Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101265
Name   oriT_PX02|unnamed1 in_silico
Organism   Raoultella ornithinolytica strain PX02
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_NJBC01000001 (1931..1980 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_PX02|unnamed1
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1226 GenBank   WP_088401876
Name   traI_CEG93_RS00180_PX02|unnamed1 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: 190588.30 Da        Isoelectric Point: 5.9980

>WP_088401876.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQSSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLHTPAEQAIHLSIPLLESQDLTFTRPQLLATALETGGDKVPMWSIEMTIK
KQIKSGQLLNVGVSPGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPHVIGLGPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDIDRALATIEQVTPERVPRKEGAWVPGSSVVEFTPTQEEEIRK
ALSKGESLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNNDRRALNGLIHDARRENGETGREEITLP
VLVTSNIRDGELRKLSTWTAHKGAVALVDNVYHRIDNVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEEITVSQGDRMRFSKSDPERGYVANSVWEVQSVSGDSVTLSDGKTTRTLTPKADEAQQHIDLAYAITA
HGAQGASEPYAIALEGMVGARKLMASFESAYVGLSRMKQHVQVYTDRREGWIKAIQHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNIGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRDRLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(11-283)

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

(576-628)

AAA domain (AAA_30)

(970-1157)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   836 GenBank   WP_088401875
Name   traD_CEG93_RS00175_PX02|unnamed1 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: 85026.96 Da        Isoelectric Point: 5.0080

>WP_088401875.1 type IV conjugative transfer system coupling protein TraD [Raoultella ornithinolytica]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVLAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLSLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFATGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRSLDTRVDTRLSALLEAREAEGSLARALFTPDAPEPGPADTESHASEQPESVSPPA
PAEMTVTPAPVKAPPTTKRPAAEPPVLPVTPVPLLNQKAAAAAATASSAGTPAAAAGGTEQELAQQPTEQ
GQDRLPAGMNDDGVIEDMDAYDAWLAGEQTQRDMQRREEVNINHSHRRDEQDDIEIGGNI

  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: 1373..29033

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CEG93_RS00005 (CEG93_00005) 157..978 + 822 WP_015065622 DUF932 domain-containing protein -
CEG93_RS30020 1026..1340 + 315 WP_001568110 DUF5983 family protein -
CEG93_RS00010 (CEG93_00010) 1373..1858 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
CEG93_RS00015 (CEG93_00015) 2249..2665 + 417 WP_074181767 conjugal transfer relaxosome DNA-binding protein TraM -
CEG93_RS00020 (CEG93_00020) 2865..3584 + 720 WP_172412520 conjugal transfer protein TrbJ -
CEG93_RS00025 (CEG93_00025) 3717..3923 + 207 WP_172412524 TraY domain-containing protein -
CEG93_RS00030 (CEG93_00030) 3985..4353 + 369 WP_004178060 type IV conjugative transfer system pilin TraA -
CEG93_RS00035 (CEG93_00035) 4367..4672 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
CEG93_RS00040 (CEG93_00040) 4692..5258 + 567 WP_004194424 type IV conjugative transfer system protein TraE traE
CEG93_RS00045 (CEG93_00045) 5245..5985 + 741 WP_088401865 type-F conjugative transfer system secretin TraK traK
CEG93_RS00050 (CEG93_00050) 5985..7409 + 1425 WP_088401866 F-type conjugal transfer pilus assembly protein TraB traB
CEG93_RS00055 (CEG93_00055) 7482..8051 + 570 WP_032456782 type IV conjugative transfer system lipoprotein TraV traV
CEG93_RS30735 8206..8637 + 432 WP_233435409 hypothetical protein -
CEG93_RS00065 (CEG93_00065) 8661..8879 + 219 WP_032456783 hypothetical protein -
CEG93_RS00070 (CEG93_00070) 8880..9191 + 312 WP_088401867 hypothetical protein -
CEG93_RS00075 (CEG93_00075) 9258..9662 + 405 WP_032456785 hypothetical protein -
CEG93_RS00080 (CEG93_00080) 9705..10004 + 300 WP_088401868 hypothetical protein -
CEG93_RS00085 (CEG93_00085) 10012..10410 + 399 WP_172412521 hypothetical protein -
CEG93_RS00090 (CEG93_00090) 10482..13121 + 2640 WP_088401870 type IV secretion system protein TraC virb4
CEG93_RS00095 (CEG93_00095) 13121..13510 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
CEG93_RS00100 (CEG93_00100) 13510..14136 + 627 WP_015065633 type-F conjugative transfer system protein TraW traW
CEG93_RS00105 (CEG93_00105) 14180..15139 + 960 WP_015065634 conjugal transfer pilus assembly protein TraU traU
CEG93_RS00110 (CEG93_00110) 15152..15790 + 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
CEG93_RS00115 (CEG93_00115) 15849..17804 + 1956 WP_088401871 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CEG93_RS00120 (CEG93_00120) 17836..18072 + 237 WP_016529263 conjugal transfer protein TrbE -
CEG93_RS31105 (CEG93_00125) 18069..18254 + 186 WP_086070806 hypothetical protein -
CEG93_RS00130 (CEG93_00130) 18300..18626 + 327 WP_016529362 hypothetical protein -
CEG93_RS00135 (CEG93_00135) 18647..19399 + 753 WP_088401872 type-F conjugative transfer system pilin assembly protein TraF traF
CEG93_RS00140 (CEG93_00140) 19410..19649 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
CEG93_RS00145 (CEG93_00145) 19621..20193 + 573 WP_032408763 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CEG93_RS00150 (CEG93_00150) 20186..20614 + 429 WP_004152689 hypothetical protein -
CEG93_RS00155 (CEG93_00155) 20601..21971 + 1371 WP_004178055 conjugal transfer pilus assembly protein TraH traH
CEG93_RS00160 (CEG93_00160) 21971..24814 + 2844 WP_088401873 conjugal transfer mating-pair stabilization protein TraG traG
CEG93_RS00165 (CEG93_00165) 24825..25349 + 525 WP_015632518 conjugal transfer entry exclusion protein -
CEG93_RS00170 (CEG93_00170) 25658..26389 + 732 WP_088401874 conjugal transfer complement resistance protein TraT -
CEG93_RS00175 (CEG93_00175) 26751..29033 + 2283 WP_088401875 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1709 GenBank   NZ_NJBC01000001
Plasmid name   PX02|unnamed1 Incompatibility group   IncFII
Plasmid size   75035 bp Coordinate of oriT [Strand]   1931..1980 [-]
Host baterium   Raoultella ornithinolytica strain PX02

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -