Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117851
Name   oriT_pKO41-2 in_silico
Organism   Klebsiella michiganensis strain KM41
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP090079 (146486..146535 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKO41-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11341 GenBank   WP_040224080
Name   traI_LW125_RS29095_pKO41-2 insolico UniProt ID   A0A7W3BA55
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190352.82 Da        Isoelectric Point: 5.9133

>WP_040224080.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVIGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMNVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASETLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   13253 GenBank   WP_023329042
Name   traD_LW125_RS29100_pKO41-2 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: 85943.90 Da        Isoelectric Point: 5.0577

>WP_023329042.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEARESEGSLARTLFMPDAPASGPADTNSHAGEQPEPISQPA
PADMTVSPAPVKAPPTTKSPAAEPSVRATEPPVLRVTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 117849..147093

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LW125_RS29100 117849..120158 - 2310 WP_023329042 type IV conjugative transfer system coupling protein TraD virb4
LW125_RS29105 120516..121247 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
LW125_RS29110 121437..121964 - 528 WP_029498351 conjugal transfer protein TraS -
LW125_RS29115 121970..124819 - 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
LW125_RS29120 124819..126198 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
LW125_RS29125 126176..126619 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
LW125_RS29130 126665..127222 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LW125_RS29135 127194..127433 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
LW125_RS29140 127444..128196 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
LW125_RS29145 128217..128543 - 327 WP_015065534 hypothetical protein -
LW125_RS29150 128556..128804 - 249 WP_004152675 hypothetical protein -
LW125_RS29155 128782..129036 - 255 WP_015065558 conjugal transfer protein TrbE -
LW125_RS29160 129068..131023 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LW125_RS29165 131082..131729 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
LW125_RS29170 131808..131984 - 177 WP_162866177 hypothetical protein -
LW125_RS29175 132005..132994 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
LW125_RS29180 132991..133392 - 402 WP_023158005 hypothetical protein -
LW125_RS29185 133427..134062 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
LW125_RS29190 134062..134451 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LW125_RS29195 134451..137090 - 2640 WP_023158007 type IV secretion system protein TraC virb4
LW125_RS29200 137162..137560 - 399 WP_023158008 hypothetical protein -
LW125_RS29205 137568..137957 - 390 WP_023158009 hypothetical protein -
LW125_RS29210 138000..138404 - 405 WP_016831042 hypothetical protein -
LW125_RS29215 138471..138782 - 312 WP_014386200 hypothetical protein -
LW125_RS29220 138783..139001 - 219 WP_014386199 hypothetical protein -
LW125_RS29225 139025..139314 - 290 Protein_149 hypothetical protein -
LW125_RS29230 139319..139729 - 411 WP_016831039 hypothetical protein -
LW125_RS29235 139861..140445 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
LW125_RS29240 140468..141064 - 597 Protein_152 conjugal transfer pilus-stabilizing protein TraP -
LW125_RS29245 141057..142481 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
LW125_RS29250 142481..143221 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
LW125_RS29255 143208..143774 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
LW125_RS29260 143794..144099 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LW125_RS29265 144113..144481 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LW125_RS29270 144543..144749 - 207 WP_171773970 TraY domain-containing protein -
LW125_RS29275 144882..145601 - 720 WP_016831034 conjugal transfer protein TrbJ -
LW125_RS29280 145801..146217 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
LW125_RS29285 146608..147093 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
LW125_RS29290 147126..147455 - 330 WP_011977736 DUF5983 family protein -
LW125_RS29295 147488..148309 - 822 WP_004182076 DUF932 domain-containing protein -
LW125_RS29300 148508..149716 + 1209 WP_001339197 IS4-like element ISVsa5 family transposase -
LW125_RS29305 150480..150893 - 414 WP_004182074 type II toxin-antitoxin system HigA family antitoxin -
LW125_RS29310 150894..151172 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
LW125_RS29315 151162..151482 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
LW125_RS29320 151563..151787 - 225 WP_020325128 hypothetical protein -
LW125_RS29325 151798..152010 - 213 WP_004182070 hypothetical protein -

Host bacterium

ID   18284 GenBank   NZ_CP090079
Plasmid name   pKO41-2 Incompatibility group   IncFII
Plasmid size   235644 bp Coordinate of oriT [Strand]   146486..146535 [+]
Host baterium   Klebsiella michiganensis strain KM41

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   fecD, fecE, arsB, arsC, merR2, merT, merP, merF, merA, merD, merE, silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9