Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104059
Name   oriT_pKP3 in_silico
Organism   Klebsiella pneumoniae strain KP3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OL804387 (57011..57060 [-], 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_pKP3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3004 GenBank   WP_237737390
Name   traI_MCP59_RS00485_pKP3 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: 190348.01 Da        Isoelectric Point: 6.0657

>WP_237737390.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDTAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWEPETRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQCREMEKQAEQTAREVAGEARKAGEPA
DRVKEAIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
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)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(11-283)


  Protein structure



No available structure.




T4CP

ID   2879 GenBank   WP_237737389
Name   traD_MCP59_RS00480_pKP3 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: 85978.04 Da        Isoelectric Point: 5.0120

>WP_237737389.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPESGPADTNSHAGEQPEPVSQPA
PADMTVSPAPVKAPPTTKMPAEEPSVRATEPSVLRLTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 56453..84568

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MCP59_RS00290 51845..52072 + 228 WP_020803451 hypothetical protein -
MCP59_RS00295 52164..52394 + 231 WP_001568051 hypothetical protein -
MCP59_RS00300 52446..53801 + 1356 WP_118860665 DUF3560 domain-containing protein -
MCP59_RS00305 53849..54412 + 564 WP_004152756 methyltransferase -
MCP59_RS00310 55237..56058 + 822 WP_237737386 DUF932 domain-containing protein -
MCP59_RS00315 56091..56420 + 330 WP_011977736 DUF5983 family protein -
MCP59_RS00320 56453..56938 - 486 WP_032440470 transglycosylase SLT domain-containing protein virB1
MCP59_RS00325 57329..57745 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
MCP59_RS00330 57945..58664 + 720 WP_172691949 conjugal transfer protein TrbJ -
MCP59_RS00335 58797..59000 + 204 WP_171486139 TraY domain-containing protein -
MCP59_RS00340 59065..59433 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
MCP59_RS00345 59447..59752 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
MCP59_RS00350 59772..60338 + 567 WP_064161971 type IV conjugative transfer system protein TraE traE
MCP59_RS00355 60325..61065 + 741 WP_172691947 type-F conjugative transfer system secretin TraK traK
MCP59_RS00360 61065..62489 + 1425 WP_185775340 F-type conjugal transfer pilus assembly protein TraB traB
MCP59_RS00365 62562..63146 + 585 WP_093998043 type IV conjugative transfer system lipoprotein TraV traV
MCP59_RS00370 63469..63687 + 219 WP_004171484 hypothetical protein -
MCP59_RS00375 63688..64005 + 318 WP_114473059 hypothetical protein -
MCP59_RS00380 64072..64476 + 405 WP_100748549 hypothetical protein -
MCP59_RS00385 64501..64899 + 399 WP_167875005 hypothetical protein -
MCP59_RS00390 64971..67610 + 2640 WP_150388098 type IV secretion system protein TraC virb4
MCP59_RS00395 67610..67999 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
MCP59_RS00400 67999..68634 + 636 WP_020325113 type-F conjugative transfer system protein TraW traW
MCP59_RS00405 68669..69070 + 402 WP_004194979 hypothetical protein -
MCP59_RS00410 69067..70056 + 990 WP_032441886 conjugal transfer pilus assembly protein TraU traU
MCP59_RS00415 70069..70707 + 639 WP_004152672 type-F conjugative transfer system pilin assembly protein TrbC trbC
MCP59_RS00420 70766..72721 + 1956 WP_237737387 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MCP59_RS00425 72753..72989 + 237 WP_114499720 conjugal transfer protein TrbE -
MCP59_RS00540 72986..73171 + 186 WP_042922350 hypothetical protein -
MCP59_RS00430 73217..73543 + 327 WP_016529362 hypothetical protein -
MCP59_RS00435 73564..74316 + 753 WP_172691972 type-F conjugative transfer system pilin assembly protein TraF traF
MCP59_RS00440 74327..74566 + 240 WP_009309875 type-F conjugative transfer system pilin chaperone TraQ -
MCP59_RS00445 74538..75095 + 558 WP_172691971 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MCP59_RS00450 75142..75588 + 447 WP_172691970 conjugal transfer protein TrbF -
MCP59_RS00455 75578..76945 + 1368 WP_185775342 conjugal transfer pilus assembly protein TraH traH
MCP59_RS00460 76945..79794 + 2850 WP_237737388 conjugal transfer mating-pair stabilization protein TraG traG
MCP59_RS00465 79800..80327 + 528 WP_040120388 conjugal transfer protein TraS -
MCP59_RS00470 80516..81247 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
MCP59_RS00475 81440..82129 + 690 WP_161283537 hypothetical protein -
MCP59_RS00480 82256..84568 + 2313 WP_237737389 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4498 GenBank   NZ_OL804387
Plasmid name   pKP3 Incompatibility group   IncFIA
Plasmid size   95192 bp Coordinate of oriT [Strand]   57011..57060 [-]
Host baterium   Klebsiella pneumoniae strain KP3

Cargo genes

Drug resistance gene   mcr-8
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -