Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114634
Name   oriT_pDCNB in_silico
Organism   Diaphorobacter sp. JS3050
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP053554 (29115..29211 [-], 97 nt)
oriT length   97 nt
IRs (inverted repeats)      24..31, 34..41  (TAACCGGC..GCCGGTTA)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 97 nt

>oriT_pDCNB
GAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9386 GenBank   WP_012478238
Name   traI_HND92_RS19080_pDCNB insolico UniProt ID   A0A1H7CDK8
Length   752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 752 a.a.        Molecular weight: 82867.55 Da        Isoelectric Point: 10.6815

>WP_012478238.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRNTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMEQHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEARLGPFEASPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALEQARRRKDRLVEAAKRSGRLRRATIKVIGESGPNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALTALRAREAAQGLKGNTIQGRGDPRPGHAPV
TDNITKKGTIIFRAGLTAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFQAQIIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTERADQRPAEHRGRAGRGPGGPGQRAATHDDAARPIAVA
RAGFGRPGGGRAGTAGVHAGAVHRKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVPRHL
EQQGTQPDHQLRRDISRPGSGVAAAPPGLAAADKYIAERESKRSKGFDIPKHARYTAGEGGLAFEGVRNI
EGQALALLKRGDEVMVMPIDQATARRMSRIAVGDAVTITPKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(420-507)


  Protein structure


Source ID Structure
AlphaFold DB A0A1H7CDK8


Auxiliary protein

ID   5507 GenBank   WP_011255188
Name   WP_011255188_pDCNB insolico UniProt ID   A0A1H7CD62
Length   123 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13964.97 Da        Isoelectric Point: 8.4531

>WP_011255188.1 MULTISPECIES: conjugal transfer transcriptional regulator TraJ [Pseudomonadota]
MEADEQPTAKRRQHLRVPVFPDEKEQIEANAKRAGVSVARYLRDVGQGYQIRGVMDYEYVRELVRVNGDL
GRLGGLLKLWLTDDPRTARFGDATILALLGRIEATQDEMSRLMKSVVQPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A1H7CD62


T4CP

ID   10895 GenBank   WP_012478237
Name   t4cp2_HND92_RS19085_pDCNB insolico UniProt ID   _
Length   634 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 634 a.a.        Molecular weight: 69616.60 Da        Isoelectric Point: 8.4953

>WP_012478237.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonadota]
MKIKMNNAVGPQVRSAKPKPSKLLPILGGVSLVGGLQAATQFFAYTFQYHASLGANLGHVYAPWSILNWS
AKWYSQYPDEIMRAGSIGMVTATVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKDAPTATGVYVGGWQDKDGNFYYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASSSGGVCWNPLDEIRVGTEAEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKARNDGGTATLPSVDAMLADPNRDIGELWMEMTTYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARSVSRSDFRIKDLMHSDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLRSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNDKGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFQARASIPAPKATDRLRQVVEAGE
GITI

  Protein domains


Predicted by InterproScan.

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

(121-618)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2536..14484

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HND92_RS18880 (HND92_18910) 308..1006 - 699 WP_012478194 TraX family protein -
HND92_RS18885 (HND92_18915) 1003..1272 - 270 WP_011255140 hypothetical protein -
HND92_RS18890 (HND92_18920) 1302..1937 - 636 WP_011255139 transglycosylase SLT domain-containing protein -
HND92_RS18895 (HND92_18925) 1939..2517 - 579 WP_011255138 TrbM/KikA/MpfK family conjugal transfer protein -
HND92_RS18900 (HND92_18930) 2536..4254 - 1719 WP_012478193 P-type conjugative transfer protein TrbL virB6
HND92_RS18905 (HND92_18935) 4266..4487 - 222 WP_011255136 entry exclusion lipoprotein TrbK -
HND92_RS18910 (HND92_18940) 4497..5270 - 774 WP_011255135 P-type conjugative transfer protein TrbJ virB5
HND92_RS18915 (HND92_18945) 5287..6666 - 1380 WP_012478192 TrbI/VirB10 family protein virB10
HND92_RS18920 (HND92_18950) 6670..7131 - 462 WP_011013267 lipoprotein -
HND92_RS18925 (HND92_18955) 7134..8027 - 894 WP_014386236 P-type conjugative transfer protein TrbG virB9
HND92_RS18930 (HND92_18960) 8045..8833 - 789 WP_011013265 conjugal transfer protein TrbF virB8
HND92_RS18935 (HND92_18965) 8830..9348 - 519 Protein_12 conjugal transfer protein TrbE -
HND92_RS18940 (HND92_18970) 9421..10509 + 1089 WP_011803559 IS5-like element ISDisp1 family transposase -
HND92_RS18945 (HND92_18975) 10500..12713 - 2214 WP_253940162 conjugal transfer protein TrbE virb4
HND92_RS18950 (HND92_18980) 12710..13021 - 312 WP_011013263 conjugal transfer protein TrbD virB3
HND92_RS18955 (HND92_18985) 13025..13489 - 465 WP_011013262 conjugal transfer system pilin TrbC virB2
HND92_RS18960 (HND92_18990) 13519..14484 - 966 WP_011013261 P-type conjugative transfer ATPase TrbB virB11
HND92_RS18965 (HND92_18995) 14799..15158 - 360 WP_011013260 transcriptional regulator -
HND92_RS18970 (HND92_19000) 15268..15606 + 339 WP_011013259 single-stranded DNA-binding protein -
HND92_RS18975 (HND92_19005) 15655..16878 + 1224 WP_011013257 plasmid replication initiator TrfA -
HND92_RS18980 (HND92_19010) 18264..18545 - 282 WP_011114071 type II toxin-antitoxin system YafQ family toxin -
HND92_RS18985 (HND92_19015) 18532..18795 - 264 WP_011114070 type II toxin-antitoxin system RelB/DinJ family antitoxin -
HND92_RS18990 (HND92_19020) 18968..19396 + 429 WP_011114069 antirestriction protein -

Host bacterium

ID   15069 GenBank   NZ_CP053554
Plasmid name   pDCNB Incompatibility group   -
Plasmid size   49405 bp Coordinate of oriT [Strand]   29115..29211 [-]
Host baterium   Diaphorobacter sp. JS3050

Cargo genes

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