Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101202
Name   oriT_pJCM_8580 in_silico
Organism   Enterobacter kobei strain JCM 8580
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MKXD01000001 (18624..18678 [-], 55 nt)
oriT length   55 nt
IRs (inverted repeats)      21..27, 31..37  (GCAAGAC..GTCTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 55 nt

>oriT_pJCM_8580
TGAAATTAAAGAATTAATCTGCAAGACAACGTCTTGCGTGGGGTGTGATGTTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1197 GenBank   WP_088222281
Name   traI_BH713_RS00280_pJCM_8580 insolico UniProt ID   _
Length   1830 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1830 a.a.        Molecular weight: 198399.88 Da        Isoelectric Point: 6.7335

>WP_088222281.1 conjugative transfer relaxase/helicase TraI [Enterobacter kobei]
MMSVAPVASAGTAAGYYSHSDNYYFLGNLQSHWLGEGARELGLDGPVRSDALTAVLEGRLPDGGRLGKEI
NGNHVHRPGHDLTFSAPKSVSILALIGGDKRMIDAHNHAVQVAAGYVEKLISARHTKDGVTSIVHTGKMV
AAAFTHDTSRNLDPLIHTHLLVANMTEYEGKWRALATDYIHNAGFIETVMKMQVTLGKIYRADLRQGVEA
LGHEVKEVGKHGMWEIKAIPDEVVEEYSSRGREVRGAVGADATLRSRDVAAKDTRRAKVDPSRIRLMERW
QTQMKEKGFDLKGYMDSVTPAESDTARPPAQIPSAADVQTRSQPDSTPEKVPARDRIPEAGKVTERDMAR
EEPSRPVTSTPPVMQAGTHAVSPVAQGAKAGPEKPHIRAEVSDAVRQAISHLSNDKTRFTWGELMLTTTE
FSDQLPDVAEVKMAIDASLKDGMIVPLDSEKGVFTSRIHLLDELSIQALSQERLKDGKVVSFARPEQYAP
RALEVVEKSPLVLMNAPTGVAGIRELTAQLTDISTAHGREVTVLASSAERASSLAKSDTLRDRLISRSHV
LSGEFSLKPQGTLIIEGAERLGLKETLVLLGEAREKDAQLVFLDSAGRQANGNAMSVLESAGVTRSRRTE
PAPGLETEVVSIADKRDRYAALASRFAELSAGSEPVTAVVLGQREQKHLTGLIRDALQNAGQLERDGVTV
EARTPVWVDNKTRRMPGTYRAGQVLEDRSDAKTTRHYVIDRIHEDTRVLSLIDSDGVLSRMKTSELTADW
RLYESENISISTGEQLIAVAGDKDAGLKAKDRLQVTGFSAGGIQVERDGLSLTLPADRPLYVKHAYVAAP
GGRDNDTGVVLAALNSRDISARTMNSLAQSGTRAEVFTAETQDRAETRLQRMNTSSSPVQLVRQLSGKDD
VSGAISALHDGVKSEAGLAVWRAINDQRGVTFSELTLLAKAAEYHPDIGAVGEHISTMVRQGDLLPVSVR
GEPALVARATWEMEKAIIRVIDAGKNTQEPLLEQVDPRLLDGLTAGQKAAARMVLGTTDQFIGIQGYAGV
GKTTQVKAVKAAIDSLPADGRPVLSGLAPTHQAVKELKDTGMPAQTVKSFLVEHDQQVNAGQKPDYRERV
FLIDESSMIGNQDTAAAYLAIQAGGGRAVSMGDIAQFEAVDAGAPFKLVQERSPMDVAIMKEIVRQKDVQ
LKGAVHDIIDNRIDAALRRIEAQPAGKIPRMAGATLPDSGIVTTEDAVGDIVRDWTERTPQARQNTLIIT
QLNADRQAVNAGIHAVLAERGELGEKSITVPVLEKISHTRHEFNKTAAWQAGMVVKRGDRYQDVVAVDKN
GSLVTVRDEDGRLGMVSPRELITGDVELFTRSTMTVNAGDELRFTATDRERGQTGNQRFTVQSVNDNGDI
VMKGAAGTKVINPAQVRAEQHIDYAWAVTGYGAQGASSEYVIALEGTEGGRKYLASQRAFYISASRAKEH
VQIYTDERSKWVAAMKQPEKEVKTAHDALQPETQRQQAKAIWAMGQPVTKTAIGRAWARHQSMAEHSLTA
RIIPATRRFPEPALALPLYDNNGKGAGLALISLVASPEGRMTQGDIRMVATEGASAAVLQRSQTGNTHVV
RHLSDALMAVREHPKDGVVWQTGEEKPSAHLMKVSRGVHQEEDAARIRAVSGLSTDITLPVTRDNPQREA
DQLSVLRAAEALRRAAEQERAGAVVDPEKLQHAVYKPESVTLPAEESIILPADLPQADTNPLFTPDSSTL
RKLAHDLTGGTEARIPAGMTRGENGTAPERAAAERASASKVVNDLAAAERDMVRQPVEGERGRAIEHEEY
AHTRTIQKER

  Protein domains


Predicted by InterproScan.

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

(644-693)

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

(702-780)

TrwC relaxase (TrwC)

(11-286)

DNA helicase TraI (TraI_C)

(1464-1575)

AAA domain (AAA_30)

(1023-1213)


  Protein structure



No available structure.




T4CP

ID   809 GenBank   WP_088222282
Name   traD_BH713_RS00275_pJCM_8580 insolico UniProt ID   _
Length   831 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 831 a.a.        Molecular weight: 93179.46 Da        Isoelectric Point: 5.0356

>WP_088222282.1 type IV conjugative transfer system coupling protein TraD [Enterobacter kobei]
MSFAGKNLTQGGQMTAYRWRMFIQVNNWIGFWVLILFVLIASSLFLWRTPQEMLDNGALYWFANLNQSFI
DLMPAGAGRFYDVHYYHAPTQTNYVLKMTLVQIYGDPYMNAMGTQVLEQLQWAALASGIFCTGVFAAISW
YISRIGKQESEDQYISGMQLTDKPADVNRLLRQNGELSDLRVGELHMVQRAEVMNYLIHGTIGVGKSTII
RWLLDYIRKRGDRAIIYDSGCTFTETHYDPRTDIILNAHDDRCANWQMWGECVDAVDYDNMAASLIPVEG
DSDPFWVSSSRTIYADLAIRMSADPDRSIEKFLKTLLSLSMQSLREYLANTPAANLVEEKIEKTAISIRS
VVTNYAKALRYLQGLDDGVKPPFTIREWMTTEKYDNSWLFISTQARHRKSVRPLISLWVSLATLMLQSMG
ENSDRRVWFIFDELPSLQRIPEFNETLAEGRKFGGCFVIGVQNMAQLVHAYGRELAKSMFDLLNTRMYGR
SPSAEMAEIVQKELGNQRKREIREQNSYGLDTVRDGISLGKDKVNNPIVDYEQIMRLPNLNFYVRLPGEY
PVVRLGLKYKKLVKRNAGLIERNIRDVLSPELEKVIQENERAATAAGLNFPTGDEVLENSNVATDTVPAV
APKPVQVKAESKPARTEVAKAEATASAKPLSVIPVSETAPEPETAPDQSNISDNVIVLKPLNVHKNPNLP
EREITASAVSRQPVTTHEAAGQDDLSSVTPALAVLRKFRQQAAGAASNEGDEDVSGGGESMSLDMHVSEL
ADGGLELSTAGTHEPGDDHPADHRASKSLAQDEENILLHRHPDDPGYSEYDLNYDDGERDL

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(181-567)

F sex factor protein N terminal (TraD_N)

(32-135)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 20665..43737

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BH713_RS00125 (BH713_21835) 15788..16015 + 228 WP_088222226 hypothetical protein -
BH713_RS00130 (BH713_21845) 16685..16987 + 303 WP_140419642 hypothetical protein -
BH713_RS00135 (BH713_21850) 17047..17868 + 822 WP_088222307 DUF932 domain-containing protein -
BH713_RS00140 (BH713_21855) 17904..18428 - 525 WP_088222313 lytic transglycosylase domain-containing protein -
BH713_RS00145 (BH713_21860) 19055..19447 + 393 WP_088222306 relaxosome protein TraM -
BH713_RS00150 (BH713_21865) 19487..20119 - 633 WP_088222305 Arc family DNA-binding protein -
BH713_RS00155 (BH713_21870) 20315..20662 + 348 WP_088222304 type IV conjugative transfer system pilin TraA -
BH713_RS00160 (BH713_21875) 20665..20967 + 303 WP_088222303 type IV conjugative transfer system protein TraL traL
BH713_RS00165 (BH713_21880) 20971..21552 + 582 WP_088222302 TraE/TraK family type IV conjugative transfer system protein traE
BH713_RS00170 (BH713_21885) 21565..22305 + 741 WP_088222301 type-F conjugative transfer system secretin TraK traK
BH713_RS00175 (BH713_21890) 22302..23693 + 1392 WP_088222300 F-type conjugal transfer pilus assembly protein TraB traB
BH713_RS00180 (BH713_21895) 23735..24280 + 546 WP_088222299 type IV conjugative transfer system lipoprotein TraV traV
BH713_RS00185 (BH713_21900) 24280..26889 + 2610 WP_088222298 type IV secretion system protein TraC virb4
BH713_RS00190 (BH713_21905) 26871..27296 + 426 WP_088222297 type-F conjugative transfer system protein TrbI -
BH713_RS00195 (BH713_21910) 27293..27928 + 636 WP_088222296 type-F conjugative transfer system protein TraW traW
BH713_RS00200 (BH713_21915) 27988..28269 + 282 WP_254915068 hypothetical protein -
BH713_RS00205 (BH713_21920) 28421..28630 + 210 WP_129364011 hypothetical protein -
BH713_RS00210 (BH713_21925) 28698..29039 + 342 WP_088222294 hypothetical protein -
BH713_RS00215 (BH713_21930) 29024..30028 + 1005 WP_088222293 conjugal transfer pilus assembly protein TraU traU
BH713_RS00220 (BH713_21935) 30036..30653 + 618 WP_088222292 type-F conjugative transfer system pilin assembly protein TrbC trbC
BH713_RS00225 (BH713_21940) 30650..32470 + 1821 WP_088222291 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BH713_RS00230 (BH713_21945) 32470..33252 + 783 WP_088222290 type-F conjugative transfer system pilin assembly protein TraF traF
BH713_RS00235 (BH713_21950) 33340..33564 + 225 WP_140419641 hypothetical protein -
BH713_RS00240 (BH713_21955) 33554..34153 + 600 WP_088222288 F-type conjugal transfer protein TrbB traF
BH713_RS00245 (BH713_21960) 34168..34437 + 270 WP_254915067 hypothetical protein -
BH713_RS00250 (BH713_21965) 34430..35794 + 1365 WP_088222287 conjugal transfer pilus assembly protein TraH traH
BH713_RS00255 (BH713_21970) 35834..39046 + 3213 WP_088222286 conjugal transfer mating-pair stabilization protein TraG traG
BH713_RS00260 (BH713_21975) 39059..39631 + 573 WP_088222285 hypothetical protein -
BH713_RS00265 (BH713_21980) 39776..40507 + 732 WP_088222284 complement resistance protein TraT -
BH713_RS00270 (BH713_21985) 40723..41094 + 372 WP_088222283 hypothetical protein -
BH713_RS00275 (BH713_21990) 41242..43737 + 2496 WP_088222282 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1646 GenBank   NZ_MKXD01000001
Plasmid name   pJCM_8580 Incompatibility group   -
Plasmid size   122368 bp Coordinate of oriT [Strand]   18624..18678 [-]
Host baterium   Enterobacter kobei strain JCM 8580

Cargo genes

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