Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117407
Name   oriT_pTMSNI47-3 in_silico
Organism   Klebsiella quasipneumoniae strain SNI47
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP019690 (48978..49027 [-], 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_pTMSNI47-3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11090 GenBank   WP_151819948
Name   traI_TMSI_RS29900_pTMSNI47-3 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: 190451.11 Da        Isoelectric Point: 5.9703

>WP_151819948.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDGGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQLELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1432-1554)

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

AAA domain (AAA_30)

(969-1156)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   12951 GenBank   WP_040215031
Name   traD_TMSI_RS29895_pTMSNI47-3 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: 85020.03 Da        Isoelectric Point: 4.9634

>WP_040215031.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLTMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDERVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 48420..78420

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
TMSI_RS31445 43544..43789 - 246 WP_306453680 hypothetical protein -
TMSI_RS29670 (TMSI_56870) 43771..44751 - 981 WP_000019445 IS5-like element ISKpn26 family transposase -
TMSI_RS29675 (TMSI_56880) 44844..45056 + 213 WP_019706020 hypothetical protein -
TMSI_RS29680 (TMSI_56890) 45067..45291 + 225 WP_014343499 hypothetical protein -
TMSI_RS29685 (TMSI_56900) 45372..45692 + 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
TMSI_RS29690 (TMSI_56910) 45682..45960 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
TMSI_RS29695 (TMSI_56920) 45961..46374 + 414 WP_023287139 type II toxin-antitoxin system HigA family antitoxin -
TMSI_RS29705 (TMSI_56940) 47204..48025 + 822 WP_004152492 DUF932 domain-containing protein -
TMSI_RS29710 (TMSI_56950) 48058..48387 + 330 WP_047066474 DUF5983 family protein -
TMSI_RS29715 (TMSI_56960) 48420..48905 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
TMSI_RS29720 (TMSI_56970) 49296..49712 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
TMSI_RS29725 (TMSI_56980) 49912..50631 + 720 WP_015065526 hypothetical protein -
TMSI_RS29730 (TMSI_56990) 50764..50967 + 204 WP_171486139 TraY domain-containing protein -
TMSI_RS29735 (TMSI_57000) 51032..51400 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
TMSI_RS29740 (TMSI_57010) 51414..51719 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
TMSI_RS29745 (TMSI_57020) 51739..52305 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
TMSI_RS29750 (TMSI_57030) 52292..53032 + 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
TMSI_RS29755 (TMSI_57040) 53032..54456 + 1425 WP_032426793 F-type conjugal transfer pilus assembly protein TraB traB
TMSI_RS29760 (TMSI_57050) 54570..55154 + 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
TMSI_RS29765 (TMSI_57060) 55286..55696 + 411 WP_004152499 hypothetical protein -
TMSI_RS29770 (TMSI_57070) 55802..56020 + 219 WP_004152501 hypothetical protein -
TMSI_RS29775 (TMSI_57080) 56021..56332 + 312 WP_004152502 hypothetical protein -
TMSI_RS29780 (TMSI_57090) 56399..56803 + 405 WP_004152503 hypothetical protein -
TMSI_RS29785 (TMSI_57100) 56846..57235 + 390 WP_004153076 hypothetical protein -
TMSI_RS29790 57243..57641 + 399 WP_011977783 hypothetical protein -
TMSI_RS29795 (TMSI_57110) 57713..60352 + 2640 WP_004152505 type IV secretion system protein TraC virb4
TMSI_RS29800 (TMSI_57120) 60352..60741 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
TMSI_RS29805 (TMSI_57130) 60741..61367 + 627 WP_004152507 type-F conjugative transfer system protein TraW traW
TMSI_RS29810 (TMSI_57140) 61409..61798 + 390 WP_032445235 hypothetical protein -
TMSI_RS29815 (TMSI_57150) 61795..62784 + 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
TMSI_RS29820 (TMSI_57160) 62797..63435 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
TMSI_RS29825 (TMSI_57170) 63494..65449 + 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
TMSI_RS29830 (TMSI_57180) 65481..65735 + 255 WP_004152674 conjugal transfer protein TrbE -
TMSI_RS29835 (TMSI_57190) 65713..65961 + 249 WP_004152675 hypothetical protein -
TMSI_RS29840 (TMSI_57200) 65974..66300 + 327 WP_004144402 hypothetical protein -
TMSI_RS29845 (TMSI_57210) 66321..67073 + 753 WP_020803149 type-F conjugative transfer system pilin assembly protein TraF traF
TMSI_RS29850 (TMSI_57220) 67084..67323 + 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
TMSI_RS29855 (TMSI_57230) 67295..67867 + 573 WP_023292147 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
TMSI_RS29860 (TMSI_57240) 67860..68288 + 429 WP_015065560 hypothetical protein -
TMSI_RS29865 (TMSI_57250) 68275..69645 + 1371 WP_004159274 conjugal transfer pilus assembly protein TraH traH
TMSI_RS29870 (TMSI_57260) 69645..72488 + 2844 WP_032420975 conjugal transfer mating-pair stabilization protein TraG traG
TMSI_RS29875 72499..73023 + 525 WP_015065538 hypothetical protein -
TMSI_RS29880 (TMSI_57280) 73352..74320 - 969 WP_072193976 IS5-like element IS903B family transposase -
TMSI_RS29885 (TMSI_57290) 74398..75129 + 732 WP_013023830 conjugal transfer complement resistance protein TraT -
TMSI_RS30815 (TMSI_57300) 75322..76011 + 690 WP_165457226 hypothetical protein -
TMSI_RS29895 (TMSI_57310) 76138..78420 + 2283 WP_040215031 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   17840 GenBank   NZ_AP019690
Plasmid name   pTMSNI47-3 Incompatibility group   IncFII
Plasmid size   89834 bp Coordinate of oriT [Strand]   48978..49027 [-]
Host baterium   Klebsiella quasipneumoniae strain SNI47

Cargo genes

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