032436745 hypothetical protein -
JJJ11_RS02020 (JJJ11_02020) 177674..177910 - 237 WP_032436746 conjugal transfer protein TrbE -
JJJ11_RS02025 (JJJ11_02025) 177942..179897 - 1956 WP_023307537 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JJJ11_RS02030 (JJJ11_02030) 179956..180594 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
JJJ11_RS02035 (JJJ11_02035) 180607..181566 - 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
JJJ11_RS02040 (JJJ11_02040) 181610..182236 - 627 WP_023307538 type-F conjugative transfer system protein TraW traW
JJJ11_RS02045 (JJJ11_02045) 182236..182625 - 390 WP_032436749 type-F conjugative transfer system protein TrbI -
JJJ11_RS02050 (JJJ11_02050) 182625..185264 - 2640 WP_016528865 type IV secretion system protein TraC virb4
JJJ11_RS02055 (JJJ11_02055) 185336..185734 - 399 WP_072158599 hypothetical protein -
JJJ11_RS02060 (JJJ11_02060) 185742..186032 - 291 WP_023307542 hypothetical protein -
JJJ11_RS02065 (JJJ11_02065) 186029..186433 - 405 WP_023307543 hypothetical protein -
JJJ11_RS02070 (JJJ11_02070) 186500..186817 - 318 WP_023307544 hypothetical protein -
JJJ11_RS02075 (JJJ11_02075) 186818..187036 - 219 WP_004171484 hypothetical protein -
JJJ11_RS02080 (JJJ11_02080) 187060..187350 - 291 WP_004152596 hypothetical protein -
JJJ11_RS02085 (JJJ11_02085) 187355..187765 - 411 WP_004152597 lipase chaperone -
JJJ11_RS02090 (JJJ11_02090) 187897..188466 - 570 WP_074186487 type IV conjugative transfer system lipoprotein TraV traV
JJJ11_RS02095 (JJJ11_02095) 188489..189085 - 597 WP_004152599 conjugal transfer pilus-stabilizing protein TraP -
JJJ11_RS02100 (JJJ11_02100) 189078..190502 - 1425 WP_004152600 F-type conjugal transfer pilus assembly protein TraB traB
JJJ11_RS02105 (JJJ11_02105) 190502..191242 - 741 WP_004152601 type-F conjugative transfer system secretin TraK traK
JJJ11_RS02110 (JJJ11_02110) 191229..191795 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
JJJ11_RS02115 (JJJ11_02115) 191815..192120 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
JJJ11_RS02120 (JJJ11_02120) 192134..192502 - 369 WP_004178060 type IV conjugative transfer system pilin TraA -
JJJ11_RS02125 (JJJ11_02125) 192556..192927 - 372 WP_004208838 TraY domain-containing protein -
JJJ11_RS02130 (JJJ11_02130) 193011..193706 - 696 WP_004178061 transcriptional regulator TraJ family protein -
JJJ11_RS02135 (JJJ11_02135) 193920..194312 - 393 WP_004178062 conjugal transfer relaxosome DNA-binding protein TraM -
JJJ11_RS02140 (JJJ11_02140) 194746..195231 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
JJJ11_RS02145 (JJJ11_02145) 195264..195593 - 330 WP_011977736 DUF5983 family protein -
JJJ11_RS02150 (JJJ11_02150) 195626..196447 - 822 WP_004178064 DUF932 domain-containing protein -
JJJ11_RS02155 (JJJ11_02155) 197281..197694 - 414 WP_004152722 helix-turn-helix domain-containing protein -
JJJ11_RS02160 (JJJ11_02160) 197695..197973 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
JJJ11_RS02165 (JJJ11_02165) 197963..198283 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
JJJ11_RS02170 (JJJ11_02170) 198364..198588 - 225 WP_004152719 hypothetical protein -
JJJ11_RS02175 (JJJ11_02175) 198599..198811 - 213 WP_004152718 hypothetical protein -
JJJ11_RS02180 (JJJ11_02180) 198872..199228 - 357 WP_004152717 hypothetical protein -
JJJ11_RS02185 (JJJ11_02185) 199864..200214 - 351 WP_004182068 hypothetical protein -

Host bacterium

ID   5806 GenBank   NZ_CP067390
Plasmid name   p5512.56-1 Incompatibility group   IncFIB
Plasmid size   232127 bp Coordinate of oriT [Strand]   194624..194673 [+]
Host baterium   Klebsiella grimontii strain 5512.56

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC, arsB, arsA, arsD, arsR, fecD, fecE, merR2, merT, merP, merF, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9