Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117752
Name   oriT_Res13-Abat-PEB01-P1-04-A|unnamednovel_1 in_silico
Organism   Raoultella terrigena strain Res13-Abat-PEB01-P1-04-A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP062917 (188820..188869 [+], 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    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_Res13-Abat-PEB01-P1-04-A|unnamednovel_1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11284 GenBank   WP_195711719
Name   traI_IMO34_RS27810_Res13-Abat-PEB01-P1-04-A|unnamednovel_1 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: 190160.51 Da        Isoelectric Point: 5.7390

>WP_195711719.1 conjugative transfer relaxase/helicase TraI [Raoultella terrigena]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAEALGLEGKVDKQVFTDLLQGKIPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLATTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATRNGDKWQTLGSDTVGKTGFSENILANHIAFGKIYQNSLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREDADKRATDIASAPVSPVKTDVPDISDVVTKTIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQARNGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVKRQNHVSVTPDASVVREAPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETLSLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKENGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKGEGVLGEKEL
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPENRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLPVAEGERLAVLGKIPETRLKGGEGVTVLKAEGGQLTVQRPGQKTTQTLAVGAGPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETELDAAIAQQKAGLHSPAEQAIHLSIPLLESNNLTFTRPQLLSTAMEFDGGGKVPMADIDRSI
QAQIKAGSLLSVPVAPGHGNDLLISRQTWDAEKSVLTRVLEGKAAMQPLMDRVPASLMTDLTSGQRAATR
MILETSDRFTVVQGYAGVGKTTQFRAVTGAIDLLPEETRPRVIGLGPTHRAVGEMQRAGVDAQTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDVNSALTTIEQVTPEQVPRKADAWVPENSVTQFTPAQEKAIV
DALKKGESVPADQPTTLYEALVMDYTGRTPEAQSQTLIITHLNNDRRALNSLIHDERVASGEVGKDEITL
PVLVTTNIRDGELRRLSTWAAHNGAVALVDNAYHRIGSVDKENQLITLTDSEGKERFISPREASAEGVTL
YRREDITVSQGDRMRFSKSDPERGYVANSVWEVKSVSGDSVTLSDGKTTRTLNPMEDEAQRHIDLAYAIT
AHGAQGASEPYAIALEGVAGGRKQMASFESTYVGLSRMKQHVQVYTDNREGWIKVIQASRSKATAHDILE
PRNDRAVKTADQLLSRARPLDESAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDSDGRLQVIGGEGRVMGNEDARFVALQGSRNGESLLAENMGEGVRVAREHPDSGVVVRLAGDDR
PWNPGAITGGSLWADKITQAPGADPVEIPLPPEVLAQKVADEAQRQEVEKQAERTAREVAGEDDKQRGPE
GQVKAVIDDVIRGVAGQKMQGERLTLPDDLEGREKAQAVQQVVSENLQRDRLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(971-1157)

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

(634-713)

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

(577-628)

DNA helicase TraI (TraI_C)

(1433-1553)


  Protein structure



No available structure.




T4CP

ID   13173 GenBank   WP_064349677
Name   traD_IMO34_RS27815_Res13-Abat-PEB01-P1-04-A|unnamednovel_1 insolico UniProt ID   _
Length   772 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 772 a.a.        Molecular weight: 86728.66 Da        Isoelectric Point: 4.9851

>WP_064349677.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGRALEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKYSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDARCAAWDIWSECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKSRPKIAEGFILRNLDTRTDARLDTLLEAREAESSHARMLFTPDAPEPEGDDKDRTASEQHEPVKQPE
PTGDPVPPVPVKAPTAAKTSVATEPVKSPETPQSVIPATRVTTVPLIRPKPASAATGTAAVAGATAHTGG
TEQELAQQAADSGQEMMPAGMNEDGEIEDMQAYDDWLAGEQTQRDMQRREEVNINNSHRRDEQDDIEIGG
NF

  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: 160642..186441

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IMO34_RS27815 (IMO34_27810) 160642..162960 - 2319 WP_064349677 type IV conjugative transfer system coupling protein TraD virb4
IMO34_RS27820 (IMO34_27815) 163155..163886 - 732 WP_064349680 conjugal transfer complement resistance protein TraT -
IMO34_RS27825 (IMO34_27820) 164080..164607 - 528 WP_195711720 conjugal transfer protein TraS -
IMO34_RS27830 (IMO34_27825) 164613..167468 - 2856 WP_195711721 conjugal transfer mating-pair stabilization protein TraG traG
IMO34_RS27835 (IMO34_27830) 167468..168838 - 1371 WP_195711722 conjugal transfer pilus assembly protein TraH traH
IMO34_RS27840 (IMO34_27835) 168825..169253 - 429 WP_101856563 conjugal transfer protein TrbF -
IMO34_RS27845 (IMO34_27840) 169246..169812 - 567 WP_101856562 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IMO34_RS27850 (IMO34_27845) 169787..170023 - 237 WP_101856561 type-F conjugative transfer system pilin chaperone TraQ -
IMO34_RS27855 (IMO34_27850) 170034..170786 - 753 WP_064361002 type-F conjugative transfer system pilin assembly protein TraF traF
IMO34_RS27860 (IMO34_27855) 170809..171135 - 327 WP_101856560 hypothetical protein -
IMO34_RS27865 (IMO34_27860) 171361..171597 - 237 WP_101856558 conjugal transfer protein TrbE -
IMO34_RS27870 (IMO34_27865) 171587..171967 - 381 WP_064360999 hypothetical protein -
IMO34_RS27875 (IMO34_27870) 172121..172591 - 471 WP_075809048 hypothetical protein -
IMO34_RS27880 (IMO34_27875) 172675..174630 - 1956 WP_064349681 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IMO34_RS27885 (IMO34_27880) 174630..175259 - 630 WP_064349684 type-F conjugative transfer system pilin assembly protein TrbC trbC
IMO34_RS27890 (IMO34_27885) 175272..176261 - 990 WP_064349687 conjugal transfer pilus assembly protein TraU traU
IMO34_RS27895 (IMO34_27890) 176272..176901 - 630 WP_195711723 type-F conjugative transfer system protein TraW traW
IMO34_RS27900 (IMO34_27895) 176898..177290 - 393 WP_064349691 type-F conjugative transfer system protein TrbI -
IMO34_RS27905 (IMO34_27900) 177290..179929 - 2640 WP_064349692 type IV secretion system protein TraC virb4
IMO34_RS27910 (IMO34_27905) 180014..180394 - 381 WP_064349750 hypothetical protein -
IMO34_RS27915 (IMO34_27910) 180409..180756 - 348 WP_074180877 hypothetical protein -
IMO34_RS27920 (IMO34_27915) 180753..181157 - 405 WP_064349693 hypothetical protein -
IMO34_RS27925 (IMO34_27920) 181154..181375 - 222 WP_064349696 hypothetical protein -
IMO34_RS27930 (IMO34_27925) 181400..181615 - 216 WP_064349698 hypothetical protein -
IMO34_RS27935 (IMO34_27930) 182226..182795 - 570 WP_195711726 type IV conjugative transfer system lipoprotein TraV traV
IMO34_RS27940 (IMO34_27935) 182818..183414 - 597 WP_064349701 conjugal transfer pilus-stabilizing protein TraP -
IMO34_RS27945 (IMO34_27940) 183407..184828 - 1422 WP_064349704 F-type conjugal transfer pilus assembly protein TraB traB
IMO34_RS27950 (IMO34_27945) 184828..185565 - 738 WP_064349705 type-F conjugative transfer system secretin TraK traK
IMO34_RS27955 (IMO34_27950) 185552..186118 - 567 WP_064349707 type IV conjugative transfer system protein TraE traE
IMO34_RS27960 (IMO34_27955) 186136..186441 - 306 WP_064349709 type IV conjugative transfer system protein TraL traL
IMO34_RS27965 (IMO34_27960) 186455..186823 - 369 WP_064349711 type IV conjugative transfer system pilin TraA -
IMO34_RS27970 (IMO34_27965) 186892..187092 - 201 WP_074180879 TraY domain-containing protein -
IMO34_RS27975 (IMO34_27970) 187178..187882 - 705 WP_064349713 hypothetical protein -
IMO34_RS27980 (IMO34_27975) 188119..188511 - 393 WP_064349715 conjugal transfer relaxosome DNA-binding protein TraM -
IMO34_RS27985 (IMO34_27980) 188944..189420 + 477 WP_064349718 transglycosylase SLT domain-containing protein -
IMO34_RS27990 (IMO34_27985) 189458..189987 - 530 Protein_192 antirestriction protein -
IMO34_RS27995 (IMO34_27990) 190805..190951 - 147 WP_064349719 hypothetical protein -
IMO34_RS28000 (IMO34_27995) 191045..191392 - 348 WP_064349720 hypothetical protein -

Host bacterium

ID   18185 GenBank   NZ_CP062917
Plasmid name   Res13-Abat-PEB01-P1-04-A|unnamednovel_1 Incompatibility group   IncFIB
Plasmid size   218566 bp Coordinate of oriT [Strand]   188820..188869 [+]
Host baterium   Raoultella terrigena strain Res13-Abat-PEB01-P1-04-A

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, arsC, arsB, arsR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -