Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102269
Name   oriT_Kp3380|unnamed3 in_silico
Organism   Klebsiella pneumoniae strain Kp3380
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_PITM01000024 (52168..52217 [+], 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_Kp3380|unnamed3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1745 GenBank   WP_043907038
Name   traI_CWR42_RS13320_Kp3380|unnamed3 insolico UniProt ID   A0A0S1TKY9
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190458.19 Da        Isoelectric Point: 6.0263

>WP_043907038.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSLSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWLTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
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)

(969-1156)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   1334 GenBank   WP_013214038
Name   traD_CWR42_RS13325_Kp3380|unnamed3 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: 86010.07 Da        Isoelectric Point: 5.1787

>WP_013214038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 24166..52775

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CWR42_RS13325 (CWR42_13335) 24166..26478 - 2313 WP_013214038 type IV conjugative transfer system coupling protein TraD virb4
CWR42_RS28685 26605..27294 - 690 WP_014343485 hypothetical protein -
CWR42_RS13335 (CWR42_13345) 27487..28218 - 732 WP_013214036 conjugal transfer complement resistance protein TraT -
CWR42_RS13340 (CWR42_13350) 28469..29071 - 603 WP_013214035 conjugal transfer protein TraS -
CWR42_RS13345 (CWR42_13355) 29094..31916 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
CWR42_RS13350 (CWR42_13360) 31916..33295 - 1380 WP_074160414 conjugal transfer pilus assembly protein TraH traH
CWR42_RS13355 (CWR42_13365) 33273..33716 - 444 WP_013214032 F-type conjugal transfer protein TrbF -
CWR42_RS13360 (CWR42_13370) 33762..34319 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CWR42_RS13365 (CWR42_13375) 34291..34530 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
CWR42_RS13370 (CWR42_13380) 34541..35293 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
CWR42_RS13375 (CWR42_13385) 35314..35640 - 327 WP_013214030 hypothetical protein -
CWR42_RS13380 (CWR42_13390) 35653..35901 - 249 WP_013214029 hypothetical protein -
CWR42_RS13385 (CWR42_13395) 35879..36133 - 255 WP_004152674 conjugal transfer protein TrbE -
CWR42_RS13390 (CWR42_13400) 36165..38120 - 1956 WP_014343489 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CWR42_RS13395 (CWR42_13405) 38179..38817 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
CWR42_RS13400 (CWR42_13410) 38830..39819 - 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
CWR42_RS13405 (CWR42_13415) 39816..40217 - 402 WP_004194979 hypothetical protein -
CWR42_RS13410 (CWR42_13420) 40252..40887 - 636 WP_013214026 type-F conjugative transfer system protein TraW traW
CWR42_RS13415 (CWR42_13425) 40887..41276 - 390 WP_013214025 type-F conjugative transfer system protein TrbI -
CWR42_RS13420 (CWR42_13430) 41276..43915 - 2640 WP_013214024 type IV secretion system protein TraC virb4
CWR42_RS13425 (CWR42_13435) 43987..44385 - 399 WP_014343490 hypothetical protein -
CWR42_RS29140 44566..44718 - 153 WP_227850486 hypothetical protein -
CWR42_RS13435 (CWR42_13445) 44761..45165 - 405 WP_004197817 hypothetical protein -
CWR42_RS13440 (CWR42_13450) 45232..45543 - 312 WP_013214022 hypothetical protein -
CWR42_RS13445 (CWR42_13455) 45544..45762 - 219 WP_004195468 hypothetical protein -
CWR42_RS13450 (CWR42_13460) 46085..46669 - 585 WP_014343493 type IV conjugative transfer system lipoprotein TraV traV
CWR42_RS13455 (CWR42_13465) 46741..48164 - 1424 Protein_42 F-type conjugal transfer pilus assembly protein TraB -
CWR42_RS13460 (CWR42_13470) 48164..48904 - 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
CWR42_RS13465 (CWR42_13475) 48891..49457 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
CWR42_RS13470 (CWR42_13480) 49477..49782 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
CWR42_RS13475 (CWR42_13485) 49796..50164 - 369 WP_104011249 type IV conjugative transfer system pilin TraA -
CWR42_RS13480 (CWR42_13490) 50226..50432 - 207 WP_171773970 TraY domain-containing protein -
CWR42_RS13485 (CWR42_13495) 50547..51283 - 737 Protein_48 conjugal transfer protein TrbJ -
CWR42_RS13490 (CWR42_13500) 51483..51899 - 417 WP_014343494 conjugal transfer relaxosome DNA-binding protein TraM -
CWR42_RS13495 (CWR42_13505) 52290..52775 + 486 WP_014343495 transglycosylase SLT domain-containing protein virB1
CWR42_RS13500 (CWR42_13510) 52808..53137 - 330 WP_013214015 DUF5983 family protein -
CWR42_RS13505 (CWR42_13515) 53170..53991 - 822 WP_004152492 DUF932 domain-containing protein -
CWR42_RS29145 (CWR42_13535) 54820..54924 - 105 Protein_53 transcriptional regulator -
CWR42_RS13530 (CWR42_13540) 54928..55206 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
CWR42_RS13535 (CWR42_13545) 55196..55516 - 321 WP_014343498 type II toxin-antitoxin system RelE/ParE family toxin -
CWR42_RS13540 (CWR42_13550) 55597..55821 - 225 WP_014343499 hypothetical protein -
CWR42_RS13545 (CWR42_13555) 55832..56044 - 213 WP_014343500 hypothetical protein -
CWR42_RS13550 (CWR42_13560) 56105..56461 - 357 WP_014343501 hypothetical protein -
CWR42_RS13560 (CWR42_13570) 57302..57619 - 318 WP_014343505 hypothetical protein -

Host bacterium

ID   2713 GenBank   NZ_PITM01000024
Plasmid name   Kp3380|unnamed3 Incompatibility group   -
Plasmid size   70302 bp Coordinate of oriT [Strand]   52168..52217 [+]
Host baterium   Klebsiella pneumoniae strain Kp3380

Cargo genes

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