Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101105
Name   oriT_pIncFII in_silico
Organism   Klebsiella pneumoniae strain BA6039
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JANTIB010000019 (42998..43047 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pIncFII
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1126 GenBank   WP_057729326
Name   traI_NXY53_RS23910_pIncFII insolico UniProt ID   A0A6G9HZM5
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190782.72 Da        Isoelectric Point: 6.1403

>WP_057729326.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELLEAAGPDASLKSRDVAALDTRKSKEAIDPAENMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETAMVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVLGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLTGDDRP
WNPGAITGGRIWAEPAPVAPVPQTGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   685 GenBank   WP_016831058
Name   traD_NXY53_RS23915_pIncFII 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: 84900.95 Da        Isoelectric Point: 5.0541

>WP_016831058.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYAAWLADDQTQRDMQRREEVNINHNHRHDEQDDVEIGGNI

  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: 13580..43605

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NXY53_RS23915 (NXY53_23895) 13580..15862 - 2283 WP_016831058 type IV conjugative transfer system coupling protein TraD virb4
NXY53_RS23920 (NXY53_23900) 15989..16678 - 690 WP_072159541 hypothetical protein -
NXY53_RS23925 (NXY53_23905) 16871..17602 - 732 WP_016831056 conjugal transfer complement resistance protein TraT -
NXY53_RS23930 (NXY53_23910) 17853..18455 - 603 WP_071604857 hypothetical protein -
NXY53_RS23935 (NXY53_23915) 18478..21300 - 2823 WP_020325096 conjugal transfer mating-pair stabilization protein TraG traG
NXY53_RS23940 (NXY53_23920) 21300..22679 - 1380 WP_072159542 conjugal transfer pilus assembly protein TraH traH
NXY53_RS23945 (NXY53_23925) 22657..23100 - 444 WP_016831053 F-type conjugal transfer protein TrbF -
NXY53_RS23950 (NXY53_23930) 23146..23703 - 558 WP_020325119 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NXY53_RS23955 (NXY53_23935) 23675..23914 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
NXY53_RS23960 (NXY53_23940) 23925..24677 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
NXY53_RS23965 (NXY53_23945) 24698..25024 - 327 WP_016831051 hypothetical protein -
NXY53_RS23970 (NXY53_23950) 25037..25285 - 249 WP_004152675 hypothetical protein -
NXY53_RS23975 (NXY53_23955) 25263..25517 - 255 WP_015065558 conjugal transfer protein TrbE -
NXY53_RS23980 (NXY53_23960) 25549..27534 - 1986 WP_020325104 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NXY53_RS23985 (NXY53_23965) 27593..28240 - 648 WP_016831049 type-F conjugative transfer system pilin assembly protein TrbC trbC
NXY53_RS23990 (NXY53_23970) 28516..29505 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
NXY53_RS23995 (NXY53_23975) 29502..29903 - 402 WP_020325101 hypothetical protein -
NXY53_RS24000 (NXY53_23980) 29938..30573 - 636 WP_020325113 type-F conjugative transfer system protein TraW traW
NXY53_RS24005 (NXY53_23985) 30573..30962 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
NXY53_RS24010 (NXY53_23990) 30962..33601 - 2640 WP_016831045 type IV secretion system protein TraC virb4
NXY53_RS24015 (NXY53_23995) 33673..34071 - 399 WP_023158008 hypothetical protein -
NXY53_RS24020 (NXY53_24000) 34079..34297 - 219 WP_072196435 hypothetical protein -
NXY53_RS24025 (NXY53_24005) 34311..34469 - 159 WP_223372464 hypothetical protein -
NXY53_RS24030 (NXY53_24010) 34512..34916 - 405 WP_016831042 hypothetical protein -
NXY53_RS24035 (NXY53_24015) 34983..35294 - 312 WP_016831041 hypothetical protein -
NXY53_RS24040 (NXY53_24020) 35295..35513 - 219 WP_014386199 hypothetical protein -
NXY53_RS24045 (NXY53_24025) 35537..35826 - 290 Protein_41 hypothetical protein -
NXY53_RS24050 (NXY53_24030) 35831..36241 - 411 WP_032433731 hypothetical protein -
NXY53_RS24055 (NXY53_24035) 36373..36957 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
NXY53_RS24060 (NXY53_24040) 36980..37576 - 597 Protein_44 conjugal transfer pilus-stabilizing protein TraP -
NXY53_RS24065 (NXY53_24045) 37569..38993 - 1425 WP_020325105 F-type conjugal transfer pilus assembly protein TraB traB
NXY53_RS24070 (NXY53_24050) 38993..39733 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
NXY53_RS24075 (NXY53_24055) 39720..40286 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
NXY53_RS24080 (NXY53_24060) 40306..40611 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
NXY53_RS24085 (NXY53_24065) 40625..40993 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
NXY53_RS24090 (NXY53_24070) 41055..41261 - 207 WP_171773970 TraY domain-containing protein -
NXY53_RS24095 (NXY53_24075) 41394..42113 - 720 WP_016831034 conjugal transfer protein TrbJ -
NXY53_RS24100 (NXY53_24080) 42313..42729 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
NXY53_RS24105 (NXY53_24085) 43120..43605 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
NXY53_RS24110 (NXY53_24090) 43638..43967 - 330 WP_011977736 DUF5983 family protein -
NXY53_RS24115 (NXY53_24095) 44000..44821 - 822 WP_004182076 DUF932 domain-containing protein -

Host bacterium

ID   1549 GenBank   NZ_JANTIB010000019
Plasmid name   pIncFII Incompatibility group   IncFII
Plasmid size   44914 bp Coordinate of oriT [Strand]   42998..43047 [+]
Host baterium   Klebsiella pneumoniae strain BA6039

Cargo genes

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