Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106640
Name   oriT_RHB08-SO-C04|unnamed1 in_silico
Organism   Klebsiella aerogenes strain RHB08-SO-C04
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099261 (144908..144957 [+], 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_RHB08-SO-C04|unnamed1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4397 GenBank   WP_279281574
Name   traI_NFJ54_RS26415_RHB08-SO-C04|unnamed1 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: 190408.22 Da        Isoelectric Point: 6.2391

>WP_279281574.1 conjugative transfer relaxase/helicase TraI [Klebsiella aerogenes]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALNTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRSHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQLELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQGAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPSQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIQK
AVSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVAGDSVTLSDGKTTRTLTPKADQTQQHIDLAYTITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATVHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGTEKMTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(970-1156)

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   1959 GenBank   WP_279281584
Name   WP_279281584_RHB08-SO-C04|unnamed1 insolico UniProt ID   _
Length   72 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 72 a.a.        Molecular weight: 7856.13 Da        Isoelectric Point: 10.2119

>WP_279281584.1 TraK [Klebsiella aerogenes]
MKTLLTSGCTNQRGAGQSGVTFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKK
ER

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   4428 GenBank   WP_086625007
Name   traD_NFJ54_RS26420_RHB08-SO-C04|unnamed1 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84895.84 Da        Isoelectric Point: 4.9578

>WP_086625007.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPESVSPPA
PAEMTVTPAPVKAPPTTKRPAAEPPVLPVTPVPLLNPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDSWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 116516..145509

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NFJ54_RS26420 (NFJ54_26380) 116516..118798 - 2283 WP_086625007 type IV conjugative transfer system coupling protein TraD virb4
NFJ54_RS26425 (NFJ54_26385) 118925..119614 - 690 WP_162985117 hypothetical protein -
NFJ54_RS26430 (NFJ54_26390) 119807..120538 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
NFJ54_RS26435 (NFJ54_26395) 120731..121258 - 528 WP_016528837 conjugal transfer entry exclusion protein TraS -
NFJ54_RS26440 (NFJ54_26400) 121264..124113 - 2850 WP_117242601 conjugal transfer mating-pair stabilization protein TraG traG
NFJ54_RS26445 (NFJ54_26405) 124113..125492 - 1380 WP_279281575 conjugal transfer pilus assembly protein TraH traH
NFJ54_RS26450 (NFJ54_26410) 125470..125913 - 444 WP_094067299 F-type conjugal transfer protein TrbF -
NFJ54_RS26455 (NFJ54_26415) 125959..126516 - 558 WP_004152678 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NFJ54_RS26460 (NFJ54_26420) 126488..126727 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
NFJ54_RS26465 (NFJ54_26425) 126738..127490 - 753 WP_029497422 type-F conjugative transfer system pilin assembly protein TraF traF
NFJ54_RS26470 (NFJ54_26430) 127511..127837 - 327 WP_279281576 hypothetical protein -
NFJ54_RS26475 (NFJ54_26435) 127850..128098 - 249 WP_004152675 hypothetical protein -
NFJ54_RS26480 (NFJ54_26440) 128076..128330 - 255 WP_004152674 conjugal transfer protein TrbE -
NFJ54_RS26485 (NFJ54_26445) 128362..130317 - 1956 WP_075253038 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NFJ54_RS26490 (NFJ54_26450) 130376..131014 - 639 WP_015065635 type-F conjugative transfer system pilin assembly protein TrbC trbC
NFJ54_RS26495 (NFJ54_26455) 131027..132016 - 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
NFJ54_RS26500 (NFJ54_26460) 132013..132414 - 402 WP_004194979 hypothetical protein -
NFJ54_RS26505 (NFJ54_26465) 132449..133084 - 636 WP_029497419 type-F conjugative transfer system protein TraW traW
NFJ54_RS26510 (NFJ54_26470) 133084..133473 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
NFJ54_RS26515 (NFJ54_26475) 133473..136112 - 2640 WP_013214024 type IV secretion system protein TraC virb4
NFJ54_RS26520 (NFJ54_26480) 136184..136582 - 399 WP_023179972 hypothetical protein -
NFJ54_RS26525 (NFJ54_26485) 136764..136916 - 153 WP_224518895 hypothetical protein -
NFJ54_RS26530 (NFJ54_26490) 136959..137363 - 405 WP_004197817 hypothetical protein -
NFJ54_RS26535 (NFJ54_26495) 137430..137741 - 312 WP_279281577 hypothetical protein -
NFJ54_RS26540 (NFJ54_26500) 137742..137960 - 219 WP_004195468 hypothetical protein -
NFJ54_RS26545 (NFJ54_26505) 138283..138867 - 585 WP_020277945 type IV conjugative transfer system lipoprotein TraV traV
NFJ54_RS26550 (NFJ54_26510) 138890..139486 - 597 WP_029497416 conjugal transfer pilus-stabilizing protein TraP -
NFJ54_RS26555 (NFJ54_26515) 139479..140903 - 1425 WP_004233801 F-type conjugal transfer pilus assembly protein TraB traB
NFJ54_RS26560 (NFJ54_26520) 140903..141643 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
NFJ54_RS26565 (NFJ54_26525) 141630..142196 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
NFJ54_RS26570 (NFJ54_26530) 142216..142521 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
NFJ54_RS26575 (NFJ54_26535) 142535..142903 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
NFJ54_RS26580 (NFJ54_26540) 142965..143171 - 207 WP_171773970 TraY domain-containing protein -
NFJ54_RS26585 (NFJ54_26545) 143304..144023 - 720 WP_075253039 conjugal transfer protein TrbJ -
NFJ54_RS26590 (NFJ54_26550) 144223..144639 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
NFJ54_RS26595 (NFJ54_26555) 145102..145509 + 408 WP_228728786 transglycosylase SLT domain-containing protein virB1
NFJ54_RS26600 (NFJ54_26560) 145547..146077 - 531 WP_049070338 antirestriction protein -
NFJ54_RS26605 (NFJ54_26565) 146269..146499 + 231 WP_049070336 hypothetical protein -
NFJ54_RS26610 (NFJ54_26570) 146737..147965 + 1229 WP_089541817 IS3 family transposase -
NFJ54_RS26615 (NFJ54_26575) 147936..148658 - 723 WP_279281578 IS6-like element IS26 family transposase -
NFJ54_RS26620 (NFJ54_26580) 148735..149661 - 927 WP_001554380 LysR family transcriptional regulator -

Host bacterium

ID   7077 GenBank   NZ_CP099261
Plasmid name   RHB08-SO-C04|unnamed1 Incompatibility group   IncFIB
Plasmid size   183022 bp Coordinate of oriT [Strand]   144908..144957 [+]
Host baterium   Klebsiella aerogenes strain RHB08-SO-C04

Cargo genes

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