Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107878
Name   oriT_pJBIWA001_2 in_silico
Organism   Raoultella planticola strain JBIWA001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP074184 (90058..90107 [-], 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_pJBIWA001_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5289 GenBank   WP_223526251
Name   traI_KGP19_RS28225_pJBIWA001_2 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: 190418.71 Da        Isoelectric Point: 5.5084

>WP_223526251.1 conjugative transfer relaxase/helicase TraI [Raoultella planticola]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPTMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALMKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKSTRTLNPKADQAQQHIDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESAYVGLSRMKQHVQVYTDNREGWIKAINNSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEAQRREMERQTEQATREVSGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVVSESLQRDRLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1552)

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

(577-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1157)

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

(634-713)


  Protein structure



No available structure.




Auxiliary protein

ID   2437 GenBank   WP_053390193
Name   WP_053390193_pJBIWA001_2 insolico UniProt ID   A0A8G2A327
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14883.89 Da        Isoelectric Point: 4.3779

>WP_053390193.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVQAYVSDEVADKINAIVEKRRVEGAKDKDISFSSISTMLLELGLRVYEAQMERKESGFNQMAFNKAL
LESVIKTQFTVNKVLGIECLSPHVSGNPRWEWPGLIENIRDDVQEVMLRFFPDEESEDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure



No available structure.




T4CP

ID   5543 GenBank   WP_128321244
Name   traD_KGP19_RS28220_pJBIWA001_2 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: 86567.35 Da        Isoelectric Point: 5.0283

>WP_128321244.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Raoultella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLILMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKHSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDIWRECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDVQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRNLDTRVDARLNALLEAREAEGSLARTLFTPDAPAPELAEKDEKVGNPPEQSQPAE
SSGTSATVKVPSTAKTPEADESGQSPEVSNPAALLTKVVTVPLTRPRPAAATGTAAVASATDVPATPAGG
TEQALETQPAEQGQDMLPPGVNEYGEIDDMHAWDEWQSGEQTQRDMQRREEVNINHSHRRDEQDDIEIGG
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: 92523..118448

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KGP19_RS28045 (KGP19_27940) 88926..89468 + 543 WP_053390246 antirestriction protein -
KGP19_RS28050 (KGP19_27945) 89491..89913 - 423 WP_077268549 transglycosylase SLT domain-containing protein -
KGP19_RS28055 (KGP19_27950) 90419..90811 + 393 WP_053390193 conjugal transfer relaxosome DNA-binding protein TraM -
KGP19_RS28060 (KGP19_27955) 91050..91724 + 675 WP_223526248 hypothetical protein -
KGP19_RS28065 (KGP19_27960) 91918..92079 + 162 WP_172686697 TraY domain-containing protein -
KGP19_RS28070 (KGP19_27965) 92144..92509 + 366 WP_020314752 type IV conjugative transfer system pilin TraA -
KGP19_RS28075 (KGP19_27970) 92523..92828 + 306 WP_020323523 type IV conjugative transfer system protein TraL traL
KGP19_RS28080 (KGP19_27975) 92844..93410 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
KGP19_RS28085 (KGP19_27980) 93397..94131 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
KGP19_RS28090 (KGP19_27985) 94131..95552 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
KGP19_RS28095 (KGP19_27990) 95545..95979 + 435 WP_020322358 conjugal transfer protein TraP -
KGP19_RS28100 (KGP19_27995) 96013..96597 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
KGP19_RS28105 (KGP19_28000) 97210..97398 + 189 WP_053390286 hypothetical protein -
KGP19_RS28110 97482..97883 + 402 WP_064343532 hypothetical protein -
KGP19_RS28115 (KGP19_28010) 97880..98179 + 300 WP_053390308 hypothetical protein -
KGP19_RS28120 (KGP19_28015) 98267..98650 + 384 WP_042946290 hypothetical protein -
KGP19_RS28125 (KGP19_28020) 98743..101382 + 2640 WP_064343533 type IV secretion system protein TraC virb4
KGP19_RS28130 (KGP19_28025) 101382..101774 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
KGP19_RS28135 (KGP19_28030) 101771..102397 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
KGP19_RS28140 (KGP19_28035) 102441..103400 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
KGP19_RS28145 (KGP19_28040) 103413..104060 + 648 WP_064343536 type-F conjugative transfer system pilin assembly protein TrbC trbC
KGP19_RS28150 (KGP19_28045) 104057..104440 + 384 WP_053390297 hypothetical protein -
KGP19_RS28155 (KGP19_28050) 104437..106392 + 1956 WP_064359956 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KGP19_RS28160 (KGP19_28055) 106424..106684 + 261 WP_053390216 hypothetical protein -
KGP19_RS28165 (KGP19_28060) 106677..107288 + 612 WP_053390217 hypothetical protein -
KGP19_RS28170 (KGP19_28065) 107278..107520 + 243 WP_053390218 conjugal transfer protein TrbE -
KGP19_RS28175 (KGP19_28070) 107566..107892 + 327 WP_053390219 hypothetical protein -
KGP19_RS28180 (KGP19_28075) 107913..108665 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
KGP19_RS28185 (KGP19_28080) 108676..108912 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
KGP19_RS28190 (KGP19_28085) 108887..109447 + 561 WP_099973675 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KGP19_RS28195 (KGP19_28090) 109434..110804 + 1371 WP_128321280 conjugal transfer pilus assembly protein TraH traH
KGP19_RS28200 (KGP19_28095) 110804..113689 + 2886 WP_128321279 conjugal transfer mating-pair stabilization protein TraG traG
KGP19_RS28205 (KGP19_28100) 113703..114248 + 546 WP_101856566 conjugal transfer entry exclusion protein TraS -
KGP19_RS28210 (KGP19_28105) 114435..115166 + 732 WP_064349680 conjugal transfer complement resistance protein TraT -
KGP19_RS28215 115358..116011 + 654 WP_223526250 hypothetical protein -
KGP19_RS28220 (KGP19_28115) 116130..118448 + 2319 WP_128321244 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   8313 GenBank   NZ_CP074184
Plasmid name   pJBIWA001_2 Incompatibility group   IncFII
Plasmid size   129579 bp Coordinate of oriT [Strand]   90058..90107 [-]
Host baterium   Raoultella planticola strain JBIWA001

Cargo genes

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