Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115687
Name   oriT_CM-1|unnamed1 in_silico
Organism   Klebsiella pasteurii strain CM-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP134212 (14933..14981 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_CM-1|unnamed1
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10043 GenBank   WP_284659195
Name   traI_RIV03_RS28180_CM-1|unnamed1 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: 190285.02 Da        Isoelectric Point: 6.0673

>WP_284659195.1 conjugative transfer relaxase/helicase TraI [Klebsiella pasteurii]
MMSIGAVKSAGSAGNYYTGKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGENKHRPGYDLTFSAPKSVSVMAMPGGDKRLIDAHNQAVMVAVKQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATHNGDKWQSLGTDTVGKTGFIENVYANQTAFGKLYREALKPLVE
KLGYETEVVGRHGMWEMKDVPVEPFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAEEIARAPVAPVKTDGPDITDVVTRAIAGLSDRKVQFTYADVLARTVGQLE
AKPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDMSVVREAP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSREYLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGRQATADIISEPDKGARYSLLAQAFAASVREGQESVAQISGTREQSVLNNVIRDTLKNEGALGSRD
MTVTALTPVWLDSKSRGVRDYYREGMVMERWDPEARSRDRFVIDRVTASSNMLTLKDREGERLDLKVSAV
DSQWTLFRADKLQVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGI
KVGHGWVESPGRSISETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLTRHTAFSVVSE
QLKARSGETDLEAAIAQQKAGLHSPAEQAIHLSVPLLESNSLTFTRPQLLATALETGGGKVPMKDIEATI
QAQIKAGSMLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAMTPLMDRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVTGLGPTHRAVGEMQSAGVEAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALTLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIERDVSRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQ
DALKEGKGIPPGTPVSLHDAIVKDYTGRTPAAQANTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTL
PVLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDGEGNTRFLSPREASAEGVTL
YRPEHITVSQGDRMRFSKSDPERGYVANSVWEVKAVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGVEGRRKTMVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PKNVRAVKNAGQLYGRAQPLDETAAGRAALQQSGLARGESPGRFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRVGRLEAIGGEGRIMGDETARFVALQNSRNGESLLAGNMSEGVRTARDHPDSGVIVRLAGDDR
PWNPEAITGGRIWADPLPNLAATDTGTDIPLPPEVLAQRAAEEAMRREMERQTEQATREVAGEEKKAGEP
GERIKEVIGDVIRGLERDRPGEEKTPLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(635-714)

AAA domain (AAA_30)

(971-1157)

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

(577-629)

DNA helicase TraI (TraI_C)

(1433-1555)

TrwC relaxase (TrwC)

(11-284)


  Protein structure



No available structure.




Auxiliary protein

ID   5902 GenBank   WP_284659152
Name   WP_284659152_CM-1|unnamed1 insolico UniProt ID   _
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14684.75 Da        Isoelectric Point: 4.6748

>WP_284659152.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Klebsiella]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNEGEIEGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-124)


  Protein structure



No available structure.




T4CP

ID   11723 GenBank   WP_284659122
Name   traD_RIV03_RS28175_CM-1|unnamed1 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85619.54 Da        Isoelectric Point: 4.9642

>WP_284659122.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pasteurii]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQSTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEAFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGSLARALFTPDAPEPEQRDADSKTPVGQPVPESAP
VSPVPVKSASTAETLAAPPSVKASEAPQAKVTTVPLTRPAPAATPAASSATASSVAATAATTGGTEQALA
QQPAEQGQEMMPAGMNEDGEIEDMQAYDAWLADEQTQREMQRREEVNINHSHRRDEQDDVEIGGNF

  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: 17358..42010

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RIV03_RS27995 (RIV03_27995) 13812..14342 + 531 WP_310810880 antirestriction protein -
RIV03_RS28000 (RIV03_28000) 14366..14860 - 495 WP_310810881 transglycosylase SLT domain-containing protein -
RIV03_RS28005 (RIV03_28005) 15293..15685 + 393 WP_284659152 conjugal transfer relaxosome DNA-binding protein TraM -
RIV03_RS28010 (RIV03_28010) 15923..16627 + 705 WP_284659151 hypothetical protein -
RIV03_RS28015 (RIV03_28015) 16711..16911 + 201 WP_284659150 TraY domain-containing protein -
RIV03_RS28020 (RIV03_28020) 16979..17344 + 366 WP_284659149 type IV conjugative transfer system pilin TraA -
RIV03_RS28025 (RIV03_28025) 17358..17663 + 306 WP_020323523 type IV conjugative transfer system protein TraL traL
RIV03_RS28030 (RIV03_28030) 17683..18249 + 567 WP_284659148 type IV conjugative transfer system protein TraE traE
RIV03_RS28035 (RIV03_28035) 18236..18976 + 741 WP_284659147 type-F conjugative transfer system secretin TraK traK
RIV03_RS28040 (RIV03_28040) 18976..20391 + 1416 WP_284659146 F-type conjugal transfer pilus assembly protein TraB traB
RIV03_RS28045 (RIV03_28045) 20384..20659 + 276 WP_310810882 hypothetical protein -
RIV03_RS28050 (RIV03_28050) 20727..20864 + 138 Protein_33 conjugal transfer protein TraP -
RIV03_RS28055 (RIV03_28055) 20887..21468 + 582 WP_284659143 type IV conjugative transfer system lipoprotein TraV traV
RIV03_RS28060 (RIV03_28060) 21634..22032 + 399 WP_284659142 hypothetical protein -
RIV03_RS28065 (RIV03_28065) 22114..22536 + 423 WP_284659141 hypothetical protein -
RIV03_RS28070 (RIV03_28070) 22561..22782 + 222 WP_284659140 hypothetical protein -
RIV03_RS28075 (RIV03_28075) 22779..23183 + 405 WP_284659139 hypothetical protein -
RIV03_RS28080 (RIV03_28080) 23180..23479 + 300 WP_284659138 hypothetical protein -
RIV03_RS28085 (RIV03_28085) 23583..26222 + 2640 WP_284659137 type IV secretion system protein TraC virb4
RIV03_RS28090 (RIV03_28090) 26222..26662 + 441 WP_310810883 type-F conjugative transfer system protein TrbI -
RIV03_RS28095 (RIV03_28095) 26659..27285 + 627 WP_284659136 type-F conjugative transfer system protein TraW traW
RIV03_RS28100 (RIV03_28100) 27305..28288 + 984 WP_284659198 conjugal transfer pilus assembly protein TraU traU
RIV03_RS28105 (RIV03_28105) 28301..28939 + 639 WP_284659135 type-F conjugative transfer system pilin assembly protein TrbC trbC
RIV03_RS28110 (RIV03_28110) 28936..29319 + 384 WP_284659134 hypothetical protein -
RIV03_RS28115 (RIV03_28115) 29316..31196 + 1881 WP_284659133 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RIV03_RS28120 (RIV03_28120) 31229..31510 + 282 WP_142480832 hypothetical protein -
RIV03_RS28125 (RIV03_28125) 31500..31760 + 261 WP_284659132 conjugal transfer protein TrbE -
RIV03_RS28130 (RIV03_28130) 31738..31986 + 249 WP_284659131 hypothetical protein -
RIV03_RS28135 (RIV03_28135) 31999..32325 + 327 WP_284659130 hypothetical protein -
RIV03_RS28140 (RIV03_28140) 32346..33098 + 753 WP_284659129 type-F conjugative transfer system pilin assembly protein TraF traF
RIV03_RS28145 (RIV03_28145) 33109..33348 + 240 WP_284659128 type-F conjugative transfer system pilin chaperone TraQ -
RIV03_RS28150 (RIV03_28150) 33320..33895 + 576 WP_284659127 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RIV03_RS28155 (RIV03_28155) 33882..35252 + 1371 WP_284659126 conjugal transfer pilus assembly protein TraH traH
RIV03_RS28160 (RIV03_28160) 35252..38110 + 2859 WP_284659125 conjugal transfer mating-pair stabilization protein TraG traG
RIV03_RS28165 (RIV03_28165) 38135..38773 + 639 WP_284659124 hypothetical protein -
RIV03_RS28170 (RIV03_28170) 38823..39494 + 672 WP_284659123 tetratricopeptide repeat protein -
RIV03_RS28175 (RIV03_28175) 39710..42010 + 2301 WP_284659122 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16120 GenBank   NZ_CP134212
Plasmid name   CM-1|unnamed1 Incompatibility group   IncFII
Plasmid size   105567 bp Coordinate of oriT [Strand]   14933..14981 [-]
Host baterium   Klebsiella pasteurii strain CM-1

Cargo genes

Drug resistance gene   -
Virulence gene   fimE, fimA, fimI, fimC, fimD, fimF, fimG, fimB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -