Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100486
Name   oriT_pNB8c in_silico
Organism   Delftia acidovorans
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019264 (47787..48377 [+], 591 nt)
oriT length   591 nt
IRs (inverted repeats)      148..160, 166..178  (AGGCGCTGCCGGT..ACCGGAAGCGCCT)
 250..255, 260..265  (GCCGGC..GCCGGC)
 318..336, 339..357  (GCGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCGC)
Location of nic site      365..366
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 591 nt

>oriT_pNB8c
TGTCGCTACCCCTTGAGCGCGTGCGCCGTGTGTCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCCGCCTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCAAGGCGCTGCCGGTCGGCAACCGGAAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGGCCGGCGGTAGCCGGCAGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAGCGAGGCGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   557 GenBank   YP_006961501
Name   TraI_pNB8c insolico UniProt ID   G9CA54
Length   752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


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

>YP_006961501.1 TraI (plasmid) [Delftia acidovorans]
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 G9CA54


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2395..13018

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS815_RS00005 (D764_p1056) 1..1224 - 1224 WP_011013257 plasmid replication initiator TrfA -
HS815_RS00010 (D764_p1055) 1273..1611 - 339 WP_011013259 single-stranded DNA-binding protein -
HS815_RS00015 (D764_p1054) 1721..2080 + 360 WP_011013260 transcriptional regulator -
HS815_RS00020 (D764_p1053) 2395..3360 + 966 WP_011013261 P-type conjugative transfer ATPase TrbB virB11
HS815_RS00025 (D764_p1052) 3390..3854 + 465 WP_011013262 conjugal transfer system pilin TrbC virB2
HS815_RS00030 (D764_p1051) 3858..4169 + 312 WP_011013263 conjugal transfer protein TrbD virB3
HS815_RS00035 (D764_p1050) 4166..6724 + 2559 WP_011013264 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS815_RS00040 (D764_p1049) 6721..7509 + 789 WP_011013265 conjugal transfer protein TrbF virB8
HS815_RS00045 (D764_p1048) 7527..8420 + 894 WP_014386236 P-type conjugative transfer protein TrbG virB9
HS815_RS00050 (D764_p1047) 8423..8884 + 462 WP_011013267 lipoprotein -
HS815_RS00055 (D764_p1046) 8888..10267 + 1380 WP_015060639 TrbI/VirB10 family protein virB10
HS815_RS00060 (D764_p1045) 10284..11057 + 774 WP_011255135 P-type conjugative transfer protein TrbJ virB5
HS815_RS00065 (D764_p1044) 11067..11288 + 222 WP_011255136 entry exclusion lipoprotein TrbK -
HS815_RS00070 (D764_p1043) 11300..13018 + 1719 WP_012478193 P-type conjugative transfer protein TrbL virB6
HS815_RS00075 (D764_p1042) 13037..13615 + 579 WP_011255138 TrbM/KikA/MpfK family conjugal transfer protein -
HS815_RS00080 (D764_p1041) 13617..14252 + 636 WP_011255139 transglycosylase SLT domain-containing protein -
HS815_RS00085 (D764_p1040) 14282..14551 + 270 WP_011255140 hypothetical protein -
HS815_RS00090 (D764_p1039) 14548..15246 + 699 WP_012478194 TraX family protein -
HS815_RS00095 (D764_p1038) 15262..15705 + 444 WP_011255142 OmpA family protein -
HS815_RS00100 (D764_p1037) 15808..16224 + 417 WP_012478195 hypothetical protein -

Host bacterium

ID   947 GenBank   NC_019264
Plasmid name   pNB8c Incompatibility group   IncP(Beta)
Plasmid size   60421 bp Coordinate of oriT [Strand]   47787..48377 [+]
Host baterium   Delftia acidovorans

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   chloroaniline degradation plasmid
Symbiosis gene   -
Anti-CRISPR   -