Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105997
Name   oriT_pKpn13-1 in_silico
Organism   Klebsiella pneumoniae strain Kpn-13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047708 (143513..143562 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKpn13-1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4032 GenBank   WP_023287123
Name   traI_GVI78_RS25750_pKpn13-1 insolico UniProt ID   A0A486VBD3
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190201.88 Da        Isoelectric Point: 6.2218

>WP_023287123.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINTTQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGAREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPAQEKAIQK
ALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   4044 GenBank   WP_023313941
Name   traD_GVI78_RS25755_pKpn13-1 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85666.78 Da        Isoelectric Point: 5.2499

>WP_023313941.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 122484..144114

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GVI78_RS25755 (GVI78_25415) 122484..124793 - 2310 WP_023313941 type IV conjugative transfer system coupling protein TraD virb4
GVI78_RS25760 124920..125609 - 690 WP_013023831 hypothetical protein -
GVI78_RS25765 (GVI78_25425) 125802..126236 - 435 Protein_122 complement resistance protein TraT -
GVI78_RS25770 (GVI78_25430) 126251..127219 + 969 WP_015958259 IS5 family transposase -
GVI78_RS25775 (GVI78_25435) 127278..128921 - 1644 Protein_124 conjugal transfer protein TraN -
GVI78_RS25780 (GVI78_25440) 128980..129618 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
GVI78_RS25785 (GVI78_25445) 129631..130620 - 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
GVI78_RS25790 (GVI78_25450) 130617..131018 - 402 WP_004194979 hypothetical protein -
GVI78_RS25795 (GVI78_25455) 131053..131688 - 636 WP_013214026 type-F conjugative transfer system protein TraW traW
GVI78_RS25800 (GVI78_25460) 131688..132077 - 390 WP_013214025 type-F conjugative transfer system protein TrbI -
GVI78_RS25805 (GVI78_25465) 132077..134716 - 2640 WP_032431388 type IV secretion system protein TraC virb4
GVI78_RS25810 (GVI78_25470) 134788..135186 - 399 WP_023179972 hypothetical protein -
GVI78_RS25815 (GVI78_25475) 135565..135969 - 405 WP_197384183 hypothetical protein -
GVI78_RS25820 (GVI78_25480) 136036..136347 - 312 WP_197384184 hypothetical protein -
GVI78_RS25825 (GVI78_25485) 136348..136566 - 219 WP_004195468 hypothetical protein -
GVI78_RS25830 (GVI78_25490) 136889..137473 - 585 WP_197384185 type IV conjugative transfer system lipoprotein TraV traV
GVI78_RS25835 (GVI78_25495) 137496..138092 - 597 WP_197384186 conjugal transfer pilus-stabilizing protein TraP -
GVI78_RS25840 (GVI78_25500) 138085..139509 - 1425 WP_004233801 F-type conjugal transfer pilus assembly protein TraB traB
GVI78_RS25845 (GVI78_25505) 139509..140249 - 741 WP_197384187 type-F conjugative transfer system secretin TraK traK
GVI78_RS25850 (GVI78_25510) 140236..140802 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
GVI78_RS25855 (GVI78_25515) 140822..141127 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
GVI78_RS25860 (GVI78_25520) 141141..141509 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
GVI78_RS25865 (GVI78_25525) 141571..141777 - 207 WP_171773970 TraY domain-containing protein -
GVI78_RS25870 (GVI78_25530) 141910..142629 - 720 WP_197384188 conjugal transfer protein TrbJ -
GVI78_RS25875 (GVI78_25535) 142828..143244 - 417 WP_167878886 conjugal transfer relaxosome DNA-binding protein TraM -
GVI78_RS25880 (GVI78_25540) 143707..144114 + 408 WP_225011827 transglycosylase SLT domain-containing protein virB1
GVI78_RS25885 (GVI78_25545) 144152..144682 - 531 WP_049070338 antirestriction protein -
GVI78_RS25890 (GVI78_25550) 144874..145104 + 231 WP_197384202 hypothetical protein -
GVI78_RS25895 (GVI78_25555) 145199..145903 - 705 WP_117048525 IS6-like element IS26 family transposase -
GVI78_RS25900 (GVI78_25560) 145980..146906 - 927 WP_001554380 LysR family transcriptional regulator -
GVI78_RS25905 (GVI78_25565) 147036..147824 + 789 WP_001554379 alpha/beta hydrolase -
GVI78_RS25910 (GVI78_25570) 148016..148195 + 180 Protein_151 hypothetical protein -

Host bacterium

ID   6434 GenBank   NZ_CP047708
Plasmid name   pKpn13-1 Incompatibility group   IncFIB
Plasmid size   181030 bp Coordinate of oriT [Strand]   143513..143562 [+]
Host baterium   Klebsiella pneumoniae strain Kpn-13

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9