Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116767
Name   oriT_p602815-CTXM in_silico
Organism   Raoultella ornithinolytica strain 170602815
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MZ753460 (106176..106224 [+], 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_p602815-CTXM
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10696 GenBank   WP_063160318
Name   traI_NLJ19_RS00385_p602815-CTXM 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: 190491.29 Da        Isoelectric Point: 6.2578

>WP_063160318.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAEALGLEGKVDKQIFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVQKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENILANRIAFGKIYQNTLRADVES
LGYRTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTSDASVVRQAPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHKTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VAHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADIAIMKEIVRQVPELRPAVYSLIERDVHHALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPTQEKAIQK
ALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKKAEQTAREMAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




Auxiliary protein

ID   6298 GenBank   WP_004197733
Name   WP_004197733_p602815-CTXM insolico UniProt ID   A0A0E3KB00
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14835.90 Da        Isoelectric Point: 4.6012

>WP_004197733.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKILGIECLSPHVKDDPRWQWKSMVLNIQEDVQEAMRNFFPDEDAEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure


Source ID Structure
AlphaFold DB A0A0E3KB00


T4CP

ID   12496 GenBank   WP_009309880
Name   traD_NLJ19_RS00390_p602815-CTXM insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85571.58 Da        Isoelectric Point: 5.1733

>WP_009309880.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPDDAGSHAGEQPEPVSQPA
PAVMTVTPAPVKSPPTTKRPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAGTAATASSAGTPAAAAGGTE
QVLAQQSAEQGQAMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDLEIGGNF

  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: 76639..106782

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NLJ19_RS00390 76639..78948 - 2310 WP_009309880 type IV conjugative transfer system coupling protein TraD virb4
NLJ19_RS00395 79074..79766 - 693 WP_009309879 hypothetical protein -
NLJ19_RS00400 80501..83374 - 2874 WP_009309878 conjugal transfer mating-pair stabilization protein TraG traG
NLJ19_RS00405 83374..84744 - 1371 WP_009309877 conjugal transfer pilus assembly protein TraH traH
NLJ19_RS00410 84731..85159 - 429 WP_004152689 hypothetical protein -
NLJ19_RS00415 85152..85724 - 573 WP_063160290 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NLJ19_RS00420 85696..85935 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
NLJ19_RS00425 85946..86698 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
NLJ19_RS00430 86719..87045 - 327 WP_004194451 hypothetical protein -
NLJ19_RS00435 87058..87306 - 249 WP_004152675 hypothetical protein -
NLJ19_RS00440 87284..87538 - 255 WP_004195500 conjugal transfer protein TrbE -
NLJ19_RS00445 87570..89525 - 1956 WP_148866277 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NLJ19_RS00450 89584..90231 - 648 WP_039698503 type-F conjugative transfer system pilin assembly protein TrbC trbC
NLJ19_RS00455 90375..90977 - 603 WP_022631520 hypothetical protein -
NLJ19_RS00460 91271..91723 + 453 WP_172686240 hypothetical protein -
NLJ19_RS00465 91698..92246 - 549 WP_022631518 hypothetical protein -
NLJ19_RS00470 92261..93244 - 984 WP_223176982 conjugal transfer pilus assembly protein TraU traU
NLJ19_RS00475 93264..93890 - 627 WP_020314628 type-F conjugative transfer system protein TraW traW
NLJ19_RS00480 93890..94282 - 393 WP_080816432 type-F conjugative transfer system protein TrbI -
NLJ19_RS00485 94279..96918 - 2640 WP_042946320 type IV secretion system protein TraC virb4
NLJ19_RS00490 96990..97388 - 399 WP_074186017 hypothetical protein -
NLJ19_RS00495 97396..97686 - 291 WP_023340940 hypothetical protein -
NLJ19_RS00500 97683..98087 - 405 WP_042939116 hypothetical protein -
NLJ19_RS00505 98154..98465 - 312 WP_023316403 hypothetical protein -
NLJ19_RS00510 98466..98684 - 219 WP_023316402 hypothetical protein -
NLJ19_RS00515 98708..98992 - 285 WP_023316401 hypothetical protein -
NLJ19_RS00520 98997..99407 - 411 WP_020805613 hypothetical protein -
NLJ19_RS00525 99539..100108 - 570 WP_023340942 type IV conjugative transfer system lipoprotein TraV traV
NLJ19_RS00530 100131..100727 - 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
NLJ19_RS00535 100720..102144 - 1425 WP_042946342 F-type conjugal transfer pilus assembly protein TraB traB
NLJ19_RS00540 102144..102884 - 741 WP_032738531 type-F conjugative transfer system secretin TraK traK
NLJ19_RS00545 102871..103437 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
NLJ19_RS00550 103457..103762 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
NLJ19_RS00555 103776..104144 - 369 WP_063267011 type IV conjugative transfer system pilin TraA -
NLJ19_RS00560 104206..104370 - 165 WP_032444506 TraY domain-containing protein -
NLJ19_RS00565 104562..105236 - 675 WP_004197737 hypothetical protein -
NLJ19_RS00570 105475..105864 - 390 WP_004197733 conjugal transfer relaxosome DNA-binding protein TraM -
NLJ19_RS00575 106297..106782 + 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
NLJ19_RS00580 106815..107144 - 330 WP_011977736 DUF5983 family protein -
NLJ19_RS00585 107177..107998 - 822 WP_004152492 DUF932 domain-containing protein -
NLJ19_RS00590 108818..109651 - 834 WP_004152751 N-6 DNA methylase -
NLJ19_RS00595 109702..109848 - 147 WP_004152750 hypothetical protein -
NLJ19_RS00600 109943..110290 - 348 WP_004152749 hypothetical protein -
NLJ19_RS00605 110347..110700 - 354 WP_004152748 hypothetical protein -
NLJ19_RS00610 111330..111680 - 351 WP_004153414 hypothetical protein -

Host bacterium

ID   17200 GenBank   NZ_MZ753460
Plasmid name   p602815-CTXM Incompatibility group   IncFII
Plasmid size   138583 bp Coordinate of oriT [Strand]   106176..106224 [+]
Host baterium   Raoultella ornithinolytica strain 170602815

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9