Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120629
Name   oriT_pCFR-eb27 in_silico
Organism   Citrobacter freundii complex sp. CFNIH9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026242 (53894..54177 [-], 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_pCFR-eb27
GTTATTGCCGCTTAATGCCGATAACGATTCGGGCTTTGCTATTTTTTTAAGCGATTAAAATTTCGTTAGCAAGCGCAGGGTTTTTTGATAAAATTCTGGTTAGTTTGGTCAAAAAGTGTTACAAGTAAGGCCAATGGATGAATGGTTAGTTTTAAGACTCAAATAGGCAGTATTAAAATTCCAAAAGTTACTTTTCATCATTCAAAAACCAAACTTTAATTTCATGTAGAAGATTAGTACAATTGTATTGACGCAAGGACAATCCGCACATGTCAGAATCAGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12997 GenBank   WP_233899731
Name   mobH_C2U43_RS27510_pCFR-eb27 insolico UniProt ID   _
Length   988 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 988 a.a.        Molecular weight: 110186.89 Da        Isoelectric Point: 4.5476

>WP_233899731.1 MobH family relaxase [Citrobacter freundii complex sp. CFNIH9]
MAELMMKDVSSLSPFAQIIGDQKYTVPDHPNLEVLKFIEYPTRPAGIQTFNEQSILSLYRDKLHSISMML
AISDGDIREDAFTFTNLVLKPLIEYIRWIHLLPASENHHHNGIGGLLSHSLEVAMISLKNANHSELRPIG
YQDEEVIRRKVYLYAAFICSLVHDAGKVYDLDIVSLNLNETLTWAPSSQSLLDWARENNVVEYEIHWRKR
IHNQHNIWSSVFLERILDPVCMSFLDRVKKERVYAKMVTALNVYNDGNDFLSKCVRTSDYYSTGTDLNVL
RDPIMGLRSNDAAARAIGTIKHNFTSININNYKSKPMHIIIVNGEVYLNENAFLDFVLSDFAAHKFNFPQ
GDAGKTVLVESLVQRGYVEPYDDERVVHYFIPGTYSENEIASIFRNGIGKLEFYNLLKLRWIGLIFDSYK
IPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRESVTRVTDTVSDAIEDTPQYGLKLVNGPDADSVN
GKSSENTEAITESVEAAGTDKATDIIDPQVTTPTDTAGTGGLDEKERVEEHEEQSQMRLVEQLHEMLLSA
PLPHNAVINIDSVPYLNLDAAIALIPGIDEAAFCDGPFFQLTYRDGSLDGMWIVRDVNNLRLIQLGDNCA
GIQVSTSEPRTTSTLKSLFDTSMYQPLDIPESPSLNEAVSPPQTPLDLPPARLNTPQAVEANSVAEQINA
HSEPETVTASEYEQYGHLLEETLDSDSEAYSDFIVADNSVVEPPQPEAKNSDVAEFHDETDQVVAPGKLN
DPEDTREPPAPNTTGKEVILTSPVSSQDPIKSEPAGEKANHLSPALARLFAVNTQAEKKHENPPVTTPVK
EAFNRSNSATVQAPIAVDQPGAEEKETLEDFTLLSGGEVTELEYVEIATMLHHILTKLSGSFKRKRKNRF
MVLTQNTFFLTQSCVEKYGTQLNAPELFNQLPQYQVTSGAIVNTKCFAFNMPTLVAASDRAKVDIELIIN
TLKDVGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(83-278)


  Protein structure



No available structure.




T4CP

ID   15261 GenBank   WP_040113316
Name   traD_C2U43_RS27515_pCFR-eb27 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: 77914.54 Da        Isoelectric Point: 8.5005

>WP_040113316.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MAKSKRTNLHAQENFYRPILEYRSASVLLICAIIMLFMGFRSDGLNIAPIILYTAAFMLLVCLYRCKTAY
PYLMAHWRVFQRQIMFISLKSLRSINKSNFFSNERKYRQLVQEYKKSNRQVPDRKTYFCNGFEWGPEHAD
RAYQIANLSSDKREIALPFALNPIARHFEAMARSMGGSNAIFAVDKRAPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVIVVIDPKNDADWRQSLMDEAAELGLPFYKFHPAQPSSSVCIDVCNAYTNVSD
LTSRLLSLVSVPGEVNPFVQYAEALVSTVITGLSYTDKKPSIYLIHKNMKSHMAILNLTVKVLECCYARH
YGPDVWMEKVKYSSNDTLQVRFKRLVEWFSAHFLNYEGAEPIDWIDTVGRLVDYSLSDPEHMSKMTAGIM
PLFSRLTEQPLNELLSPSPNSLTSREIVTSDGIFSTGGVLYISLDGLSNPESARAISQLIMSDLTSCAGS
RYNSDDGDMSSHSRISIFVDEAHSAINNSMINLLAQGRAAQIALFICTQTISDFIAAANIETANRITGLC
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   15262 GenBank   WP_004883099
Name   trbE_C2U43_RS28220_pCFR-eb27 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   15263 GenBank   WP_004883083
Name   t4cp2_C2U43_RS28245_pCFR-eb27 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: 163260..172878

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C2U43_RS28165 (C2U43_28165) 159258..160139 + 882 WP_015063085 RepB family plasmid replication initiator protein -
C2U43_RS28170 (C2U43_28170) 160727..161242 - 516 WP_015063086 hypothetical protein -
C2U43_RS29665 161431..161757 + 327 WP_015063087 hypothetical protein -
C2U43_RS29520 161804..161962 - 159 WP_022652137 hypothetical protein -
C2U43_RS28175 (C2U43_28175) 162071..162343 + 273 WP_022652138 hypothetical protein -
C2U43_RS28180 (C2U43_28180) 162333..162728 + 396 WP_223203170 DNA-binding protein -
C2U43_RS28185 (C2U43_28185) 163021..163263 - 243 WP_004883121 DUF2274 domain-containing protein -
C2U43_RS28190 (C2U43_28190) 163260..164540 - 1281 WP_004883119 TrbI/VirB10 family protein virB10
C2U43_RS28195 (C2U43_28195) 164543..165535 - 993 WP_004883112 P-type conjugative transfer protein TrbG virB9
C2U43_RS28200 (C2U43_28200) 165532..166236 - 705 WP_004883108 conjugal transfer protein TrbF virB8
C2U43_RS28205 (C2U43_28205) 166266..167630 - 1365 WP_004883106 P-type conjugative transfer protein TrbL virB6
C2U43_RS28210 (C2U43_28210) 167627..167953 - 327 WP_004883103 hypothetical protein -
C2U43_RS28215 (C2U43_28215) 167966..168703 - 738 WP_004883101 P-type conjugative transfer protein TrbJ virB5
C2U43_RS28220 (C2U43_28220) 168700..171150 - 2451 WP_004883099 conjugal transfer protein TrbE virb4
C2U43_RS28225 (C2U43_28225) 171162..171434 - 273 WP_004883097 VirB3 family type IV secretion system protein virB3
C2U43_RS28230 (C2U43_28230) 171431..171814 - 384 WP_004883090 TrbC/VirB2 family protein virB2
C2U43_RS28235 (C2U43_28235) 171811..172878 - 1068 WP_004883088 P-type conjugative transfer ATPase TrbB virB11
C2U43_RS28240 (C2U43_28240) 172875..173339 - 465 WP_004883086 ribbon-helix-helix protein, CopG family -
C2U43_RS28245 (C2U43_28245) 173336..175351 - 2016 WP_004883083 conjugal transfer protein TraG -
C2U43_RS28250 (C2U43_28250) 175634..175909 - 276 WP_004883082 EexN family lipoprotein -
C2U43_RS28255 (C2U43_28255) 175906..176850 - 945 WP_004883081 LysR family transcriptional regulator -

Region 2: 227075..236243

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C2U43_RS28475 (C2U43_28475) 222436..222636 - 201 WP_022652148 hypothetical protein -
C2U43_RS28480 (C2U43_28480) 222654..223727 - 1074 WP_022652149 hypothetical protein -
C2U43_RS28485 (C2U43_28485) 224269..225144 + 876 WP_015063098 RepB family plasmid replication initiator protein -
C2U43_RS29525 226195..226380 + 186 WP_032610388 hypothetical protein -
C2U43_RS28495 (C2U43_28495) 226670..227023 + 354 WP_015063100 hypothetical protein -
C2U43_RS28500 (C2U43_28500) 227075..227392 + 318 WP_022652151 type IV conjugative transfer system protein TraL traL
C2U43_RS28505 (C2U43_28505) 227404..228189 + 786 WP_022652152 TraE/TraK family type IV conjugative transfer system protein traE
C2U43_RS28510 (C2U43_28510) 228192..229430 + 1239 WP_015063103 type-F conjugative transfer system secretin TraK traK
C2U43_RS28515 (C2U43_28515) 229432..229872 + 441 WP_015063104 plasmid transfer protein HtdO -
C2U43_RS28520 (C2U43_28520) 229862..231220 + 1359 WP_022652153 IncHI-type conjugal transfer protein TrhB traB
C2U43_RS28525 (C2U43_28525) 231229..231735 + 507 WP_015063106 hypothetical protein -
C2U43_RS28530 (C2U43_28530) 231841..232593 + 753 WP_185757620 protein-disulfide isomerase HtdT -
C2U43_RS28535 (C2U43_28535) 232603..233553 + 951 WP_015063108 TraV family lipoprotein traV
C2U43_RS28540 (C2U43_28540) 233562..236243 + 2682 WP_040113303 IncHI-type conjugal transfer ATPase TrhC virb4
C2U43_RS28550 (C2U43_28550) 238604..239857 + 1254 WP_015063110 ParA family protein -
C2U43_RS28555 (C2U43_28555) 239854..240858 + 1005 WP_022652164 ParB family protein -

Host bacterium

ID   21058 GenBank   NZ_CP026242
Plasmid name   pCFR-eb27 Incompatibility group   IncHI1B
Plasmid size   355789 bp Coordinate of oriT [Strand]   53894..54177 [-]
Host baterium   Citrobacter freundii complex sp. CFNIH9

Cargo genes

Drug resistance gene   blaSHV-5, dfrA1, ant(3'')-Ia, aac(3)-Ia, qacE, sul1, qnrA1
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW, merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -