Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103784
Name   oriT_pCHS4.2-2 in_silico
Organism   Klebsiella pneumoniae strain CHS4.2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OL964515 (111456..111505 [-], 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_pCHS4.2-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2812 GenBank   WP_029498346
Name   traI_L7A80_RS00780_pCHS4.2-2 insolico UniProt ID   A0A2R4NEL5
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190742.66 Da        Isoelectric Point: 6.1403

>WP_029498346.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELLEAAGPDASLKSRDVAALDTRKSKEAIDPAENMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETAMVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLLEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRIWAEPAPVAPVPQTGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

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

(576-628)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   2634 GenBank   WP_048255491
Name   traD_L7A80_RS00775_pCHS4.2-2 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84914.98 Da        Isoelectric Point: 5.0560

>WP_048255491.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYAAWLADEQTQRDMQRREEVNINHNHRHDEQDDVEIGGNI

  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: 110898..140110

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L7A80_RS00565 106287..106514 + 228 WP_004182050 hypothetical protein -
L7A80_RS00570 106606..106836 + 231 WP_001568051 hypothetical protein -
L7A80_RS00575 106888..108243 + 1356 WP_004182052 DUF3560 domain-containing protein -
L7A80_RS00580 108291..108854 + 564 WP_004182054 methyltransferase -
L7A80_RS00585 109682..110503 + 822 WP_004182076 DUF932 domain-containing protein -
L7A80_RS00590 110536..110865 + 330 WP_011977736 DUF5983 family protein -
L7A80_RS00595 110898..111383 - 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
L7A80_RS00600 111774..112190 + 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
L7A80_RS00605 112390..113109 + 720 WP_016831034 conjugal transfer protein TrbJ -
L7A80_RS00610 113242..113448 + 207 WP_171773970 TraY domain-containing protein -
L7A80_RS00615 113510..113878 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
L7A80_RS00620 113892..114197 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
L7A80_RS00625 114217..114783 + 567 WP_016831035 type IV conjugative transfer system protein TraE traE
L7A80_RS00630 114770..115510 + 741 WP_047670045 type-F conjugative transfer system secretin TraK traK
L7A80_RS00635 115510..116934 + 1425 WP_015632498 F-type conjugal transfer pilus assembly protein TraB traB
L7A80_RS00640 116927..117523 + 597 WP_047670043 conjugal transfer pilus-stabilizing protein TraP -
L7A80_RS00645 117546..118130 + 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
L7A80_RS00650 118262..118672 + 411 WP_015632501 hypothetical protein -
L7A80_RS00655 118677..118946 + 270 WP_032433956 hypothetical protein -
L7A80_RS00660 118985..119203 + 219 WP_004171484 hypothetical protein -
L7A80_RS00665 119204..119515 + 312 WP_015632502 hypothetical protein -
L7A80_RS00670 119582..119986 + 405 WP_032433941 hypothetical protein -
L7A80_RS00675 120029..120418 + 390 WP_015632504 hypothetical protein -
L7A80_RS00680 120426..120824 + 399 WP_015632505 hypothetical protein -
L7A80_RS00685 120896..123535 + 2640 WP_015632506 type IV secretion system protein TraC virb4
L7A80_RS00690 123535..123924 + 390 WP_015632507 type-F conjugative transfer system protein TrbI -
L7A80_RS00695 123924..124559 + 636 WP_236940752 type-F conjugative transfer system protein TraW traW
L7A80_RS00700 124594..124995 + 402 WP_004194979 hypothetical protein -
L7A80_RS00705 124992..125981 + 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
L7A80_RS00710 126257..126904 + 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
L7A80_RS00715 126963..128918 + 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
L7A80_RS00720 128950..129204 + 255 WP_032433943 conjugal transfer protein TrbE -
L7A80_RS00725 129182..129430 + 249 WP_004152675 hypothetical protein -
L7A80_RS00730 129443..129769 + 327 WP_015632512 hypothetical protein -
L7A80_RS00735 129790..130542 + 753 WP_015632513 type-F conjugative transfer system pilin assembly protein TraF traF
L7A80_RS00740 130553..130792 + 240 WP_048255490 type-F conjugative transfer system pilin chaperone TraQ -
L7A80_RS00745 130764..131321 + 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
L7A80_RS00750 131367..131810 + 444 WP_023158001 F-type conjugal transfer protein TrbF -
L7A80_RS00755 131788..133167 + 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
L7A80_RS00760 133167..136016 + 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
L7A80_RS00765 136022..136549 + 528 WP_029498351 conjugal transfer protein TraS -
L7A80_RS00770 136739..137470 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
L7A80_RS00775 137828..140110 + 2283 WP_048255491 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4224 GenBank   NZ_OL964515
Plasmid name   pCHS4.2-2 Incompatibility group   IncFIB
Plasmid size   204092 bp Coordinate of oriT [Strand]   111456..111505 [-]
Host baterium   Klebsiella pneumoniae strain CHS4.2

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, qnrS1, blaLAP-2, aac(3)-IId, blaCTX-M-14
Virulence gene   -
Metal resistance gene   fecD, fecE, arsC, arsB, arsA, arsD, arsR, pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -