Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115914
Name   oriT_pIncFIB_Silv108 in_silico
Organism   Raoultella ornithinolytica strain MQB_Silv_108
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104452 (102751..102800 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..13, 18..24  (GCAAAAT..ATTTTGC)
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_pIncFIB_Silv108
AAATCTGCAAAATATTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10186 GenBank   WP_076752116
Name   traI_N2J37_RS29495_pIncFIB_Silv108 insolico UniProt ID   A0A9Q9JMY5
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190488.11 Da        Isoelectric Point: 5.7342

>WP_076752116.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGGKWQSLGTDTVGKTGFIENVYANQIAFGKLYREVLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKESGFDIHSYREDADKRAAEINRAPVSPAKTDGPDISDVVTKAIAGLSDRKVQFTYADMLARTVSQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRHAPF
SDAVSVLAQDRPAMGIVYGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLVGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETLSLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGNQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGVREQGVLNGIIREVLKNEGTLGAKEM
TVTTLTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFLIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVASGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQTLAVGAGPFDGIK
VGHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIALQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDSVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQLRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQITPEQVPRKDGAWVPENSVVEFTPAQEETIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTLNPKADQAQQHVDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESSYVGLSRMKQHVQVYTDNREGWIRAINHSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKVGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVATESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1552)

AAA domain (AAA_30)

(970-1156)

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

(576-628)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   11896 GenBank   WP_032736842
Name   traD_N2J37_RS29490_pIncFIB_Silv108 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85398.61 Da        Isoelectric Point: 5.0675

>WP_032736842.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTICVVTFFVASWVLGRQGKL
QSEDENTGGRQLSDKPKDVARQMKRDGAASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMRGDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYNPRPKIAEGFIQRRLDTRIDERLSAQLEAREAEGSLVRALFTPDEPVSEPAEEKAGVQPEQTKPAKDS
VLPVPVKTSSMAAEGAGKTPAVPLSGAPVTRVKTVPLIRPKPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLEGEQIQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 105176..128236

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2J37_RS29325 (N2J37_29325) 101210..101440 - 231 WP_076752135 hypothetical protein -
N2J37_RS29330 (N2J37_29330) 101632..102162 + 531 WP_076752134 antirestriction protein -
N2J37_RS29335 (N2J37_29335) 102200..102676 - 477 WP_076752132 transglycosylase SLT domain-containing protein -
N2J37_RS29340 (N2J37_29340) 103108..103500 + 393 WP_032736874 conjugal transfer relaxosome DNA-binding protein TraM -
N2J37_RS29345 (N2J37_29345) 103739..104440 + 702 WP_223526258 hypothetical protein -
N2J37_RS29350 (N2J37_29350) 104525..104725 + 201 WP_060415469 TraY domain-containing protein -
N2J37_RS29355 (N2J37_29355) 104794..105162 + 369 WP_032736871 type IV conjugative transfer system pilin TraA -
N2J37_RS29360 (N2J37_29360) 105176..105481 + 306 WP_032736870 type IV conjugative transfer system protein TraL traL
N2J37_RS29365 (N2J37_29365) 105501..106067 + 567 WP_032736869 type IV conjugative transfer system protein TraE traE
N2J37_RS29370 (N2J37_29370) 106054..106788 + 735 WP_032736867 type-F conjugative transfer system secretin TraK traK
N2J37_RS29375 (N2J37_29375) 106788..108209 + 1422 WP_032736866 F-type conjugal transfer pilus assembly protein TraB traB
N2J37_RS29380 (N2J37_29380) 108202..108363 + 162 WP_154235504 hypothetical protein -
N2J37_RS29385 (N2J37_29385) 108383..108952 + 570 WP_042946293 type IV conjugative transfer system lipoprotein TraV traV
N2J37_RS29390 (N2J37_29390) 109064..109342 + 279 WP_032736865 hypothetical protein -
N2J37_RS29395 (N2J37_29395) 109427..109828 + 402 WP_032736864 hypothetical protein -
N2J37_RS29400 (N2J37_29400) 109825..110124 + 300 WP_032736863 hypothetical protein -
N2J37_RS29405 (N2J37_29405) 110212..110595 + 384 WP_042946290 hypothetical protein -
N2J37_RS29410 (N2J37_29410) 110688..113327 + 2640 WP_032736861 type IV secretion system protein TraC virb4
N2J37_RS29415 (N2J37_29415) 113327..113716 + 390 WP_032736860 type-F conjugative transfer system protein TrbI -
N2J37_RS29420 (N2J37_29420) 113713..114339 + 627 WP_042946288 type-F conjugative transfer system protein TraW traW
N2J37_RS29425 (N2J37_29425) 114383..115342 + 960 WP_088912317 conjugal transfer pilus assembly protein TraU traU
N2J37_RS29430 (N2J37_29430) 115355..115981 + 627 WP_032736857 type-F conjugative transfer system pilin assembly protein TrbC trbC
N2J37_RS29435 (N2J37_29435) 115978..117921 + 1944 WP_032736856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
N2J37_RS29440 (N2J37_29440) 118035..118646 + 612 WP_032736855 hypothetical protein -
N2J37_RS29445 (N2J37_29445) 118636..118872 + 237 WP_076752122 conjugal transfer protein TrbE -
N2J37_RS29450 (N2J37_29450) 118869..119054 + 186 WP_032736852 hypothetical protein -
N2J37_RS29455 (N2J37_29455) 119101..119427 + 327 WP_032736851 hypothetical protein -
N2J37_RS29460 (N2J37_29460) 119448..120200 + 753 WP_042946285 type-F conjugative transfer system pilin assembly protein TraF traF
N2J37_RS29465 (N2J37_29465) 120211..120447 + 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
N2J37_RS29470 (N2J37_29470) 120434..120997 + 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
N2J37_RS29475 (N2J37_29475) 120984..122354 + 1371 WP_076752120 conjugal transfer pilus assembly protein TraH traH
N2J37_RS29480 (N2J37_29480) 122354..125197 + 2844 WP_076752118 conjugal transfer mating-pair stabilization protein TraG traG
N2J37_RS29485 (N2J37_29485) 125208..125735 + 528 WP_032736843 hypothetical protein -
N2J37_RS29490 (N2J37_29490) 125942..128236 + 2295 WP_032736842 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16347 GenBank   NZ_CP104452
Plasmid name   pIncFIB_Silv108 Incompatibility group   IncFIB
Plasmid size   138718 bp Coordinate of oriT [Strand]   102751..102800 [-]
Host baterium   Raoultella ornithinolytica strain MQB_Silv_108

Cargo genes

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