Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120813
Name   oriT_p23_B in_silico
Organism   Raoultella ornithinolytica strain 23
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048351 (107093..107141 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_p23_B
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13126 GenBank   WP_110246679
Name   traI_GZS10_RS29395_p23_B 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: 190470.20 Da        Isoelectric Point: 6.0801

>WP_110246679.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGQQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMESWDPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTIQ
AQIWSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIKK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(970-1156)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   7321 GenBank   WP_087829209
Name   WP_087829209_p23_B insolico UniProt ID   _
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14907.97 Da        Isoelectric Point: 4.5248

>WP_087829209.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure



No available structure.




T4CP

ID   15406 GenBank   WP_095033689
Name   traD_GZS10_RS29390_p23_B insolico UniProt ID   _
Length   761 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 761 a.a.        Molecular weight: 85308.33 Da        Isoelectric Point: 4.9677

>WP_095033689.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFIFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRSLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPAEVTV
SPAPVKATQTTKMPAEEPSVRATEPPVLRVTTVPLIKPKAAGTAATASSAGTPVAPAGGTEQELVQHSTE
QGRDMLPAGMNEDGVIEDMQAYDAWLADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 106535..135305

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GZS10_RS29160 (GZS10_29160) 101639..101989 + 351 WP_004153414 hypothetical protein -
GZS10_RS29175 (GZS10_29175) 102619..102972 + 354 WP_004152748 hypothetical protein -
GZS10_RS29180 (GZS10_29180) 103029..103376 + 348 WP_004152749 hypothetical protein -
GZS10_RS29185 (GZS10_29185) 103471..103617 + 147 WP_004152750 hypothetical protein -
GZS10_RS29190 (GZS10_29190) 103668..104501 + 834 WP_004152751 N-6 DNA methylase -
GZS10_RS29200 (GZS10_29200) 105319..106140 + 822 WP_004152492 DUF932 domain-containing protein -
GZS10_RS29205 (GZS10_29205) 106173..106502 + 330 WP_011977736 DUF5983 family protein -
GZS10_RS29210 (GZS10_29210) 106535..107020 - 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
GZS10_RS29215 (GZS10_29215) 107453..107842 + 390 WP_087829209 conjugal transfer relaxosome DNA-binding protein TraM -
GZS10_RS29220 (GZS10_29220) 108081..108755 + 675 WP_095033684 hypothetical protein -
GZS10_RS29225 (GZS10_29225) 108947..109111 + 165 WP_032444506 TraY domain-containing protein -
GZS10_RS29230 (GZS10_29230) 109173..109541 + 369 WP_087829211 type IV conjugative transfer system pilin TraA -
GZS10_RS29235 (GZS10_29235) 109555..109860 + 306 WP_087829212 type IV conjugative transfer system protein TraL traL
GZS10_RS29240 (GZS10_29240) 109880..110446 + 567 WP_064373744 type IV conjugative transfer system protein TraE traE
GZS10_RS29245 (GZS10_29245) 110433..111173 + 741 WP_020804840 type-F conjugative transfer system secretin TraK traK
GZS10_RS29250 (GZS10_29250) 111173..112597 + 1425 WP_023316397 F-type conjugal transfer pilus assembly protein TraB traB
GZS10_RS29255 (GZS10_29255) 112590..113186 + 597 WP_023316398 conjugal transfer pilus-stabilizing protein TraP -
GZS10_RS29260 (GZS10_29260) 113209..113778 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
GZS10_RS29265 (GZS10_29265) 113910..114320 + 411 WP_023316400 hypothetical protein -
GZS10_RS29270 (GZS10_29270) 114325..114609 + 285 WP_023316401 hypothetical protein -
GZS10_RS29275 (GZS10_29275) 114633..114851 + 219 WP_023316402 hypothetical protein -
GZS10_RS29280 (GZS10_29280) 114852..115163 + 312 WP_023316403 hypothetical protein -
GZS10_RS29285 (GZS10_29285) 115230..115634 + 405 WP_023316404 hypothetical protein -
GZS10_RS29290 (GZS10_29290) 115631..115921 + 291 WP_020323516 hypothetical protein -
GZS10_RS29295 (GZS10_29295) 115929..116327 + 399 WP_072156904 hypothetical protein -
GZS10_RS29300 (GZS10_29300) 116399..119038 + 2640 WP_020323518 type IV secretion system protein TraC virb4
GZS10_RS29305 (GZS10_29305) 119038..119427 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
GZS10_RS29310 (GZS10_29310) 119427..120053 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
GZS10_RS29315 (GZS10_29315) 120097..121056 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
GZS10_RS29320 (GZS10_29320) 121069..121707 + 639 WP_064182677 type-F conjugative transfer system pilin assembly protein TrbC trbC
GZS10_RS29325 (GZS10_29325) 121766..123721 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GZS10_RS29330 (GZS10_29330) 123754..124035 + 282 WP_022644736 hypothetical protein -
GZS10_RS29335 (GZS10_29335) 124025..124252 + 228 WP_012540032 conjugal transfer protein TrbE -
GZS10_RS29340 (GZS10_29340) 124263..124589 + 327 WP_020323521 hypothetical protein -
GZS10_RS29345 (GZS10_29345) 124610..125362 + 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
GZS10_RS29350 (GZS10_29350) 125817..126056 + 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
GZS10_RS29355 (GZS10_29355) 126028..126585 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GZS10_RS29360 (GZS10_29360) 126631..127074 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
GZS10_RS29365 (GZS10_29365) 127052..128431 + 1380 WP_162495503 conjugal transfer pilus assembly protein TraH traH
GZS10_RS29370 (GZS10_29370) 128431..131280 + 2850 WP_032744228 conjugal transfer mating-pair stabilization protein TraG traG
GZS10_RS29375 (GZS10_29375) 131286..131813 + 528 WP_020803849 hypothetical protein -
GZS10_RS31285 131996..132664 + 669 WP_020803846 hypothetical protein -
GZS10_RS29385 (GZS10_29385) 132688..132948 + 261 WP_020803850 hypothetical protein -
GZS10_RS29390 (GZS10_29390) 133020..135305 + 2286 WP_095033689 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21242 GenBank   NZ_CP048351
Plasmid name   p23_B Incompatibility group   IncFII
Plasmid size   146470 bp Coordinate of oriT [Strand]   107093..107141 [-]
Host baterium   Raoultella ornithinolytica strain 23

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9