Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100393
Name   oriT_pTB30 in_silico
Organism   Comamonas testosteroni
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_016968 (66654..67244 [+], 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_pTB30
TGTCGCTACCCCTTGAGCGCGTGCGCCGTGTGTCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCCGCCTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCAAGGCGCTGCCGGTCGGCAACCGGAAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGGCCGGCGGTAGCCGGCAGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAGCGAGGCGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   464 GenBank   YP_005351585
Name   TraI_pTB30 insolico UniProt ID   G9C9H2
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_005351585.1 TraI (plasmid) [Comamonas testosteroni]
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 G9C9H2


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2394..13017

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS892_RS00005 (PTB30_p01) 1..1224 - 1224 WP_011013257 plasmid replication initiator TrfA -
HS892_RS00010 (PTB30_p02) 1273..1611 - 339 WP_011013259 single-stranded DNA-binding protein -
HS892_RS00015 (PTB30_p03) 1720..2079 + 360 WP_011013260 transcriptional regulator -
HS892_RS00020 (PTB30_p04) 2394..3359 + 966 WP_014386235 P-type conjugative transfer ATPase TrbB virB11
HS892_RS00025 (PTB30_p05) 3389..3853 + 465 WP_011013262 conjugal transfer system pilin TrbC virB2
HS892_RS00030 (PTB30_p06) 3857..4168 + 312 WP_011013263 conjugal transfer protein TrbD virB3
HS892_RS00035 (PTB30_p07) 4165..6723 + 2559 WP_011013264 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS892_RS00040 (PTB30_p08) 6720..7508 + 789 WP_011013265 conjugal transfer protein TrbF virB8
HS892_RS00045 (PTB30_p09) 7526..8419 + 894 WP_014386236 P-type conjugative transfer protein TrbG virB9
HS892_RS00050 (PTB30_p10) 8422..8883 + 462 WP_011013267 lipoprotein -
HS892_RS00055 (PTB30_p11) 8887..10266 + 1380 WP_012478192 TrbI/VirB10 family protein virB10
HS892_RS00060 (PTB30_p12) 10283..11056 + 774 WP_011255135 P-type conjugative transfer protein TrbJ virB5
HS892_RS00065 11066..11287 + 222 WP_011255136 entry exclusion lipoprotein TrbK -
HS892_RS00070 (PTB30_p14) 11299..13017 + 1719 WP_012478193 P-type conjugative transfer protein TrbL virB6
HS892_RS00075 (PTB30_p15) 13036..13614 + 579 WP_011255138 TrbM/KikA/MpfK family conjugal transfer protein -
HS892_RS00080 (PTB30_p16) 13616..14251 + 636 WP_011255139 transglycosylase SLT domain-containing protein -
HS892_RS00085 (PTB30_p17) 14281..14550 + 270 WP_011255140 hypothetical protein -
HS892_RS00090 (PTB30_p18) 14547..15245 + 699 WP_012478194 TraX family protein -
HS892_RS00095 (PTB30_p19) 15261..15704 + 444 WP_011255142 OmpA family protein -
HS892_RS00100 (PTB30_p20) 15807..16223 + 417 WP_012478195 hypothetical protein -

Host bacterium

ID   854 GenBank   NC_016968
Plasmid name   pTB30 Incompatibility group   IncP(Beta)
Plasmid size   79291 bp Coordinate of oriT [Strand]   66654..67244 [+]
Host baterium   Comamonas testosteroni

Cargo genes

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