Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121812
Name   oriT_p2562_2 in_silico
Organism   Klebsiella michiganensis strain 2563
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP116216 (155113..155162 [+], 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_p2562_2
AAATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13769 GenBank   WP_040118408
Name   traI_PHA56_RS30625_p2562_2 insolico UniProt ID   _
Length   1754 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1754 a.a.        Molecular weight: 190278.01 Da        Isoelectric Point: 5.9989

>WP_040118408.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKPVDKAVFTEILKGKLPDGSDLTRM
QDGTNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTKALQQVETLAATRVMTDGKSETVLTGNL
IVAKFTHDTNRNEEPQLHTHAVVMNATQNGDKWQSLGTDTVGKTGFIENVYANQIAFGKIYREELKPLVE
ILGYKTEVVGKHGMWEMNEVPVEPFSTRTQEVREAAGPDASLKSRDVAALDTRKSKAAIDPAEKMVEWMN
TMKETGFDMRSYREDADKRAAELASAPVSPVKTDGPDISDVVTKAIAGLSDRKVQFTYADLLARTVSQLE
AKPGVFEQARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRQAP
FSDAVSVLAQDRPAMGIVSGQGGAAGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQVTADIISEPDKGARYSLLAQEFAASVREGQESVAQISGTREQNVLNSVIRDTLKNEGVLGEKE
MTVTALTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFVIDRVTASSNMLTLKDKEGECLDMKVSAV
DSQWTLFRADKLPVAEGERLAVLGKIPDTRLKGGESITVLKSGDGQLTVQRPGQKTTQSLSVGSSPFDGI
EVGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTMEKLARHTAFSVVSE
QLKARSGETDLDAAIAQQKAGLHTPAEQAIHLSVPLLESDDLTFTRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVSVSSGHGNDLLISRQTWDAEKSILTRVLEGKDAVAPLMDRVPASLMTGLTAGQRASTR
MILETPDRFTVVQGYAGVGKTTQFRAVTSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTLLLLLRNGQTPDFSNTLFLIDESSMVGLSDKAKALSLIAAGGGRAVSSGDTDQLQSISPGQPFRLMQQ
RSAADVAIMKEIVRQVPELRPAVYSLIDRDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTRAQEKAI
QEALKKGESVPAGQPATLYEALVKDYAGRTPEAQSQTLVITHLNKDRRALNGLIHDARRENGETGKEEIT
LPVLVTSNIRDGELRRLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVT
LYRREDITVSEGDRMRFSKSDPERGYVANSVWEVKSVSGDSVTFSDGKTSRTLNPKADEAQRHIDLAYAI
TAHGAQGASEPFAIALEGVAEGRKAMASFESAYVGLSRMKQHVQVYTDSREGWIKAINASPSKATAHDIL
APRNDRAVHTAEQLFSRARPMNETAAGRAALQQSGLAKGISPGKFISPGKQYPQPHVALPVYDKNGKEAG
IWLSSLTDSDGRLQVMGGVGRVMGNEDARFVALQGSRNGESLLAGNMGEGVRVARDNPDSGVVVRLAGDD
RPWNPGAITGGRVWADPIPVVSPEAAGTDIPLPPEVLAQRAAEEAQRQNMEKQAEQTAREVAGDGRKAGE
SEDRVKEVIGDVIRGLEREKPGEEKMTLPDDPQTRKQEAAVQQVAQESLQRERLQQMERDMVRDLNREKT
LGGD

  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)

DNA helicase TraI (TraI_C)

(1434-1553)

AAA domain (AAA_30)

(971-1158)

TrwC relaxase (TrwC)

(10-284)


  Protein structure



No available structure.




Auxiliary protein

ID   7603 GenBank   WP_032700831
Name   WP_032700831_p2562_2 insolico UniProt ID   A0A485D480
Length   129 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14705.63 Da        Isoelectric Point: 4.4711

>WP_032700831.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Klebsiella/Raoultella group]
MARVQAYASDEVAEKINAIVEKRKAEGAKDKDVSFSSVASMLLELGLRVYEAQMERKESGFNQAEFNKML
LENVIKTQFSISKVLAMESLSPHIQGDERFDFKSMVMNIRDDAKEVVERFFPDTDDEES

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A485D480


T4CP

ID   16094 GenBank   WP_040118437
Name   traD_PHA56_RS30630_p2562_2 insolico UniProt ID   _
Length   776 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 776 a.a.        Molecular weight: 86788.85 Da        Isoelectric Point: 4.9734

>WP_040118437.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella/Raoultella group]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFIIFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTINYYGRSLEYNAEQILADKYTIWCGEQLWTSFVLAAVVSLVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILLNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLSLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFATGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRSLDTRVDTRLSALLEAREAEGSLARALFTPDAPAPDPAEKDVKVGNTPEQSQPAE
SIESPATVKVPATAKTPAADEIGQSPETPEPAAPVTKVVTVPLIRPRSATATGTAAVATTAASTTSATTV
PAGGTEQELAQQPTEQGQDRLPAGMNDDGVIEDMDAYDAWLAGEQTQRDMQRREEVNINHSHRRDEQDDI
EIGGNF

  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: 126645..155715

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PHA56_RS30630 (PHA56_30630) 126645..128975 - 2331 WP_040118437 type IV conjugative transfer system coupling protein TraD virb4
PHA56_RS30635 (PHA56_30635) 129169..129900 - 732 WP_032716670 conjugal transfer complement resistance protein TraT -
PHA56_RS30640 (PHA56_30640) 130095..130709 - 615 WP_032732092 hypothetical protein -
PHA56_RS30645 (PHA56_30645) 130735..133557 - 2823 WP_040118409 conjugal transfer mating-pair stabilization protein TraG traG
PHA56_RS30650 (PHA56_30650) 133557..134927 - 1371 WP_032700807 conjugal transfer pilus assembly protein TraH traH
PHA56_RS30655 (PHA56_30655) 134914..135342 - 429 WP_032700808 conjugal transfer protein TrbF -
PHA56_RS30660 (PHA56_30660) 135335..135901 - 567 WP_032732090 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PHA56_RS30665 (PHA56_30665) 135876..136112 - 237 WP_032700810 type-F conjugative transfer system pilin chaperone TraQ -
PHA56_RS30670 (PHA56_30670) 136123..136875 - 753 WP_040118410 type-F conjugative transfer system pilin assembly protein TraF traF
PHA56_RS30675 (PHA56_30675) 136898..137224 - 327 WP_032700812 hypothetical protein -
PHA56_RS30680 (PHA56_30680) 137514..138482 - 969 WP_077255412 IS5 family transposase -
PHA56_RS30685 (PHA56_30685) 138562..140517 - 1956 WP_040118411 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PHA56_RS30690 (PHA56_30690) 140517..141146 - 630 WP_032700817 type-F conjugative transfer system pilin assembly protein TrbC trbC
PHA56_RS30695 (PHA56_30695) 141159..142118 - 960 WP_032716690 conjugal transfer pilus assembly protein TraU traU
PHA56_RS30700 (PHA56_30700) 142159..142788 - 630 WP_032716660 type-F conjugative transfer system protein TraW traW
PHA56_RS30705 (PHA56_30705) 142785..143177 - 393 WP_032716659 type-F conjugative transfer system protein TrbI -
PHA56_RS30710 (PHA56_30710) 143177..145816 - 2640 WP_032716658 type IV secretion system protein TraC virb4
PHA56_RS30715 (PHA56_30715) 145896..146285 - 390 WP_040118412 hypothetical protein -
PHA56_RS30720 (PHA56_30720) 146662..147066 - 405 WP_040118414 hypothetical protein -
PHA56_RS30725 (PHA56_30725) 147063..147284 - 222 WP_032732073 hypothetical protein -
PHA56_RS30730 (PHA56_30730) 147766..148245 - 480 WP_223306708 hypothetical protein -
PHA56_RS30735 (PHA56_30735) 148352..148921 - 570 WP_071889124 type IV conjugative transfer system lipoprotein TraV traV
PHA56_RS30740 (PHA56_30740) 148940..149146 - 207 WP_032700826 hypothetical protein -
PHA56_RS30745 (PHA56_30745) 149127..149723 - 597 WP_119834738 conjugal transfer protein TraP -
PHA56_RS30750 (PHA56_30750) 149716..151134 - 1419 WP_040118415 F-type conjugal transfer pilus assembly protein TraB traB
PHA56_RS30755 (PHA56_30755) 151134..151868 - 735 WP_040118416 type-F conjugative transfer system secretin TraK traK
PHA56_RS30760 (PHA56_30760) 151855..152421 - 567 WP_040118417 type IV conjugative transfer system protein TraE traE
PHA56_RS30765 (PHA56_30765) 152441..152746 - 306 WP_020323523 type IV conjugative transfer system protein TraL traL
PHA56_RS30770 (PHA56_30770) 152760..153128 - 369 WP_047665734 type IV conjugative transfer system pilin TraA -
PHA56_RS30775 (PHA56_30775) 153190..153354 - 165 WP_032444506 TraY domain-containing protein -
PHA56_RS30780 (PHA56_30780) 153532..154221 - 690 WP_071889125 hypothetical protein -
PHA56_RS30785 (PHA56_30785) 154422..154811 - 390 WP_032700831 conjugal transfer relaxosome DNA-binding protein TraM -
PHA56_RS30790 (PHA56_30790) 155236..155715 + 480 WP_032716648 transglycosylase SLT domain-containing protein virB1
PHA56_RS30795 (PHA56_30795) 155753..156283 - 531 WP_032716647 antirestriction protein -
PHA56_RS30800 (PHA56_30800) 156968..157114 - 147 WP_032700834 hypothetical protein -
PHA56_RS30805 (PHA56_30805) 157208..157555 - 348 WP_032700835 hypothetical protein -
PHA56_RS30810 (PHA56_30810) 157581..157739 - 159 WP_162180130 hypothetical protein -
PHA56_RS30815 (PHA56_30815) 157796..158071 - 276 WP_032700867 hypothetical protein -
PHA56_RS30820 (PHA56_30820) 158890..159171 - 282 WP_004118961 helix-turn-helix transcriptional regulator -
PHA56_RS30825 (PHA56_30825) 159152..159481 - 330 WP_004118963 type II toxin-antitoxin system RelE/ParE family toxin -
PHA56_RS30830 (PHA56_30830) 159801..159888 - 88 Protein_166 theronine dehydrogenase -
PHA56_RS30835 (PHA56_30835) 159885..160613 - 729 WP_004118966 plasmid SOS inhibition protein A -

Host bacterium

ID   22239 GenBank   NZ_CP116216
Plasmid name   p2562_2 Incompatibility group   IncFIB
Plasmid size   183276 bp Coordinate of oriT [Strand]   155113..155162 [+]
Host baterium   Klebsiella michiganensis strain 2563

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsR, arsD, arsA, arsB, arsC, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -