Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105144
Name   oriT_pRHBSTW-00001_2 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055594 (76153..76202 [-], 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_pRHBSTW-00001_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3560 GenBank   WP_151819948
Name   traI_HV026_RS26180_pRHBSTW-00001_2 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   3525 GenBank   WP_040215031
Name   traD_HV026_RS26175_pRHBSTW-00001_2 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: 75595..105595

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV026_RS25960 (HV026_25975) 70693..71043 + 351 WP_004153414 hypothetical protein -
HV026_RS25965 (HV026_25980) 71677..72030 + 354 WP_004152748 hypothetical protein -
HV026_RS25970 (HV026_25985) 72087..72434 + 348 WP_004152749 hypothetical protein -
HV026_RS25975 (HV026_25990) 72529..72675 + 147 WP_004152750 hypothetical protein -
HV026_RS25980 (HV026_25995) 72726..73559 + 834 WP_004152751 N-6 DNA methylase -
HV026_RS25985 (HV026_26000) 74379..75200 + 822 WP_004152492 DUF932 domain-containing protein -
HV026_RS25990 (HV026_26005) 75233..75562 + 330 WP_011977736 DUF5983 family protein -
HV026_RS25995 (HV026_26010) 75595..76080 - 486 WP_022631514 transglycosylase SLT domain-containing protein virB1
HV026_RS26000 (HV026_26015) 76471..76887 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
HV026_RS26005 (HV026_26020) 77087..77806 + 720 WP_015065526 hypothetical protein -
HV026_RS26010 (HV026_26025) 77939..78142 + 204 WP_171486139 TraY domain-containing protein -
HV026_RS26015 (HV026_26030) 78207..78575 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
HV026_RS26020 (HV026_26035) 78589..78894 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
HV026_RS26025 (HV026_26040) 78914..79480 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
HV026_RS26030 (HV026_26045) 79467..80207 + 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
HV026_RS26035 (HV026_26050) 80207..81631 + 1425 WP_032426793 F-type conjugal transfer pilus assembly protein TraB traB
HV026_RS26040 (HV026_26055) 81745..82329 + 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
HV026_RS26045 (HV026_26060) 82461..82871 + 411 WP_004152499 hypothetical protein -
HV026_RS26050 (HV026_26065) 82977..83195 + 219 WP_004152501 hypothetical protein -
HV026_RS26055 (HV026_26070) 83196..83507 + 312 WP_004152502 hypothetical protein -
HV026_RS26060 (HV026_26075) 83574..83978 + 405 WP_004152503 hypothetical protein -
HV026_RS26065 (HV026_26080) 84021..84410 + 390 WP_004153076 hypothetical protein -
HV026_RS26070 (HV026_26085) 84418..84816 + 399 WP_023179972 hypothetical protein -
HV026_RS26075 (HV026_26090) 84888..87527 + 2640 WP_004152505 type IV secretion system protein TraC virb4
HV026_RS26080 (HV026_26095) 87527..87916 + 390 WP_004152506 type-F conjugative transfer system protein TrbI -
HV026_RS26085 (HV026_26100) 87916..88542 + 627 WP_181467186 type-F conjugative transfer system protein TraW traW
HV026_RS26090 (HV026_26105) 88584..88973 + 390 WP_032445235 hypothetical protein -
HV026_RS26095 (HV026_26110) 88970..89959 + 990 WP_011977785 conjugal transfer pilus assembly protein TraU traU
HV026_RS26100 (HV026_26115) 89972..90610 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV026_RS26105 (HV026_26120) 90669..92624 + 1956 WP_030003482 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV026_RS26110 (HV026_26125) 92656..92910 + 255 WP_004152674 conjugal transfer protein TrbE -
HV026_RS26115 (HV026_26130) 92888..93136 + 249 WP_004152675 hypothetical protein -
HV026_RS26120 (HV026_26135) 93149..93475 + 327 WP_004144402 hypothetical protein -
HV026_RS26125 (HV026_26140) 93496..94248 + 753 WP_020803149 type-F conjugative transfer system pilin assembly protein TraF traF
HV026_RS26130 (HV026_26145) 94259..94498 + 240 WP_004152687 type-F conjugative transfer system pilin chaperone TraQ -
HV026_RS26135 (HV026_26150) 94470..95042 + 573 WP_023292147 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV026_RS26140 (HV026_26155) 95035..95463 + 429 WP_015065560 hypothetical protein -
HV026_RS26145 (HV026_26160) 95450..96820 + 1371 WP_004159274 conjugal transfer pilus assembly protein TraH traH
HV026_RS26150 (HV026_26165) 96820..99663 + 2844 WP_032420975 conjugal transfer mating-pair stabilization protein TraG traG
HV026_RS26155 (HV026_26170) 99674..100198 + 525 WP_015065538 hypothetical protein -
HV026_RS26160 (HV026_26175) 100527..101495 - 969 WP_072193976 IS5-like element IS903B family transposase -
HV026_RS26165 (HV026_26180) 101573..102304 + 732 WP_013023830 conjugal transfer complement resistance protein TraT -
HV026_RS26170 (HV026_26185) 102497..103186 + 690 WP_165457226 hypothetical protein -
HV026_RS26175 (HV026_26190) 103313..105595 + 2283 WP_040215031 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5582 GenBank   NZ_CP055594
Plasmid name   pRHBSTW-00001_2 Incompatibility group   IncFIB
Plasmid size   116760 bp Coordinate of oriT [Strand]   76153..76202 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00001

Cargo genes

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