Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102823
Name   oriT_pKp_Goe_414-3 in_silico
Organism   Klebsiella pneumoniae isolate Kp_Goe_154414
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP018340 (2125..2173 [-], 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_pKp_Goe_414-3
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2091 GenBank   WP_073558196
Name   traI_BB788_RS29285_pKp_Goe_414-3 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: 190619.72 Da        Isoelectric Point: 6.3386

>WP_073558196.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKDAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGGRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQLRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLTQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRLEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

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

(635-714)

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)


  Protein structure



No available structure.




T4CP

ID   1750 GenBank   WP_077272951
Name   traD_BB788_RS29280_pKp_Goe_414-3 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85921.92 Da        Isoelectric Point: 5.0577

>WP_077272951.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPASGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1567..30392

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BB788_RS29090 (BB788_28855) 353..1172 + 820 Protein_0 DUF932 domain-containing protein -
BB788_RS29095 (BB788_28860) 1205..1534 + 330 WP_011977736 DUF5983 family protein -
BB788_RS29100 (BB788_28865) 1567..2052 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
BB788_RS29105 (BB788_28870) 2484..2876 + 393 WP_073558191 conjugal transfer relaxosome DNA-binding protein TraM -
BB788_RS29110 (BB788_28875) 3106..3807 + 702 WP_004194113 hypothetical protein -
BB788_RS29115 (BB788_28880) 3893..4093 + 201 WP_004194116 TraY domain-containing protein -
BB788_RS29120 (BB788_28885) 4162..4530 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
BB788_RS29125 (BB788_28890) 4544..4849 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
BB788_RS29130 (BB788_28895) 4869..5435 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
BB788_RS29135 (BB788_28900) 5422..6162 + 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
BB788_RS29140 (BB788_28905) 6162..7586 + 1425 WP_073558192 F-type conjugal transfer pilus assembly protein TraB traB
BB788_RS29145 (BB788_28910) 7700..8284 + 585 WP_009309868 type IV conjugative transfer system lipoprotein TraV traV
BB788_RS29150 (BB788_28915) 8416..8826 + 411 WP_009309869 hypothetical protein -
BB788_RS29155 (BB788_28920) 8932..9150 + 219 WP_004195468 hypothetical protein -
BB788_RS29160 (BB788_28925) 9151..9462 + 312 WP_004195465 hypothetical protein -
BB788_RS29165 (BB788_28930) 9529..9933 + 405 WP_004197817 hypothetical protein -
BB788_RS33090 9976..10128 + 153 WP_224518895 hypothetical protein -
BB788_RS29180 (BB788_28940) 10309..10707 + 399 WP_023179972 hypothetical protein -
BB788_RS29185 (BB788_28945) 10779..13418 + 2640 WP_023284638 type IV secretion system protein TraC virb4
BB788_RS29190 (BB788_28950) 13418..13807 + 390 WP_004197815 type-F conjugative transfer system protein TrbI -
BB788_RS29195 (BB788_28955) 13807..14433 + 627 WP_009309871 type-F conjugative transfer system protein TraW traW
BB788_RS29200 (BB788_28960) 14475..14864 + 390 WP_004194992 hypothetical protein -
BB788_RS29205 (BB788_28965) 14861..15850 + 990 WP_073558193 conjugal transfer pilus assembly protein TraU traU
BB788_RS29210 (BB788_28970) 15863..16501 + 639 WP_011977786 type-F conjugative transfer system pilin assembly protein TrbC trbC
BB788_RS29215 (BB788_28975) 16560..18515 + 1956 WP_004152673 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BB788_RS29220 (BB788_28980) 18547..18801 + 255 WP_073558194 conjugal transfer protein TrbE -
BB788_RS29225 (BB788_28985) 18779..19027 + 249 WP_004152675 hypothetical protein -
BB788_RS29230 (BB788_28990) 19040..19366 + 327 WP_004152676 hypothetical protein -
BB788_RS29235 (BB788_28995) 19387..20139 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
BB788_RS29240 (BB788_29000) 20150..20389 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
BB788_RS29245 (BB788_29005) 20361..20918 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
BB788_RS29250 (BB788_29010) 20964..21407 + 444 WP_004194305 F-type conjugal transfer protein TrbF -
BB788_RS29255 (BB788_29015) 21385..22764 + 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
BB788_RS29260 (BB788_29020) 22764..25616 + 2853 WP_073558195 conjugal transfer mating-pair stabilization protein TraG traG
BB788_RS29265 (BB788_29025) 25619..26152 + 534 WP_014343486 conjugal transfer protein TraS -
BB788_RS29270 (BB788_29030) 26338..27069 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
BB788_RS32730 27262..27951 + 690 WP_072101983 hypothetical protein -
BB788_RS29280 (BB788_29040) 28080..30392 + 2313 WP_077272951 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3266 GenBank   NZ_CP018340
Plasmid name   pKp_Goe_414-3 Incompatibility group   IncFII
Plasmid size   81939 bp Coordinate of oriT [Strand]   2125..2173 [-]
Host baterium   Klebsiella pneumoniae isolate Kp_Goe_154414

Cargo genes

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