Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100297
Name   oriT_pCNB in_silico
Organism   Comamonas testosteroni CNB-1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_010935 (90599..91181 [+], 583 nt)
oriT length   583 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: 583 nt

>oriT_pCNB
TGTCGCTACCCCTTGAGCGCGTGCGCCGTGTGTCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCCGCCTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCAAGGCGCTGCCGGTCGGCAACCGGAAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGGCCGGCGGTAGCCGGCAGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGATAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   368 GenBank   YP_001967734
Name   Relaxase_pCNB insolico UniProt ID   A7K7N1
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_001967734.1 DNA relaxase (plasmid) [Comamonas testosteroni CNB-1]
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 A7K7N1


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 19873..30496

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H8R99_RS00105 (pCNB_p22) 15512..15817 - 306 WP_000130000 PadR family transcriptional regulator -
H8R99_RS00110 (pCNB_p23) 15828..17033 - 1206 WP_000184001 chromate efflux transporter -
H8R99_RS00115 17184..17510 + 327 WP_185767474 hypothetical protein -
H8R99_RS00120 (pCNB_p24) 17479..18702 - 1224 WP_011013257 plasmid replication initiator TrfA -
H8R99_RS00125 (pCNB_p25) 18751..19089 - 339 WP_011013259 single-stranded DNA-binding protein -
H8R99_RS00130 (pCNB_p26) 19199..19558 + 360 WP_011013260 transcriptional regulator -
H8R99_RS00135 (pCNB_p27) 19873..20838 + 966 WP_012478191 P-type conjugative transfer ATPase TrbB virB11
H8R99_RS00140 (pCNB_p28) 20868..21332 + 465 WP_011013262 conjugal transfer system pilin TrbC virB2
H8R99_RS00145 (pCNB_p29) 21336..21647 + 312 WP_011013263 conjugal transfer protein TrbD virB3
H8R99_RS00150 (pCNB_p30) 21644..24202 + 2559 WP_011013264 VirB4 family type IV secretion/conjugal transfer ATPase virb4
H8R99_RS00155 (pCNB_p31) 24199..24987 + 789 WP_011013265 conjugal transfer protein TrbF virB8
H8R99_RS00160 (pCNB_p32) 25005..25898 + 894 WP_014386236 P-type conjugative transfer protein TrbG virB9
H8R99_RS00165 (pCNB_p33) 25901..26362 + 462 WP_011013267 lipoprotein -
H8R99_RS00170 (pCNB_p34) 26366..27745 + 1380 WP_012478192 TrbI/VirB10 family protein virB10
H8R99_RS00175 (pCNB_p35) 27762..28535 + 774 WP_011255135 P-type conjugative transfer protein TrbJ virB5
H8R99_RS00180 (pCNB_p36) 28545..28766 + 222 WP_011255136 entry exclusion lipoprotein TrbK -
H8R99_RS00185 (pCNB_p37) 28778..30496 + 1719 WP_012478193 P-type conjugative transfer protein TrbL virB6
H8R99_RS00190 (pCNB_p38) 30515..31093 + 579 WP_011255138 TrbM/KikA/MpfK family conjugal transfer protein -
H8R99_RS00195 (pCNB_p39) 31095..31730 + 636 WP_011255139 transglycosylase SLT domain-containing protein -
H8R99_RS00200 (pCNB_p40) 31760..32029 + 270 WP_011255140 hypothetical protein -
H8R99_RS00205 (pCNB_p41) 32026..32724 + 699 WP_012478194 TraX family protein -
H8R99_RS00210 (pCNB_p42) 32740..33183 + 444 WP_011255142 OmpA family protein -
H8R99_RS00215 (pCNB_p43) 33286..33702 + 417 WP_012478195 hypothetical protein -

Host bacterium

ID   759 GenBank   NC_010935
Plasmid name   pCNB Incompatibility group   IncP(Beta)
Plasmid size   91181 bp Coordinate of oriT [Strand]   90599..91181 [+]
Host baterium   Comamonas testosteroni CNB-1

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   resistance to arsenate and chromate
Degradation gene   degradation of 4-chloronitrobenzene (4CNB)
Symbiosis gene   -
Anti-CRISPR   -