Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102793
Name   oriT_pUCLAOXA232-6 in_silico
Organism   Klebsiella pneumoniae strain UCLAOXA232KP
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP012567 (54037..54086 [-], 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_pUCLAOXA232-6
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2065 GenBank   WP_071854302
Name   traI_AM277_RS30465_pUCLAOXA232-6 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190549.09 Da        Isoelectric Point: 6.0386

>WP_071854302.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   1723 GenBank   WP_014386205
Name   traD_AM277_RS30460_pUCLAOXA232-6 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: 85924.97 Da        Isoelectric Point: 5.1787

>WP_014386205.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAVAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 53479..82129

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AM277_RS30220 (AM277_28855) 48530..48880 + 351 WP_014386186 hypothetical protein -
AM277_RS30235 (AM277_28860) 49517..49843 + 327 WP_014386187 hypothetical protein -
AM277_RS30240 (AM277_28865) 49905..50117 + 213 WP_014386188 hypothetical protein -
AM277_RS30245 (AM277_28870) 50128..50352 + 225 WP_014386189 hypothetical protein -
AM277_RS30250 (AM277_28875) 50433..50753 + 321 WP_014386190 type II toxin-antitoxin system RelE/ParE family toxin -
AM277_RS30255 (AM277_28880) 50743..51021 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
AM277_RS30260 (AM277_28885) 51022..51435 + 414 WP_013023817 helix-turn-helix domain-containing protein -
AM277_RS30280 (AM277_28890) 52268..53088 + 821 Protein_62 DUF932 domain-containing protein -
AM277_RS33085 53121..53447 + 327 Protein_63 DUF5983 family protein -
AM277_RS30285 (AM277_28895) 53479..53964 - 486 WP_001568108 transglycosylase SLT domain-containing protein virB1
AM277_RS30290 (AM277_28900) 54355..54771 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
AM277_RS30295 (AM277_28905) 54970..55689 + 720 WP_162899473 conjugal transfer protein TrbJ -
AM277_RS30300 55822..56025 + 204 WP_171486139 TraY domain-containing protein -
AM277_RS30305 (AM277_28910) 56090..56458 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
AM277_RS30310 (AM277_28915) 56472..56777 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
AM277_RS30315 (AM277_28920) 56797..57363 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
AM277_RS30320 (AM277_28925) 57350..58090 + 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
AM277_RS30325 (AM277_28930) 58090..59514 + 1425 WP_032426793 F-type conjugal transfer pilus assembly protein TraB traB
AM277_RS30330 (AM277_28935) 59628..60212 + 585 WP_004161368 type IV conjugative transfer system lipoprotein TraV traV
AM277_RS30335 (AM277_28940) 60535..60753 + 219 WP_004195468 hypothetical protein -
AM277_RS30340 (AM277_28945) 60754..61065 + 312 WP_013214022 hypothetical protein -
AM277_RS30345 (AM277_28950) 61132..61536 + 405 WP_004197817 hypothetical protein -
AM277_RS30360 (AM277_28955) 61913..62311 + 399 WP_014343490 hypothetical protein -
AM277_RS30365 (AM277_28960) 62383..65022 + 2640 WP_013214024 type IV secretion system protein TraC virb4
AM277_RS30370 (AM277_28965) 65022..65411 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
AM277_RS30375 (AM277_28970) 65411..66046 + 636 WP_013214026 type-F conjugative transfer system protein TraW traW
AM277_RS30380 (AM277_28975) 66081..66482 + 402 WP_004194979 hypothetical protein -
AM277_RS30385 (AM277_28980) 66479..67468 + 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
AM277_RS30390 (AM277_28985) 67481..68119 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
AM277_RS30395 (AM277_28990) 68178..70133 + 1956 WP_014343489 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AM277_RS30400 (AM277_28995) 70165..70419 + 255 WP_004152674 conjugal transfer protein TrbE -
AM277_RS30405 (AM277_29000) 70397..70645 + 249 WP_013214029 hypothetical protein -
AM277_RS30410 (AM277_29005) 70658..70984 + 327 WP_013214030 hypothetical protein -
AM277_RS30415 (AM277_29010) 71005..71757 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
AM277_RS30420 (AM277_29015) 71768..72007 + 240 WP_032440623 type-F conjugative transfer system pilin chaperone TraQ -
AM277_RS30425 (AM277_29020) 71979..72536 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AM277_RS30430 (AM277_29025) 72582..73025 + 444 WP_013214032 F-type conjugal transfer protein TrbF -
AM277_RS30435 (AM277_29030) 73003..74382 + 1380 WP_072157884 conjugal transfer pilus assembly protein TraH traH
AM277_RS30440 (AM277_29035) 74382..77204 + 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
AM277_RS30445 77227..77829 + 603 WP_013214035 conjugal transfer protein TraS -
AM277_RS30450 (AM277_29040) 78080..78811 + 732 WP_013214036 conjugal transfer complement resistance protein TraT -
AM277_RS32755 79004..79693 + 690 WP_014343485 hypothetical protein -
AM277_RS30460 (AM277_29050) 79820..82129 + 2310 WP_014386205 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3236 GenBank   NZ_CP012567
Plasmid name   pUCLAOXA232-6 Incompatibility group   IncFIB
Plasmid size   196706 bp Coordinate of oriT [Strand]   54037..54086 [-]
Host baterium   Klebsiella pneumoniae strain UCLAOXA232KP

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, blaOXA-1
Virulence gene   -
Metal resistance gene   arsR, arsD, arsA, arsB, arsC, arsH, pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9