Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106465
Name   oriT_p3045-2 in_silico
Organism   Raoultella planticola strain RP_3045
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP114774 (185606..185655 [+], 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_p3045-2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4310 GenBank   WP_278078318
Name   traI_O4J57_RS29360_p3045-2 insolico UniProt ID   _
Length   1757 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1757 a.a.        Molecular weight: 190670.54 Da        Isoelectric Point: 6.0521

>WP_278078318.1 conjugative transfer relaxase/helicase TraI [Raoultella planticola]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKPVDKAVFTEILKGKLPDGSDLTRM
QDGTNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTKALQQVETLAATRVMTDGKSETVLTGNL
IVAKFTHDTNRNEEPQLHTHAVVMNATQNGDKWQSLGTDTVGKTGFIENVYANQIAFGKIYREELKPLVE
ILGYKTEVVGKHGMWEMNEVPVEPFSTRTQEVREAAGPDASLKSRDVAALDTRKSKAAIDPAEKMVEWMN
TMKETGFDMRSYREDADKRAAELASAPVSPVKTDGPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLE
AKPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRQAP
FSDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQVTADIISEPDKGARYSLLAQEFAASVREGQESVAQISGTREQNVLNSVIRDTLKNEGVLGEKE
MTVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLKDKEGERLDMKVSAV
DSQWTLFRADKLPVAEGERLAVLGKIPDTRLKGGESITVLKSGDGQLTVQRPGQKTTQSLSVGSSPFDGI
EVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTMEKLARHTAFSVVSE
QLKARSGETDLDAAIAQQKAGLHTPAEQAIHLSVPLLESDDLTFTRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVSVSSGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTGLTAGQRASTR
MILETPDRFTVVQGYAGVGKTTQFRAVTSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTLLLLLLLLRNGQTPDFSNTLFLIDESSMVGLSDKAKALSLIAAGGGRAVSSGDTDQLQSISPGQPFRL
MQQRSAADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTRAQE
KAIQEALKKGESVPAGQPATLYEALVKDYAGRTPEAQSQTLVITHLNKDRRALNGLIHDARRENGETGKE
EITLPVLVTSNIRDGELRRLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAE
GVTLYRREDITVSEGDRMRFSKSDPERGYVANSVWEVKSVSGDSVTFSDGKTSRTLNPKADEAQRHIDLA
YAITAHGAQGASEPFAIALEGVAEGRKAMASFESAYVGLSRMKQHVQVYTDSREGWIKAINASPSKATAH
DILAPRNDRAVHTAEQLFSRARPMNETAAGRAALQQSGLAKGISPGKFISPGKQYPQPHVALPVYDKNGK
EAGIWLSSLTDSDGRLQVMGGVGRVMGNEDARFVALQGSRNGESLLAGNMGEGVRVARDNPDSGVVVRLA
GDDRPWNPGAITGGRVWADPIPVVSPEAAGTDIPLPPEVLAQRAAEEAQRQNMEKQAEQTAREVAGDGRK
AGESEDRVKEVIGDVIRGLEREKPGEEKMTLPDDPQTRKQEAAVQQVAQESLQRERLQQMERDMVRDLNR
EKTLGGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

DNA helicase TraI (TraI_C)

(1437-1556)

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

(577-629)

AAA domain (AAA_30)

(971-1161)

TrwC relaxase (TrwC)

(10-284)


  Protein structure



No available structure.




Auxiliary protein

ID   1913 GenBank   WP_032700831
Name   WP_032700831_p3045-2 insolico UniProt ID   A0A485D480
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14705.63 Da        Isoelectric Point: 4.4711

>WP_032700831.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Klebsiella/Raoultella group]
MARVQAYASDEVAEKINAIVEKRKAEGAKDKDVSFSSVASMLLELGLRVYEAQMERKESGFNQAEFNKML
LENVIKTQFSISKVLAMESLSPHIQGDERFDFKSMVMNIRDDAKEVVERFFPDTDDEES

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A485D480


T4CP

ID   4338 GenBank   WP_040118437
Name   traD_O4J57_RS29365_p3045-2 insolico UniProt ID   _
Length   776 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 776 a.a.        Molecular weight: 86788.85 Da        Isoelectric Point: 4.9734

>WP_040118437.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGRSLEYNAEQILADKYTIWCGEQLWTSFVLAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLSLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFATGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRSLDTRVDTRLSALLEAREAEGSLARALFTPDAPAPDPAEKDVKVGNTPEQSQPAE
SIESPATVKVPATAKTPAADEIGQSPETPEPAAPVTKVVTVPLIRPRSATATGTAAVATTAASTTSATTV
PAGGTEQELAQQPTEQGQDRLPAGMNDDGVIEDMDAYDAWLAGEQTQRDMQRREEVNINHSHRRDEQDDI
EIGGNF

  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: 157141..186208

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
O4J57_RS29365 (O4J57_29360) 157141..159471 - 2331 WP_040118437 type IV conjugative transfer system coupling protein TraD virb4
O4J57_RS29370 (O4J57_29365) 159665..160396 - 732 WP_032716670 conjugal transfer complement resistance protein TraT -
O4J57_RS29375 (O4J57_29370) 160591..161205 - 615 WP_032732092 hypothetical protein -
O4J57_RS29380 (O4J57_29375) 161231..164053 - 2823 WP_047665748 conjugal transfer mating-pair stabilization protein TraG traG
O4J57_RS29385 (O4J57_29380) 164053..165423 - 1371 WP_032700807 conjugal transfer pilus assembly protein TraH traH
O4J57_RS29390 (O4J57_29385) 165410..165838 - 429 WP_032700808 conjugal transfer protein TrbF -
O4J57_RS29395 (O4J57_29390) 165831..166397 - 567 WP_032732090 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
O4J57_RS29400 (O4J57_29395) 166372..166608 - 237 WP_032700810 type-F conjugative transfer system pilin chaperone TraQ -
O4J57_RS29405 (O4J57_29400) 166619..167371 - 753 WP_040118410 type-F conjugative transfer system pilin assembly protein TraF traF
O4J57_RS29410 (O4J57_29405) 167394..167720 - 327 WP_032700812 hypothetical protein -
O4J57_RS29415 (O4J57_29410) 168010..168978 - 969 WP_077255412 IS5 family transposase -
O4J57_RS29420 (O4J57_29415) 169058..171013 - 1956 WP_040118411 type-F conjugative transfer system mating-pair stabilization protein TraN traN
O4J57_RS29425 (O4J57_29420) 171013..171642 - 630 WP_032700817 type-F conjugative transfer system pilin assembly protein TrbC trbC
O4J57_RS29430 (O4J57_29425) 171655..172614 - 960 WP_032716690 conjugal transfer pilus assembly protein TraU traU
O4J57_RS29435 (O4J57_29430) 172655..173284 - 630 WP_032716660 type-F conjugative transfer system protein TraW traW
O4J57_RS29440 (O4J57_29435) 173281..173673 - 393 WP_032716659 type-F conjugative transfer system protein TrbI -
O4J57_RS29445 (O4J57_29440) 173673..176312 - 2640 WP_032716658 type IV secretion system protein TraC virb4
O4J57_RS29450 (O4J57_29445) 176392..176781 - 390 WP_040118412 hypothetical protein -
O4J57_RS29455 (O4J57_29450) 177158..177562 - 405 WP_040118414 hypothetical protein -
O4J57_RS29460 (O4J57_29455) 177559..177780 - 222 WP_032732073 hypothetical protein -
O4J57_RS29465 (O4J57_29460) 178262..178741 - 480 WP_223306708 hypothetical protein -
O4J57_RS29470 (O4J57_29465) 178848..179417 - 570 WP_071889124 type IV conjugative transfer system lipoprotein TraV traV
O4J57_RS29475 (O4J57_29470) 179436..179642 - 207 WP_032700826 hypothetical protein -
O4J57_RS29480 (O4J57_29475) 179623..180219 - 597 WP_119834738 conjugal transfer protein TraP -
O4J57_RS29485 (O4J57_29480) 180212..181630 - 1419 WP_040118415 F-type conjugal transfer pilus assembly protein TraB traB
O4J57_RS29490 (O4J57_29485) 181630..182364 - 735 WP_040118416 type-F conjugative transfer system secretin TraK traK
O4J57_RS29495 (O4J57_29490) 182351..182917 - 567 WP_040118417 type IV conjugative transfer system protein TraE traE
O4J57_RS29500 (O4J57_29495) 182937..183242 - 306 WP_020323523 type IV conjugative transfer system protein TraL traL
O4J57_RS29505 (O4J57_29500) 183256..183624 - 369 WP_047665734 type IV conjugative transfer system pilin TraA -
O4J57_RS29510 (O4J57_29505) 183686..183850 - 165 WP_032444506 TraY domain-containing protein -
O4J57_RS29515 (O4J57_29510) 184028..184717 - 690 WP_071889125 hypothetical protein -
O4J57_RS29520 (O4J57_29515) 184915..185304 - 390 WP_032700831 conjugal transfer relaxosome DNA-binding protein TraM -
O4J57_RS29525 (O4J57_29520) 185729..186208 + 480 WP_032716648 transglycosylase SLT domain-containing protein virB1
O4J57_RS29530 (O4J57_29525) 186246..186776 - 531 WP_032716647 antirestriction protein -
O4J57_RS29535 (O4J57_29530) 187461..187607 - 147 WP_032700834 hypothetical protein -
O4J57_RS29540 (O4J57_29535) 187701..188048 - 348 WP_032700835 hypothetical protein -
O4J57_RS29545 (O4J57_29540) 188074..188232 - 159 WP_162180130 hypothetical protein -
O4J57_RS29550 (O4J57_29545) 188289..188564 - 276 WP_032700867 hypothetical protein -
O4J57_RS29555 (O4J57_29550) 189383..189664 - 282 WP_004118961 helix-turn-helix transcriptional regulator -
O4J57_RS29560 (O4J57_29555) 189645..189974 - 330 WP_004118963 type II toxin-antitoxin system RelE/ParE family toxin -
O4J57_RS29565 (O4J57_29560) 190294..190381 - 88 Protein_195 theronine dehydrogenase -
O4J57_RS29570 (O4J57_29565) 190378..191106 - 729 WP_004118966 plasmid SOS inhibition protein A -

Host bacterium

ID   6902 GenBank   NZ_CP114774
Plasmid name   p3045-2 Incompatibility group   IncFIB
Plasmid size   212569 bp Coordinate of oriT [Strand]   185606..185655 [+]
Host baterium   Raoultella planticola strain RP_3045

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