Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104409
Name   oriT_pRHBSTW-00405_5 in_silico
Organism   Klebsiella pneumoniae strain RHBSTW-00405
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055521 (35789..35836 [-], 48 nt)
oriT length   48 nt
IRs (inverted repeats)      5..12, 15..22  (GCAAAATT..AATTTTGC)
Location of nic site      31..32
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 48 nt

>oriT_pRHBSTW-00405_5
ATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3213 GenBank   WP_181466069
Name   traI_HV185_RS28660_pRHBSTW-00405_5 insolico UniProt ID   _
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190098.84 Da        Isoelectric Point: 6.1737

>WP_181466069.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTVAVKQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQTAFGKLYREALKPLVE
KLGYETKVVGKHGMWEMKDVPVEAFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADAHAAELARAPVAPEKTDGPDITDVVTRAIAGLSDRKVQFTYADVLARTVGQLE
AKPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDAGVVREKP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSREFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGKQATADIISEPDKSARYSRLAQEFAASVREGQESVAQISGAREQNVLNNVIRDTLKNEGALGNRD
MAVTALTPVWLDSKSRGVRDFYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAV
DSQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGNHIRLYSAQDAARTTEKLARHTAFSVVSE
QLKARSGEADLEAAIAQQKAGLHTPAEQAVHLSIPLLESNSLTFTRPQLLAAALETGDGKVPMKDIEATI
QAQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMGRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFKAVMSAISLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDISRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQ
DALKEGKEIPPGTPVSLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTL
PVLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTL
YRPEHITVSQGDRMRFSKSDPERGYVANSVWEVKTVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGVEGRRKALVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PQNARAVKNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRDGRLEAIGGEGRIMGDETARFVALQSSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDR
PWNPEAITGGRIWADPLPNPPLPDTGTDIPLPPEVLAQRAAEEAQRREMEKQAEQATREVAGEEKKAGEP
GERIKEVIGDVIRGLERDRPGEEKTRLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(577-629)

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

(635-714)

AAA domain (AAA_30)

(971-1157)

TrwC relaxase (TrwC)

(10-284)

DNA helicase TraI (TraI_C)

(1433-1555)


  Protein structure



No available structure.




T4CP

ID   3127 GenBank   WP_064174013
Name   traD_HV185_RS28655_pRHBSTW-00405_5 insolico UniProt ID   _
Length   766 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 766 a.a.        Molecular weight: 85728.45 Da        Isoelectric Point: 4.8494

>WP_064174013.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGSLARALFTPDAPEPEQSDADSRTSPGQPEPESAP
VSPAPVKSASTAETLAAQPSVKASEAPQAKVTTVPLTRPVPAATTTAAASATGSSAAATATTGGTEQELA
QQPAEQGQEMMPAGMNEDGEIEDMQAYDAWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  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: 38287..61800

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV185_RS28490 (HV185_28500) 34657..35199 + 543 WP_181466071 antirestriction protein -
HV185_RS28495 (HV185_28505) 35222..35644 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
HV185_RS28500 (HV185_28510) 36137..36532 + 396 WP_022644714 conjugal transfer relaxosome DNA-binding protein TraM -
HV185_RS28505 (HV185_28515) 36704..37390 + 687 WP_022644713 transcriptional regulator TraJ family protein -
HV185_RS28510 (HV185_28520) 37469..37849 + 381 WP_032409797 TraY domain-containing protein -
HV185_RS28515 (HV185_28525) 37908..38273 + 366 WP_020314752 type IV conjugative transfer system pilin TraA -
HV185_RS28520 (HV185_28530) 38287..38592 + 306 WP_020323523 type IV conjugative transfer system protein TraL traL
HV185_RS28525 (HV185_28535) 38612..39178 + 567 WP_064373744 type IV conjugative transfer system protein TraE traE
HV185_RS28530 (HV185_28540) 39165..39905 + 741 WP_181466067 type-F conjugative transfer system secretin TraK traK
HV185_RS28535 (HV185_28545) 39905..41320 + 1416 WP_064362917 F-type conjugal transfer pilus assembly protein TraB traB
HV185_RS28540 (HV185_28550) 41313..41915 + 603 WP_115723427 conjugal transfer protein TraP -
HV185_RS29900 (HV185_28555) 41983..42120 + 138 Protein_61 conjugal transfer protein TraP -
HV185_RS28550 (HV185_28560) 42143..42706 + 564 WP_181466068 type IV conjugative transfer system lipoprotein TraV traV
HV185_RS28555 (HV185_28565) 42853..43056 + 204 WP_064362911 hypothetical protein -
HV185_RS28560 (HV185_28570) 43297..43710 + 414 WP_020315139 hypothetical protein -
HV185_RS28565 (HV185_28575) 43739..44038 + 300 WP_020315144 hypothetical protein -
HV185_RS28570 (HV185_28580) 44055..44279 + 225 WP_022644711 hypothetical protein -
HV185_RS28575 (HV185_28585) 44276..44680 + 405 WP_064362909 hypothetical protein -
HV185_RS28580 (HV185_28590) 44813..47452 + 2640 WP_064362907 type IV secretion system protein TraC virb4
HV185_RS28585 (HV185_28595) 47485..47886 + 402 WP_064362936 type-F conjugative transfer system protein TrbI -
HV185_RS28590 (HV185_28600) 47883..48509 + 627 WP_064362905 type-F conjugative transfer system protein TraW traW
HV185_RS28595 (HV185_28605) 48529..49512 + 984 WP_155553410 conjugal transfer pilus assembly protein TraU traU
HV185_RS28600 (HV185_28610) 49525..50142 + 618 WP_064362903 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV185_RS28605 (HV185_28615) 50139..52019 + 1881 WP_064362901 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV185_RS28610 (HV185_28620) 52057..52338 + 282 WP_064174416 hypothetical protein -
HV185_RS28615 (HV185_28625) 52328..52555 + 228 WP_064174417 conjugal transfer protein TrbE -
HV185_RS28620 (HV185_28630) 52566..52892 + 327 WP_064362899 hypothetical protein -
HV185_RS28625 (HV185_28635) 52911..53663 + 753 WP_040118488 type-F conjugative transfer system pilin assembly protein TraF traF
HV185_RS28630 (HV185_28640) 53674..53913 + 240 WP_047722563 type-F conjugative transfer system pilin chaperone TraQ -
HV185_RS28635 (HV185_28645) 53885..54463 + 579 WP_064362897 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV185_RS28640 (HV185_28650) 54450..55820 + 1371 WP_064362895 conjugal transfer pilus assembly protein TraH traH
HV185_RS28645 (HV185_28655) 55820..58690 + 2871 WP_064362893 conjugal transfer mating-pair stabilization protein TraG traG
HV185_RS28650 (HV185_28660) 58824..59264 + 441 WP_224313869 conjugal transfer protein TraS -
HV185_RS28655 (HV185_28665) 59500..61800 + 2301 WP_064174013 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   4848 GenBank   NZ_CP055521
Plasmid name   pRHBSTW-00405_5 Incompatibility group   IncFII
Plasmid size   71963 bp Coordinate of oriT [Strand]   35789..35836 [-]
Host baterium   Klebsiella pneumoniae strain RHBSTW-00405

Cargo genes

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