Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104566
Name   oriT_STIN_84|unnamed1 in_silico
Organism   Klebsiella pneumoniae strain STIN_84
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP054998 (158665..158714 [+], 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_STIN_84|unnamed1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3292 GenBank   WP_239594436
Name   traI_HUZ56_RS25615_STIN_84|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: 190502.01 Da        Isoelectric Point: 5.7557

>WP_239594436.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDSAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNSTLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFNVVSEQ
LKARSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGDGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLSDTAKALSLIAAGGGRAVLSGDTDQLQSISPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDIDRALATIEQVTPERVPRKEGAWVPGSSVVEFTPTQEEEIRK
ALSKGESLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNNDRRALNGLIHDARRENGETGREEITLP
VLVTSNIRDGELRKLSTWTAHKGAVALVDNVYHRIDNVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEEITVSQGDRMRFSKSDPERGYVANSVWEVQSVSGDSVTLSDGKTTRTLTPKADEAQQHIDLAYAITA
HGAQGASEPYAIALEGMVGARKLMASFESAYVGLSRMKQHVQVYTDRREGWIKAIQHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNIGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPV
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1157)

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   3232 GenBank   WP_239594437
Name   traD_HUZ56_RS25620_STIN_84|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: 84993.90 Da        Isoelectric Point: 4.9159

>WP_239594437.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLSDLSCYVTLPGPYPAVKLAL
KYKPRPKITEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTESQASEQPESVSPPA
PAEMTVTPAPVKAPPTTKRPAAEPPVLPVTPVPLLNQKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 129557..156278

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ56_RS25620 (HUZ56_25565) 129557..131839 - 2283 WP_239594437 type IV conjugative transfer system coupling protein TraD virb4
HUZ56_RS25625 (HUZ56_25570) 132199..132930 - 732 WP_032415736 conjugal transfer complement resistance protein TraT -
HUZ56_RS25630 (HUZ56_25575) 133181..133783 - 603 WP_023280878 hypothetical protein -
HUZ56_RS25635 (HUZ56_25580) 133807..136629 - 2823 WP_114435908 conjugal transfer mating-pair stabilization protein TraG traG
HUZ56_RS25640 (HUZ56_25585) 136629..138008 - 1380 WP_164875722 conjugal transfer pilus assembly protein TraH traH
HUZ56_RS25645 (HUZ56_25590) 137986..138429 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
HUZ56_RS25650 (HUZ56_25595) 138475..139032 - 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ56_RS25655 (HUZ56_25600) 139004..139243 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
HUZ56_RS25660 (HUZ56_25605) 139254..140006 - 753 WP_114435907 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ56_RS25665 (HUZ56_25610) 140027..140353 - 327 WP_016529362 hypothetical protein -
HUZ56_RS25670 (HUZ56_25615) 140439..141407 - 969 WP_004099053 IS5-like element IS903B family transposase -
HUZ56_RS26760 141464..141649 - 186 WP_042922350 hypothetical protein -
HUZ56_RS25675 (HUZ56_25620) 141646..141882 - 237 WP_239594438 conjugal transfer protein TrbE -
HUZ56_RS25680 (HUZ56_25625) 141914..143869 - 1956 WP_114435906 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ56_RS25685 (HUZ56_25630) 143928..144566 - 639 WP_046622838 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ56_RS25690 (HUZ56_25635) 144579..145568 - 990 WP_239594439 conjugal transfer pilus assembly protein TraU traU
HUZ56_RS25695 (HUZ56_25640) 145565..145954 - 390 WP_128206239 hypothetical protein -
HUZ56_RS25700 (HUZ56_25645) 145996..146622 - 627 WP_032445234 type-F conjugative transfer system protein TraW traW
HUZ56_RS25705 (HUZ56_25650) 146622..147011 - 390 WP_004152591 type-F conjugative transfer system protein TrbI -
HUZ56_RS25710 (HUZ56_25655) 147011..149650 - 2640 WP_016528865 type IV secretion system protein TraC virb4
HUZ56_RS25715 (HUZ56_25660) 149722..150120 - 399 WP_239594440 hypothetical protein -
HUZ56_RS25720 (HUZ56_25665) 150145..150549 - 405 WP_023320104 hypothetical protein -
HUZ56_RS25725 (HUZ56_25670) 150616..150933 - 318 WP_016530481 hypothetical protein -
HUZ56_RS25730 (HUZ56_25675) 150934..151152 - 219 WP_004171484 hypothetical protein -
HUZ56_RS25735 (HUZ56_25680) 151176..151466 - 291 WP_032426790 hypothetical protein -
HUZ56_RS25740 151495..151893 - 399 WP_223177007 hypothetical protein -
HUZ56_RS25745 (HUZ56_25690) 152049..152618 - 570 WP_239594441 type IV conjugative transfer system lipoprotein TraV traV
HUZ56_RS25750 (HUZ56_25695) 152638..152793 - 156 WP_153587559 hypothetical protein -
HUZ56_RS25755 (HUZ56_25700) 152830..153243 - 414 Protein_156 conjugal transfer pilus-stabilizing protein TraP -
HUZ56_RS25760 (HUZ56_25705) 153236..154660 - 1425 WP_239594442 F-type conjugal transfer pilus assembly protein TraB traB
HUZ56_RS25765 (HUZ56_25710) 154660..155400 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
HUZ56_RS25770 (HUZ56_25715) 155387..155953 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
HUZ56_RS25775 (HUZ56_25720) 155973..156278 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HUZ56_RS25780 (HUZ56_25725) 156292..156660 - 369 WP_064147976 type IV conjugative transfer system pilin TraA -
HUZ56_RS25785 (HUZ56_25730) 156722..156928 - 207 WP_172412524 TraY domain-containing protein -
HUZ56_RS25790 (HUZ56_25735) 157061..157780 - 720 WP_239594443 conjugal transfer protein TrbJ -
HUZ56_RS25795 (HUZ56_25740) 157980..158396 - 417 WP_074181767 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ56_RS25800 (HUZ56_25745) 158859..159266 + 408 WP_226331063 transglycosylase SLT domain-containing protein -
HUZ56_RS25805 (HUZ56_25750) 159304..159834 - 531 WP_023292160 antirestriction protein -

Host bacterium

ID   5005 GenBank   NZ_CP054998
Plasmid name   STIN_84|unnamed1 Incompatibility group   IncFIB
Plasmid size   197765 bp Coordinate of oriT [Strand]   158665..158714 [+]
Host baterium   Klebsiella pneumoniae strain STIN_84

Cargo genes

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