Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105179
Name   oriT_pRHBSTW-00883_2 in_silico
Organism   Klebsiella variicola strain RHBSTW-00883
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056146 (121654..121703 [+], 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_pRHBSTW-00883_2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3571 GenBank   WP_181482101
Name   traI_HV312_RS26920_pRHBSTW-00883_2 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190676.71 Da        Isoelectric Point: 6.1411

>WP_181482101.1 conjugative transfer relaxase/helicase TraI [Klebsiella variicola]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGQGAEALGIDGKAVDKTLFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQTLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRTQEVREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRAHDRFVIDRVTASSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDKATLNQLEQSGSHLRLYSAQDAARTTEKLARHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLAAALETGGGKVPMADIDTTI
QAQIRSGQLLDVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAMAPLMDRVPASLMTDLTAGQREATR
MILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVSRKEGAWAPGSSVVEFTPKQEKAIQ
KALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSDGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEEAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILE
PRNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNIGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAITGGRVWADPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
AERVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRDRLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1433-1555)

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

(577-629)

TrwC relaxase (TrwC)

(10-284)

AAA domain (AAA_30)

(971-1157)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   3535 GenBank   WP_047665855
Name   traD_HV312_RS26925_pRHBSTW-00883_2 insolico UniProt ID   _
Length   768 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 768 a.a.        Molecular weight: 85847.91 Da        Isoelectric Point: 5.0689

>WP_047665855.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSQPA
PAEVTVSPAPVKAPPTTKSPAAEPSARAAEPPVLRVTTVPLIKPKAAAAAAAAATASSVGTPAAGGTEQE
LAQQSAEQGQEMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINRSHRHDEQDDVEIGGNF

  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: 97013..119156

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV312_RS26925 (HV312_26930) 97013..99319 - 2307 WP_047665855 type IV conjugative transfer system coupling protein TraD virb4
HV312_RS27600 99393..99488 - 96 Protein_98 hypothetical protein -
HV312_RS26930 (HV312_26935) 99681..100412 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
HV312_RS26935 (HV312_26940) 100602..101129 - 528 WP_047665858 conjugal transfer protein TraS -
HV312_RS26940 (HV312_26945) 101135..103984 - 2850 WP_181482102 conjugal transfer mating-pair stabilization protein TraG traG
HV312_RS26945 (HV312_26950) 103984..105354 - 1371 WP_087846395 conjugal transfer pilus assembly protein TraH traH
HV312_RS26950 (HV312_26955) 105341..105604 - 264 WP_087846397 hypothetical protein -
HV312_RS26955 (HV312_26960) 105601..106026 - 426 WP_109910419 HNH endonuclease signature motif containing protein -
HV312_RS26960 (HV312_26965) 106030..106233 - 204 WP_087846401 hypothetical protein -
HV312_RS26965 (HV312_26970) 106235..106636 - 402 WP_087846403 hypothetical protein -
HV312_RS26970 (HV312_26975) 106629..107201 - 573 WP_087846405 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV312_RS26975 (HV312_26980) 107173..107412 - 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
HV312_RS26980 (HV312_26985) 107423..108175 - 753 WP_087846407 type-F conjugative transfer system pilin assembly protein TraF traF
HV312_RS26985 (HV312_26990) 108196..108522 - 327 WP_086070807 hypothetical protein -
HV312_RS26990 (HV312_26995) 108750..108986 - 237 WP_087846411 conjugal transfer protein TrbE -
HV312_RS26995 (HV312_27000) 109018..110973 - 1956 WP_087846413 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV312_RS27000 (HV312_27005) 111032..111670 - 639 WP_032456788 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV312_RS27005 (HV312_27010) 111683..112672 - 990 WP_009309872 conjugal transfer pilus assembly protein TraU traU
HV312_RS27010 (HV312_27015) 112669..113058 - 390 WP_040107935 hypothetical protein -
HV312_RS27015 (HV312_27020) 113100..113726 - 627 WP_087846415 type-F conjugative transfer system protein TraW traW
HV312_RS27020 (HV312_27025) 113726..114115 - 390 WP_040107933 type-F conjugative transfer system protein TrbI -
HV312_RS27025 (HV312_27030) 114115..116754 - 2640 WP_040107932 type IV secretion system protein TraC virb4
HV312_RS27030 (HV312_27035) 116826..117218 - 393 WP_087846417 hypothetical protein -
HV312_RS27035 (HV312_27040) 117232..117585 - 354 WP_228725554 hypothetical protein -
HV312_RS27040 (HV312_27045) 117565..118533 + 969 WP_181481626 IS5 family transposase -
HV312_RS27045 (HV312_27050) 118592..118831 - 240 Protein_122 TraE/TraK family type IV conjugative transfer system protein -
HV312_RS27050 (HV312_27055) 118851..119156 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV312_RS27055 (HV312_27060) 119170..119538 - 369 WP_048295882 type IV conjugative transfer system pilin TraA -
HV312_RS27060 (HV312_27065) 119592..119963 - 372 WP_004208838 TraY domain-containing protein -
HV312_RS27065 (HV312_27070) 120047..120742 - 696 WP_075212577 transcriptional regulator TraJ family protein -
HV312_RS27070 (HV312_27075) 120949..121341 - 393 WP_087846435 conjugal transfer relaxosome DNA-binding protein TraM -
HV312_RS27075 (HV312_27080) 121848..122255 + 408 WP_226615017 transglycosylase SLT domain-containing protein -
HV312_RS27080 (HV312_27085) 122293..122823 - 531 WP_087846439 antirestriction protein -

Host bacterium

ID   5617 GenBank   NZ_CP056146
Plasmid name   pRHBSTW-00883_2 Incompatibility group   IncFIB
Plasmid size   165251 bp Coordinate of oriT [Strand]   121654..121703 [+]
Host baterium   Klebsiella variicola strain RHBSTW-00883

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   fecD, fecE
Degradation gene   bphA
Symbiosis gene   -
Anti-CRISPR   -