Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104183
Name   oriT_pKLO00015_4 in_silico
Organism   Klebsiella michiganensis strain KLO00015
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OP378639 (208446..208729 [-], 284 nt)
oriT length   284 nt
IRs (inverted repeats)      183..188, 190..195  (AAAAGT..ACTTTT)
 45..50, 55..60  (TTTTAA..TTAAAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 284 nt

>oriT_pKLO00015_4
GTTATTGCCGCTTAATGCCGATAACGATTCGGGCTTTGCTATTTTTTTAAGCGATTAAAATTTCGTTAGCAAGCGCAGGGTTTTTTGATAAAATTCTGGTTAGTTTGGTCAAAAAGTGTTACAAGTAAGGCCAATGGATGAATGGTTAGTTTTAAGACTCAAATAGGCAGTATTAAAATTCCAAAAGTTACTTTTCATCATTCAAAAACCAAACTTTAATTTCATGTAGAAGATTAGTACAATTGTATTGACGCAAGGACAATCCGCACATGTCAGAATCAGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3075 GenBank   WP_015063004
Name   mobH_PWC61_RS01055_pKLO00015_4 insolico UniProt ID   A0A706EP88
Length   1011 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1011 a.a.        Molecular weight: 112820.93 Da        Isoelectric Point: 4.5727

>WP_015063004.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MNFRALFLSIQRVLGIFSSRENDVAELMMKDVSSLSPFAQIIGDQKYTVPDHPNLEVLKFIEYPTRPAGI
QTFNEQSILSLYRDKLHSISMMLAISDGDIREDAFTFTNLVLKPLIEYIRWIHLLPASENHHHNGIGGLL
SHSLEVAMISLKNANHSELRPIGYQDEEVIRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLNETLTWAPS
SQSLLDWARENNVVEYEIHWRKRIHNQHNIWSSVFLERILDPVCMSFLDRVKKERVYAKMVTALNVYNDG
NDFLSKCVRTSDYYSTGTDLNVLRDPIMGLRSNDAAARAIGTIKHNFTSININNYKSKPMHIIIVNGEVY
LNENAFLDFVLSDFAAHKFNFPQGDAGKTVLVESLVQRGYVEPYDDERVVHYFIPGTYSENEIASIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRESVTRVTDTVS
DAIEDTPQYGLKLVNGPDADSVNGKSSENTEAITESVEAAGTDKATDIIDPQVTTPTDTAGTGGLDEKER
VEEHEEQSQMRLVEQLHEMLLSAPLPHNAVINIDSVPYLNLDAAIALIPGIDEAAFCDGPFFQLTYRDGS
LDGMWIVRDVNNLRLIQLGDNCAGIQVSTSEPRTTSTLKSLFDTSMYQPLDIPESPSLNEAVSPPQTPLD
LPPARLNTPQAVEANSVAEQINAHSEPETVTASEYEQYGHLLEETLDSDSEAYSDFIVADNSVVEPPQPE
AKNSDVAEFHDETDQVVAPGKLNDPEDTREPPAPNTTGKEVILTSPVSSQDPIKSEPAGEKANHLSPALA
RLFAVNTQAEKKHENPPVTTPVKEAFNRSNSATVQAPIAVDQPGAEEKETLEDFTLLSGGEVTELEYVEI
ATMLHHILTKLSGSFKRKRKNRFMVLTQNTFFLTQSCVEKYGTQLNAPELFNQLPQYQVTSGAIVNTKCF
AFNMPTLVAASDRAKVDIELIINTLKDVGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-301)


  Protein structure


Source ID Structure
AlphaFold DB A0A706EP88


T4CP

ID   2970 GenBank   WP_015063005
Name   traD_PWC61_RS01060_pKLO00015_4 insolico UniProt ID   _
Length   694 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 694 a.a.        Molecular weight: 77900.52 Da        Isoelectric Point: 8.5005

>WP_015063005.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MAKSKRTNLHAQENFYRPILEYRSASVLLICAIIMLFMGFRSDGLNIAPIILYTAAFMLLVCLYRCKTAY
PYLMAHWRVFQRQIMFISLKSLRSINKSNFFSNERKYRQLVQEYKKSNRQVPDRKTYFCNGFEWGPEHAD
RAYQIANLSSDKREIALPFALNPIARHFEAMARSMGGSNAIFAVDKRAPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVIVVIDPKNDADWRQSLMDEAAELGLPFYKFHPAQPSSSVCIDVCNAYTNVSD
LTSRLLSLVSVPGEVNPFVQYAEALVSTVITGLSYTDKKPSIYLIHKNMKSHMAILNLTVKVLECCYARH
YGPDVWMEKVKYSSNDTLQVRFKRLVEWFSAHFLNYEGAEPIDWIDTVGRLVDYSLSDPEHMSKMTAGIM
PLFSRLTEQPLNELLSPSPNSLTSREIVTSDGIFSTGGVLYISLDGLSNPESARAISQLIMSDLTSCAGS
RYNSDDGDMSSHSRISIFVDEAHSAINNSMINLLAQGRAAQIALFICTQTISDFIAAANVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSPISTNMVTYTTGSETTLPHNNFSGSISERKQTTLEESIPKELLGQV
PKFHIVARLQDGRKVVGQIPIAVSENSMRPNTTLLEMFLKPAGKVTLRQNVGLDYLNKHLRKLH

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(505-627)

  Protein structure



No available structure.



ID   2971 GenBank   WP_004883099
Name   trbE_PWC61_RS01520_pKLO00015_4 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 89531.64 Da        Isoelectric Point: 5.2838

>WP_004883099.1 MULTISPECIES: conjugal transfer protein TrbE [Pseudomonadota]
MLNLAEYRQRPALLADWLPWAGLIAPGVVLNKDGSFQRTARFRGPDLDSATQGELIATTARLNNALRRLG
SGWALFVEAERQSAADYPHSDFPEPLSWLVDEERRAAFEESGNHYESSYHLTLAYLPPEESRARAAKLLY
EHAPGDGVDWRGRLDAFLAETDRVFDLLDGVMPEIVWLDDAATLTYLHATVSTRRYRLAVPEVPFHLDAL
LADSALVGGLAPMLGDQHLRVVSVRGFPTSTWPGLLDDLNRLGFAYRWSTRFLCLDKAEAEKELGRLRRQ
WFAKRKNVIALLRETIFQQESPLVDTDASNKAADADAALQELGSDQVAFGYLTATVTVFDDDPAVADEKL
RMVERVIQGRGFVTIPETLNAVDAWLSSIPGNAYANVRQPIVSTLNLAHMMPVSAVWAGPEKNAHLDGPP
LIVTRTDGATPFRLVTHIGDVGHTLVAGPTGMGKSVLLAMLALQFRRYGGSRIFAFDMGRSMRATVLGLG
GEHYDLGADGAIAFQPLARIDSEGYRTWAAEWIEGRLLHEGVTVGPDEKAAIWSALGSLAGAPVEQRTMT
GLSVLLQSNALRQALSPYVLGGAHGKLLDADRDRLGSGDVQGFEMEELMHSPAAVQAVLRYLFARFDARF
DGAPTLLILDEAWLFLDEPSFAARIRQWLKTLRKKNVSVIFATQSLADIKDSTIAPAIIESCASRIFLPN
PQATEPQIRTVYEGFGLNSRQIEIVATAQPKRDYYYQSRLGNRLFDLDLGPAALAFSGASTPQDQRDIDR
VLTQAGAPGFAGAWLRHRGLDWAADLLPSSPSAASFLATQPLEISP

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(571-726)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(187-388)

  Protein structure



No available structure.



ID   2972 GenBank   WP_004883083
Name   t4cp2_PWC61_RS01545_pKLO00015_4 insolico UniProt ID   _
Length   671 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 671 a.a.        Molecular weight: 73455.71 Da        Isoelectric Point: 6.5506

>WP_004883083.1 MULTISPECIES: conjugal transfer protein TraG [Pseudomonadota]
MQGTNVLFGQIAVVFGIVIAGVWGATQWTAAALGYQVRLGSPWFDFLGTPIYLPWKLFEWWFFFDAYAPR
VFDTGGAIAGGSGLLAVVVAVCMSIWRSRQSRLVTTYGSARWASTEDIRKAGLTQPIGVFLGQHDGKYLR
HEGPEHILTFAPTRSGKGVGLVVPTLLSWPASAVVHDIKGENWQITAGWRSRYSHCLLFNPTDAKSAAYN
PLLEVRRGAHEVRDVQNIADILVDPEGALEKRNHWEKTSHALLVGAILHVLYAGEDKTLRGVANFLSDPA
SPFELTLHRMMTTQHLVNVEGGGPHPVVASAAREVLNKSDNERSGVLSTAMSFLGLYRDPTVAEVTSRCD
WRIADLIASEHPVSLYLVVPPSDISRTKPLIRLILNQIGRRLTESLDGSDGIERRHKLLLMLDEFPALGR
LDFFETALAFMAGYGIRSFLIAQSLNQIDKAYGQNHSILDNCHVRVTFATNDERTAKRISETLGTATELR
AQRNYAGHRLAPWLGHLMVSRQETARPLLTPGEVMQLPTEEAVVMVSSVAPIKAKKLRYYADANFKNRVL
PPPVLAAGQYADAPPARPDDWSGLSIPAVSTVRAAGLSGDGTGTADDGGPRRQPELSEVSEYSPEPLLAG
HDLTLLDDDDDLPLPLPGQLDPAMQRTARLASLDPNDGIDL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(112-562)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2815..11983

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PWC61_RS00005 1..876 + 876 WP_015063098 RepB family plasmid replication initiator protein -
PWC61_RS00010 1935..2120 + 186 WP_032610388 hypothetical protein -
PWC61_RS00015 2410..2763 + 354 WP_015063100 hypothetical protein -
PWC61_RS00020 2815..3132 + 318 WP_022652151 type IV conjugative transfer system protein TraL traL
PWC61_RS00025 3144..3929 + 786 WP_022652152 TraE/TraK family type IV conjugative transfer system protein traE
PWC61_RS00030 3932..5170 + 1239 WP_015063103 type-F conjugative transfer system secretin TraK traK
PWC61_RS00035 5172..5612 + 441 WP_015063104 plasmid transfer protein HtdO -
PWC61_RS00040 5602..6960 + 1359 WP_022652153 IncHI-type conjugal transfer protein TrhB traB
PWC61_RS00045 6969..7475 + 507 WP_015063106 hypothetical protein -
PWC61_RS00050 7581..8333 + 753 WP_185757620 protein-disulfide isomerase HtdT -
PWC61_RS00055 8343..9293 + 951 WP_015063108 TraV family lipoprotein traV
PWC61_RS00060 9302..11983 + 2682 WP_015063109 IncHI-type conjugal transfer ATPase TrhC virb4
PWC61_RS00065 13500..13694 - 195 WP_044713619 hypothetical protein -
PWC61_RS00070 14344..15597 + 1254 WP_015063110 ParA family protein -
PWC61_RS00075 15594..16598 + 1005 WP_022652164 ParB family protein -

Region 2: 273612..281947

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PWC61_RS01460 269797..270312 - 516 WP_015063086 hypothetical protein -
PWC61_RS01465 270501..270827 + 327 WP_015063087 hypothetical protein -
PWC61_RS01470 270874..271032 - 159 WP_022652137 hypothetical protein -
PWC61_RS01475 271141..271413 + 273 WP_022652138 hypothetical protein -
PWC61_RS01480 271403..271798 + 396 WP_223203170 DNA-binding protein -
PWC61_RS01485 272091..272333 - 243 WP_004883121 DUF2274 domain-containing protein -
PWC61_RS01490 272330..273609 - 1280 Protein_298 TrbI/VirB10 family protein -
PWC61_RS01495 273612..274604 - 993 WP_004883112 P-type conjugative transfer protein TrbG virB9
PWC61_RS01500 274601..275305 - 705 WP_004883108 conjugal transfer protein TrbF virB8
PWC61_RS01505 275335..276699 - 1365 WP_004883106 P-type conjugative transfer protein TrbL virB6
PWC61_RS01510 276696..277022 - 327 WP_004883103 hypothetical protein -
PWC61_RS01515 277035..277772 - 738 WP_004883101 P-type conjugative transfer protein TrbJ virB5
PWC61_RS01520 277769..280219 - 2451 WP_004883099 conjugal transfer protein TrbE virb4
PWC61_RS01525 280231..280503 - 273 WP_004883097 VirB3 family type IV secretion system protein virB3
PWC61_RS01530 280500..280883 - 384 WP_004883090 TrbC/VirB2 family protein virB2
PWC61_RS01535 280880..281947 - 1068 WP_004883088 P-type conjugative transfer ATPase TrbB virB11
PWC61_RS01540 281944..282408 - 465 WP_004883086 ribbon-helix-helix protein, CopG family -
PWC61_RS01545 282405..284420 - 2016 WP_004883083 conjugal transfer protein TraG -
PWC61_RS01550 284695..284970 - 276 WP_004883082 EexN family lipoprotein -
PWC61_RS01555 284967..285911 - 945 WP_004883081 LysR substrate-binding domain-containing protein -

Host bacterium

ID   4622 GenBank   NZ_OP378639
Plasmid name   pKLO00015_4 Incompatibility group   IncHI1A
Plasmid size   333303 bp Coordinate of oriT [Strand]   208446..208729 [-]
Host baterium   Klebsiella michiganensis strain KLO00015

Cargo genes

Drug resistance gene   mcr-9
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoS, pcoE, ncrC, rcnR/yohL, terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -