Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119144
Name   oriT_pKOXM1B in_silico
Organism   Klebsiella michiganensis strain M1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP008843 (24308..24356 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pKOXM1B
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12106 GenBank   WP_040118495
Name   traI_HR38_RS28440_pKOXM1B insolico UniProt ID   A0A7H9GIQ2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190247.71 Da        Isoelectric Point: 6.0516

>WP_040118495.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVTGSMEERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLAGTRVQKDGVSETVLTGNLI
IARFNHDTSRAQEPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSENLLANRIALGKIYQSALRADIES
MGYKTVDAGKHGMWEMKDVPVEAFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADAHAAELARAPAAPVKTDGPDIADVVTRAIAGLSDRKVQFTYADVLARTVGQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVMREKPF
SDAVSVLAQDRPAMGIVAGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGRQATADIISEPDKSVRYSRLAQEFAVSVREGQESVAQISGTREQNVLNNVIRDTLKNEGALGNRDM
TVTALTPVWLDSKSRGVRDYYREGMVMERWDPEARKHDRFVIDRVTASSNMLTLKDREGERLDLKVSVVD
SQWTLFRTDKLPVAEGERLAVLGKIPDTRLKGGESVTVLKAEAGQLTVQRPGQKTTQTLPVGSSPFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKVRSGEADLEAAIAQQKAGLHTPAEQAIHLSVPLLESNSLTFTRTQLLATALETGGGKVPMTDIDATIQ
AQIKAGSLLNVPVASGHGNDLLISRQTWDAEKSVLTRVLEGKDAMTPLMDRVPGSLMTDLTAGQRAATRM
ILETPDRFTVVQGYAGVGKTTQFKSVMSAISLLPEEARSRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLQQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDISRALSTIEQVTPEQVPRKDGAWVPENSVTEFTPAQEKAIQD
ALKEGKEIPPDTPASLHDAIVKDYTGRTPAAQASTLIITHLNADRRALNGLIHDARVQNGEVSKEEVTLP
VLVTSNIRDGELRKLSTWSEHQGAVALLDNTYQRIESVDKENQLITLKDNEGNIRLLSPREASAEGVTLY
RPEHITVSQGDRMRFSKSDPERGYVANSVWEVKAFSGDSVTLTDGKTTRTLNPKADEAQRHIDLAYAITA
HGAQGASEPFAIALEGVEGRRKALVSFESAYVALSRMKQHAQVYTDNREGWTTAVSRSQEKASAHDVLEP
QNARAVRNAGQLYGRAQPLDETAAGRAALQQSGLARGRSPGKFISPGKKYPQPHVALPAFDKNGKEAGIW
LSPLTDRDGRLEAIGGEGRIMGDETARFVALQNSRNGESLLAGNMGEGVRAARNHPDSGVIVRLAGDDRP
WNPEAITGGRVWADPLPNTPLPDTGTDIPLPPDVLAQRAAEEVQRREMEKQAEQTAREVAGEEKKAGEPG
ERIKEVIGDVIRGLERDRPGEEKTLLPDDPQTRRQEAAIQQVASESLQRERLQQMERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   6932 GenBank   WP_020804860
Name   WP_020804860_pKOXM1B insolico UniProt ID   A0A7H9GLQ1
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 15022.07 Da        Isoelectric Point: 4.5248

>WP_020804860.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MGKVQAYPSDEVCEKINAIVEKRRMEGAKDKDVSFSSISTMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESVVKTQFSVNKVLGIECLSPHVKDDPRWQWKGMVQNIQEDVQEVMRTFFPDEQEEADE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A7H9GLQ1


T4CP

ID   14180 GenBank   WP_040118494
Name   traD_HR38_RS28435_pKOXM1B 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: 85764.48 Da        Isoelectric Point: 4.8107

>WP_040118494.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
EIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKDVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRCYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRTLDTRVDARLSALLEAREAEGNLARALFTPDAPEPEQRDADSRTSPGQPEPENAP
VSPAPVKSASTAETLAAPPSVKASEAPQATVTTVPLTRPAPATTPAASSATASSVAATAATTGGTEQELA
QQPADTGQEVMPAGMNEDGEIEDMQAYDTWLADEQTQREMQRREEVNINHSHRRDEQDDIEIGGNF

  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: 26774..50289

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HR38_RS32135 22813..22983 - 171 WP_162933663 hypothetical protein -
HR38_RS28280 (HR38_28955) 23176..23718 + 543 WP_040118470 antirestriction protein -
HR38_RS28285 (HR38_28960) 23741..24163 - 423 WP_051800693 transglycosylase SLT domain-containing protein -
HR38_RS28290 (HR38_28965) 24668..25060 + 393 WP_020804860 conjugal transfer relaxosome DNA-binding protein TraM -
HR38_RS28295 (HR38_28970) 25298..25990 + 693 WP_032426082 conjugal transfer protein TrbJ -
HR38_RS30910 26165..26329 + 165 WP_032426810 TraY domain-containing protein -
HR38_RS28300 (HR38_28975) 26392..26760 + 369 WP_040118418 type IV conjugative transfer system pilin TraA -
HR38_RS28305 (HR38_28980) 26774..27079 + 306 WP_020323523 type IV conjugative transfer system protein TraL traL
HR38_RS28310 (HR38_28985) 27099..27665 + 567 WP_040118472 type IV conjugative transfer system protein TraE traE
HR38_RS28315 (HR38_28990) 27652..28392 + 741 WP_040118473 type-F conjugative transfer system secretin TraK traK
HR38_RS28320 (HR38_28995) 28392..29807 + 1416 WP_040118474 F-type conjugal transfer pilus assembly protein TraB traB
HR38_RS31935 29800..30396 + 597 WP_117146400 conjugal transfer protein TraP -
HR38_RS28330 (HR38_29005) 30636..31217 + 582 WP_040118475 type IV conjugative transfer system lipoprotein TraV traV
HR38_RS28335 (HR38_29010) 31364..31567 + 204 WP_020315141 hypothetical protein -
HR38_RS28340 (HR38_29015) 31808..32221 + 414 WP_040118476 hypothetical protein -
HR38_RS28345 (HR38_29020) 32250..32549 + 300 WP_040118477 hypothetical protein -
HR38_RS28350 (HR38_29025) 32566..32790 + 225 WP_040118478 hypothetical protein -
HR38_RS28355 (HR38_29030) 32787..33191 + 405 WP_040118479 hypothetical protein -
HR38_RS28360 (HR38_29035) 33324..35963 + 2640 WP_040118480 type IV secretion system protein TraC virb4
HR38_RS28365 (HR38_29040) 35996..36397 + 402 WP_051800694 type-F conjugative transfer system protein TrbI -
HR38_RS28370 (HR38_29045) 36394..37020 + 627 WP_040118481 type-F conjugative transfer system protein TraW traW
HR38_RS28375 (HR38_29050) 37040..38023 + 984 WP_074423225 conjugal transfer pilus assembly protein TraU traU
HR38_RS28380 (HR38_29055) 38036..38653 + 618 WP_040118483 type-F conjugative transfer system pilin assembly protein TrbC trbC
HR38_RS28385 (HR38_29060) 38650..40530 + 1881 WP_040118484 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HR38_RS28390 (HR38_29065) 40568..40849 + 282 WP_040118485 hypothetical protein -
HR38_RS28395 (HR38_29070) 40839..41066 + 228 WP_040118486 conjugal transfer protein TrbE -
HR38_RS28400 (HR38_29075) 41077..41403 + 327 WP_040118487 hypothetical protein -
HR38_RS28405 (HR38_29080) 41422..42174 + 753 WP_040118488 type-F conjugative transfer system pilin assembly protein TraF traF
HR38_RS28410 (HR38_29085) 42185..42424 + 240 WP_040118489 type-F conjugative transfer system pilin chaperone TraQ -
HR38_RS28415 (HR38_29090) 42396..42971 + 576 WP_040118490 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HR38_RS28420 (HR38_29095) 42958..44328 + 1371 WP_040118491 conjugal transfer pilus assembly protein TraH traH
HR38_RS28425 (HR38_29100) 44328..47201 + 2874 WP_040118492 conjugal transfer mating-pair stabilization protein TraG traG
HR38_RS28430 (HR38_29105) 47212..47745 + 534 WP_040118493 hypothetical protein -
HR38_RS28435 (HR38_29110) 47989..50289 + 2301 WP_040118494 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19574 GenBank   NZ_CP008843
Plasmid name   pKOXM1B Incompatibility group   IncFII
Plasmid size   183015 bp Coordinate of oriT [Strand]   24308..24356 [-]
Host baterium   Klebsiella michiganensis strain M1

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   ncrY, ncrC, ncrB, ncrA, chrA, merR, merT, merP, merA, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9