Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120814
Name   oriT_p23_C in_silico
Organism   Raoultella ornithinolytica strain 23
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048352 (105535..105583 [-], 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_C
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13127 GenBank   WP_162661895
Name   traI_GZS10_RS30260_p23_C 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: 190356.62 Da        Isoelectric Point: 5.5084

>WP_162661895.1 conjugative transfer relaxase/helicase TraI [Raoultella ornithinolytica]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTNNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLGSDTVGKTGFSENILANRIAFGKIYQSTLRADVES
MGYKTVDAGKHGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADTRAKELASAPAAPVKTDVPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLEA
KPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDTAVVRQSPF
SDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHIIAADNRSREFLSADARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKMSLKETLSMLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGKQATADIISEPEKGARYSRLAQEFAASVREGQESVAQISGSREQGILNGLIRETLKSEGVLGEKDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRQHDRFVIDRVTASSNMLTLRDKEGERLDMKVSAVD
SQWTLFRADKLTVAEGERLAVLGKIPDTRLKGGESVTVLKAEEGQLTVQRPGQKTTQSLSVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQGTARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIASQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
SQIQAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDNVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQFRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQVTPEQVPRKDGAWVPENSVVEFTPAQEEAIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
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   7322 GenBank   WP_020805752
Name   WP_020805752_p23_C insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   15407 GenBank   WP_075606915
Name   traD_GZS10_RS30255_p23_C 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: 86712.47 Da        Isoelectric Point: 5.0825

>WP_075606915.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLILMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGKSLEYNSEQILADKYTIWCGEQLWTSFVFAAIVSLTVCIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKHSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDIWRECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFSEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLKNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLGMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKSRPKIAEGFILRNLDTRTDARLDTLLEAREAESSHARTLFTPDAPAPELAEKDEKVGNPPEQSQPAE
SSGTPATVKVPSTAKTPEADESGQSPEVSNPAALLTKVVTVPLTRPRPAAATGTAAVASATDVRATPAGG
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: 104977..132760

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GZS10_RS30030 (GZS10_30030) 100002..100352 + 351 WP_023287104 hypothetical protein -
GZS10_RS30045 (GZS10_30045) 100984..101340 + 357 WP_019706019 hypothetical protein -
GZS10_RS30050 (GZS10_30050) 101401..101613 + 213 WP_019706020 hypothetical protein -
GZS10_RS30055 (GZS10_30055) 101624..101848 + 225 WP_014343499 hypothetical protein -
GZS10_RS30060 (GZS10_30060) 101929..102249 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
GZS10_RS30065 (GZS10_30065) 102239..102517 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
GZS10_RS30070 (GZS10_30070) 102518..102931 + 414 WP_023287139 type II toxin-antitoxin system HigA family antitoxin -
GZS10_RS30085 (GZS10_30085) 103761..104582 + 822 WP_004152492 DUF932 domain-containing protein -
GZS10_RS30090 (GZS10_30090) 104615..104944 + 330 WP_011977736 DUF5983 family protein -
GZS10_RS30095 (GZS10_30095) 104977..105462 - 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
GZS10_RS30100 (GZS10_30100) 105894..106286 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
GZS10_RS31315 106524..107225 + 702 WP_223174962 hypothetical protein -
GZS10_RS30110 (GZS10_30110) 107311..107511 + 201 WP_048289787 TraY domain-containing protein -
GZS10_RS30115 (GZS10_30115) 107580..107948 + 369 WP_064343525 type IV conjugative transfer system pilin TraA -
GZS10_RS30120 (GZS10_30120) 107962..108267 + 306 WP_064343526 type IV conjugative transfer system protein TraL traL
GZS10_RS30125 (GZS10_30125) 108283..108849 + 567 WP_064359954 type IV conjugative transfer system protein TraE traE
GZS10_RS30130 (GZS10_30130) 108836..109570 + 735 WP_064343528 type-F conjugative transfer system secretin TraK traK
GZS10_RS30135 (GZS10_30135) 109570..110991 + 1422 WP_053390199 F-type conjugal transfer pilus assembly protein TraB traB
GZS10_RS30140 (GZS10_30140) 110984..111418 + 435 WP_020322358 conjugal transfer protein TraP -
GZS10_RS30145 (GZS10_30145) 111452..112036 + 585 WP_064343530 type IV conjugative transfer system lipoprotein TraV traV
GZS10_RS30150 (GZS10_30150) 112649..112837 + 189 WP_053390286 hypothetical protein -
GZS10_RS31320 112921..113322 + 402 WP_064343532 hypothetical protein -
GZS10_RS30160 (GZS10_30160) 113319..113618 + 300 WP_053390308 hypothetical protein -
GZS10_RS30165 (GZS10_30165) 113706..114089 + 384 WP_064359955 hypothetical protein -
GZS10_RS30170 (GZS10_30170) 114182..116821 + 2640 WP_064343533 type IV secretion system protein TraC virb4
GZS10_RS30175 (GZS10_30175) 116821..117213 + 393 WP_064343534 type-F conjugative transfer system protein TrbI -
GZS10_RS30180 (GZS10_30180) 117210..117836 + 627 WP_064343535 type-F conjugative transfer system protein TraW traW
GZS10_RS30185 (GZS10_30185) 117880..118839 + 960 WP_229295972 conjugal transfer pilus assembly protein TraU traU
GZS10_RS30190 (GZS10_30190) 118852..119478 + 627 WP_075606921 type-F conjugative transfer system pilin assembly protein TrbC trbC
GZS10_RS30195 (GZS10_30195) 119475..121430 + 1956 WP_162661894 type-F conjugative transfer system mating-pair stabilization protein TraN traN
GZS10_RS30200 (GZS10_30200) 121462..121722 + 261 WP_053390216 hypothetical protein -
GZS10_RS30205 (GZS10_30205) 121715..122326 + 612 WP_053390217 hypothetical protein -
GZS10_RS30210 (GZS10_30210) 122316..122558 + 243 WP_053390218 conjugal transfer protein TrbE -
GZS10_RS30215 (GZS10_30215) 122604..122930 + 327 WP_053390219 hypothetical protein -
GZS10_RS30220 (GZS10_30220) 122951..123703 + 753 WP_053390220 type-F conjugative transfer system pilin assembly protein TraF traF
GZS10_RS30225 (GZS10_30225) 123714..123950 + 237 WP_053390221 type-F conjugative transfer system pilin chaperone TraQ -
GZS10_RS30230 (GZS10_30230) 123925..124485 + 561 WP_039698500 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
GZS10_RS30235 (GZS10_30235) 124472..125842 + 1371 WP_075606918 conjugal transfer pilus assembly protein TraH traH
GZS10_RS30240 (GZS10_30240) 125842..128697 + 2856 WP_075606917 conjugal transfer mating-pair stabilization protein TraG traG
GZS10_RS30245 (GZS10_30245) 128714..129385 + 672 WP_088883382 hypothetical protein -
GZS10_RS31325 129631..130323 + 693 WP_202395549 hypothetical protein -
GZS10_RS30255 (GZS10_30255) 130442..132760 + 2319 WP_075606915 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21243 GenBank   NZ_CP048352
Plasmid name   p23_C Incompatibility group   IncFIB
Plasmid size   143891 bp Coordinate of oriT [Strand]   105535..105583 [-]
Host baterium   Raoultella ornithinolytica strain 23

Cargo genes

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