Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102666
Name   oriT_GZWM139|p2 in_silico
Organism   Nitratireductor sp. GZWM139
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAMQML010000023 (32046..32145 [+], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      24..31, 35..42  (TAATCGGC..GCCGATTA)
Location of nic site      61..62
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 100 nt

>oriT_GZWM139|p2
GAATAAGGGAGAGTGAAGATAGTTAATCGGCTCCGCCGATTAGCTAACTTCACCTATCCTGCCCGCCTTACGGCGTTGTTTACACCAAGGAAAGTGTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1973 GenBank   WP_283801641
Name   Relaxase_NDI72_RS20575_GZWM139|p2 insolico UniProt ID   _
Length   762 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 762 a.a.        Molecular weight: 84222.45 Da        Isoelectric Point: 10.5684

>WP_283801641.1 TraI/MobA(P) family conjugative relaxase [Nitratireductor sp. GZWM139]
MIAKHVPMRSLKKSDFAGLVKYITDEQSKTERLGLVNATNCEADTMQAVIGEVLATQQGNTRAKGDKTYH
LIVSFPAGEKPEDDVLKAVEERICAGLGYADHQRVSAVHHDTDNVHIHIAINKIHPTRNTMHEPYQDYRT
LGGLCDALEDEYGLQKDNHQGRKSVSQGRASDMERHAGIESLVSWIKRECLEEIKTAKTWEELHQVMSDN
GLEIRQRANGFVIESEDGTQVKASTVARDLSKPKLEARLGAFEETAAQAERKAKRRYDKRPTHFKVNTTE
LYARYQEEQKNLTAARKVEWNNARGRKDRRIEAAKRSNRLRRSAIKLMGGSRISKKLLYAQAHKALKDEI
QSINKDYKREKQELYDQYKRRAWADWLKQQVLNGDKKALEALRAREQSKGLQGDTIKGEGGSKPGHAPVT
DNITKKGTIIFRTGKSAVRDDGDKLQVSKAANGDTVTEALRVAMERYGSRITVTGSPQFKAQVIVAAATS
NLPITFADAGLERRRQQLLQQENSNDRRNEQARRGNERGRADRRSNGRAERGPADDNGRGRGTADSRAAT
TGRAGDGQRGRGQSTSTGSTTAGGRNDAGNGGRPILNKPHVGRIGGEPPSFAKNRLRTLSSLGVVRFARG
GEVLLPGNAPGELEHQGAKPDNQLRWGVSGSGGITPDQTNAADKYIAEREAKRLKGFDIPKHSRYTNQDG
AVTYGGTRNVQGQALALLNRGDEVLVLPIDKATAQRMKRVRIGEAVTVTPQGSLKRSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(419-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure



No available structure.




Auxiliary protein

ID   797 GenBank   WP_269129272
Name   WP_269129272_GZWM139|p2 insolico UniProt ID   _
Length   123 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13797.90 Da        Isoelectric Point: 9.4637

>WP_269129272.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Pseudomonadota]
MSEEKKPGKKRSHHLRVPVFDDEKETIEAQAARAGMSVARYLREVGQGYQIKGVVDYEQVRELARINGDL
GRLGGLLKLWLTDDVRTAQFGQSTILAVLSKIEATQEEMGKVMTKVVMPRSEP

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   1609 GenBank   WP_283801650
Name   t4cp2_NDI72_RS20445_GZWM139|p2 insolico UniProt ID   _
Length   845 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 845 a.a.        Molecular weight: 94123.89 Da        Isoelectric Point: 6.3396

>WP_283801650.1 VirB4 family type IV secretion/conjugal transfer ATPase [Nitratireductor sp. GZWM139]
MIQAISFAIAVCGAALLLILFARIRAVDAELKLKKHRSKDAGLADLLNYAAVVDDGVIVCKNGAFMASWL
YKGDDNASSTDEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERNTSAFPDPVSAAIDEERRQLF
EGLGAMYEGYFVLTLTWFPPLLAQRKFVELMFDDDAEVVGKKARTKGLINQFKREISSIENRLTTAVKLT
RLRGQKIVNEDGSKVTHDDFLSWLQFCVTGVSHPVQLPNNPMYMDAYIGGQEMWGGVVPKVGRKFIQVVS
IEGFPLESHPGILSALAELPVEYRWSSRFIFMDQHESVKHLDKFRKKWKQKVRGFFDQVFNTNSGNVDQD
ALTMVQDAESAIAEVNSGLVAVGYYTSVVVLMDESRDRLEQSARQVEKSINRLGFAARTETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSTIWTGSADAPCPMYPPLSPALMHCVTSGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLALIAAQLRRYAGMSIFAFDKGMSMYPLTKAVGGLHFSVGADDDRLSFCPLQYLET
KSDRAWAMEWIDTILALNGVQSTPAQRNEIAHAIVSMHESGARTLSEFSLTIQDESIREAIRQYTVDGSM
GHLLDADEDGLSLTDFTTFEIEELMNLGEKFALPVLLYLFRRIERSLKGQPAVIILDEAWLMLGHPAFRE
KIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMGLNARQIE
ILATAIPKRQYYYVSENGRRLYDLALGPLALSFVGASDKESVAAIKQLEAKYGEQWVHEWLAGRGLKLDN
YLEAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(618-747)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(221-431)

  Protein structure



No available structure.



ID   1610 GenBank   WP_014579486
Name   t4cp2_NDI72_RS20570_GZWM139|p2 insolico UniProt ID   _
Length   635 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 69921.78 Da        Isoelectric Point: 7.3667

>WP_014579486.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKPKINNAVGPQVRDRKPKKQRLLPALGAVSVLGGLQAATQFFAYTFNYQDNLGGHINHVYAPWSILSWA
SDWYSIYPDEFMRSGSIGMVVTTVGLLGVAIAKVVTSNSSKASEYLHGSARWAEKKDIQAAGLLPRERTA
LEVVTGKDAPTSTGVYVGGWEDKDGNFFYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPQSSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSNGGVCWNPLDEIRIGTEYEVGDVQNLATLIVDPDGKGMDSHWQ
KTSYALLVGVILHALYKSKNEGTPATLPVVDAMLADPERDTGELWMEMATYGHVDGQNHPAVGSAARDMM
DRPEEEGGSVLSTAKSYLALYRDPVVARNVSKSEFRIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVLTN
MIIRLLADEMSFEKGRPVAHYKHRLLAMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDLNQLKSRET
GYGPDETITSNCHVQNAYPPNRIETAEHLSRLTGQTTVVKEQITTSGRRTSAMLGQVSRTIQEVQRPLLT
PDECLRMPGPTKNAAGDIEKAGDMVIYVAGYPAVYGKQPLYFKDPVFQARASVDAPKISDKLRIVAEPEG
EGVTI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(121-617)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4148..14936

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NDI72_RS20415 (NDI72_20405) 1782..2921 - 1140 WP_283801649 plasmid replication initiator TrfA -
NDI72_RS20420 (NDI72_20410) 3069..3413 - 345 WP_283801628 single-stranded DNA-binding protein -
NDI72_RS20425 (NDI72_20415) 3513..3896 + 384 WP_041646689 transcriptional regulator -
NDI72_RS20430 (NDI72_20420) 4148..5107 + 960 WP_014579515 P-type conjugative transfer ATPase TrbB virB11
NDI72_RS20435 (NDI72_20425) 5133..5558 + 426 WP_014579514 conjugal transfer system pilin TrbC virB2
NDI72_RS20440 (NDI72_20430) 5561..5872 + 312 WP_008929954 conjugal transfer protein TrbD virB3
NDI72_RS20445 (NDI72_20435) 5872..8409 + 2538 WP_283801650 VirB4 family type IV secretion/conjugal transfer ATPase virb4
NDI72_RS20450 (NDI72_20440) 8409..9191 + 783 WP_269129290 conjugal transfer protein TrbF virB8
NDI72_RS20455 (NDI72_20445) 9209..10114 + 906 WP_283801629 P-type conjugative transfer protein TrbG virB9
NDI72_RS20460 (NDI72_20450) 10117..10626 + 510 WP_283801630 conjugal transfer protein TrbH -
NDI72_RS20465 (NDI72_20455) 10630..12057 + 1428 WP_269129287 TrbI/VirB10 family protein virB10
NDI72_RS20470 (NDI72_20460) 12076..12837 + 762 WP_269129286 P-type conjugative transfer protein TrbJ virB5
NDI72_RS20475 (NDI72_20465) 12847..13074 + 228 WP_269129285 entry exclusion lipoprotein TrbK -
NDI72_RS20480 (NDI72_20470) 13086..14936 + 1851 WP_283801631 P-type conjugative transfer protein TrbL virB6
NDI72_RS20485 (NDI72_20475) 14956..15438 + 483 WP_283801632 hypothetical protein -
NDI72_RS20490 (NDI72_20480) 15450..16085 + 636 WP_283801633 muramidase -
NDI72_RS20495 (NDI72_20485) 16082..16810 + 729 WP_283801634 TraX family protein -
NDI72_RS20500 (NDI72_20490) 16824..17249 + 426 WP_014579501 OmpA family protein -
NDI72_RS20505 (NDI72_20495) 17268..17537 + 270 WP_283801635 hypothetical protein -
NDI72_RS20510 (NDI72_20500) 17562..17816 + 255 WP_283801636 hypothetical protein -
NDI72_RS20515 (NDI72_20505) 17821..18327 + 507 WP_283801637 hypothetical protein -
NDI72_RS20520 (NDI72_20510) 18412..18717 + 306 WP_283801638 hypothetical protein -
NDI72_RS20525 (NDI72_20515) 18738..19361 - 624 WP_283801639 recombinase family protein -
NDI72_RS20530 19370..19501 - 132 WP_269129278 hypothetical protein -

Host bacterium

ID   3110 GenBank   NZ_JAMQML010000023
Plasmid name   GZWM139|p2 Incompatibility group   -
Plasmid size   42560 bp Coordinate of oriT [Strand]   32046..32145 [+]
Host baterium   Nitratireductor sp. GZWM139

Cargo genes

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