Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105235
Name   oriT_pRHBSTW-00634_7 in_silico
Organism   Klebsiella grimontii strain RHBSTW-00634
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056688 (38680..38729 [-], 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    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pRHBSTW-00634_7
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3597 GenBank   WP_064174014
Name   traI_HV252_RS32185_pRHBSTW-00634_7 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: 190116.90 Da        Isoelectric Point: 6.2259

>WP_064174014.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMEERWQGKGAEALGLDGKAVDKAVFTELLKGKLPDGSDLTRM
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTVAVKQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQLHTHAVVINATQNGDKWQSLGTDTVGKTGFIENVYANQTAFGKLYREALKPLVE
KLGYETKVVGKHGMWEMKDVPVEAFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMN
TLKETGFDIRGYREAADAHAAELARAPVAPEKTDGPDITDVVTRAIAGLSDRKVQFTYADVLARTVGQLE
AKPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEIQRQNHVSVTPDAGVVREKP
FSDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSREFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGKQATADIISEPDKSARYSRLAQEFAASVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGNRD
MAVTALTPVWLDSKSRGVRDFYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSAV
DSQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGI
KVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGNHIRLYSAQDAARTTEKLARHTAFSVVSE
QLKARSGEADLEAAIAQQKAGLHTPAEQAVHLSIPLLESNSLTFTRPQLLATALETGGGKVPMKDIEATI
QAQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAVAPLMGRVPGSLMTDLTAGQRAATR
MILETPDRFTVVQGYAGVGKTTQFKAVMSAISLLPEETRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLH
DTQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQR
SAADVAIMKEIVRQVPELRPAVYSLIDRDISRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQ
DALKEGKEIPPGTPVSLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTL
PVLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTL
YRPEHITVSQGDRMRFSKSDLERGYVANSVWEVKTVSGDSVTLSDGKTTRTLNPKADEAQRHIDLAYAIT
AHGAQGASEPFAIALEGVEGRRKALVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLE
PQNARAVKNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGI
WLSPLTDRDGRLEAIGGEGRIMGDETARFVALQSSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDR
PWNPEAITGGRIWADPLPNPPLPDTGTDIPLPPEVLAQRAAEEAQRREMEKQAEQATREVAGEEKKAGEP
GERIKEVIGDVIRGLERDRPGEEKTRLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)

TrwC relaxase (TrwC)

(10-284)


  Protein structure



No available structure.




T4CP

ID   3557 GenBank   WP_064174013
Name   traD_HV252_RS32180_pRHBSTW-00634_7 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: 41188..65068

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV252_RS32010 (HV252_32015) 37548..38090 + 543 WP_020804853 antirestriction protein -
HV252_RS32015 (HV252_32020) 38113..38535 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
HV252_RS32020 (HV252_32025) 39029..39427 + 399 WP_064174027 conjugal transfer relaxosome DNA-binding protein TraM -
HV252_RS32025 (HV252_32030) 39601..40287 + 687 WP_064174026 transcriptional regulator TraJ family protein -
HV252_RS32030 (HV252_32035) 40366..40752 + 387 WP_064174025 TraY domain-containing protein -
HV252_RS32035 (HV252_32040) 40806..41174 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
HV252_RS32040 (HV252_32045) 41188..41493 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HV252_RS32045 (HV252_32050) 41513..42079 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
HV252_RS32050 (HV252_32055) 42066..42806 + 741 WP_064174024 type-F conjugative transfer system secretin TraK traK
HV252_RS32055 (HV252_32060) 42806..44230 + 1425 WP_042946342 F-type conjugal transfer pilus assembly protein TraB traB
HV252_RS32060 (HV252_32065) 44223..44819 + 597 WP_023340943 conjugal transfer pilus-stabilizing protein TraP -
HV252_RS32065 (HV252_32070) 44842..45411 + 570 WP_181511930 type IV conjugative transfer system lipoprotein TraV traV
HV252_RS32070 (HV252_32075) 45543..45953 + 411 WP_023316400 hypothetical protein -
HV252_RS32075 (HV252_32080) 45958..46242 + 285 WP_023316401 hypothetical protein -
HV252_RS32080 (HV252_32085) 46266..46484 + 219 WP_181511931 hypothetical protein -
HV252_RS32085 (HV252_32090) 46485..46796 + 312 WP_023316403 hypothetical protein -
HV252_RS32090 (HV252_32095) 46863..47267 + 405 WP_023316404 hypothetical protein -
HV252_RS32095 (HV252_32100) 47264..47554 + 291 WP_020323516 hypothetical protein -
HV252_RS32100 (HV252_32105) 47562..47960 + 399 WP_072156904 hypothetical protein -
HV252_RS32105 (HV252_32110) 48032..50671 + 2640 WP_040212846 type IV secretion system protein TraC virb4
HV252_RS32110 (HV252_32115) 50671..51060 + 390 WP_021312677 type-F conjugative transfer system protein TrbI -
HV252_RS32115 (HV252_32120) 51060..51686 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
HV252_RS32120 (HV252_32125) 51730..52689 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
HV252_RS32125 (HV252_32130) 52702..53340 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
HV252_RS32130 (HV252_32135) 53399..55354 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HV252_RS32135 (HV252_32140) 55387..55668 + 282 WP_022644736 hypothetical protein -
HV252_RS32140 (HV252_32145) 55658..55885 + 228 WP_012540032 conjugal transfer protein TrbE -
HV252_RS32145 (HV252_32150) 55896..56222 + 327 WP_020323521 hypothetical protein -
HV252_RS32150 (HV252_32155) 56243..56995 + 753 WP_064174011 type-F conjugative transfer system pilin assembly protein TraF traF
HV252_RS32155 (HV252_32160) 57006..57245 + 240 WP_020315123 type-F conjugative transfer system pilin chaperone TraQ -
HV252_RS32160 (HV252_32165) 57217..57792 + 576 WP_020315129 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HV252_RS32165 (HV252_32170) 57779..59149 + 1371 WP_020315127 conjugal transfer pilus assembly protein TraH traH
HV252_RS32170 (HV252_32175) 59149..61998 + 2850 WP_064174012 conjugal transfer mating-pair stabilization protein TraG traG
HV252_RS32175 (HV252_32180) 62004..62531 + 528 WP_020315130 hypothetical protein -
HV252_RS32180 (HV252_32185) 62768..65068 + 2301 WP_064174013 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5673 GenBank   NZ_CP056688
Plasmid name   pRHBSTW-00634_7 Incompatibility group   IncFII
Plasmid size   75825 bp Coordinate of oriT [Strand]   38680..38729 [-]
Host baterium   Klebsiella grimontii strain RHBSTW-00634

Cargo genes

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