Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100786
Name   oriT_pX1 in_silico
Organism   Cupriavidus nantongensis strain X1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014846 (46565..47155 [-], 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_pX1
TGTCGCTACCCCTTGAGCGCGTGCGCCGTGTGTCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCCGCCTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCAAGGCGCTGCCGGTCGGCAACCGGAAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGGCCGGCGGTAGCCGGCAGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCCCGCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAGCGAGGCGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   858 GenBank   WP_012478238
Name   TraI_pX1 insolico UniProt ID   A0A142JWQ4
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

>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 A0A142JWQ4


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 21500..32123

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A2G96_RS31895 (A2G96_31895) 16593..17159 + 567 WP_003159185 recombinase family protein -
A2G96_RS31900 (A2G96_31900) 17193..17489 + 297 Protein_16 helix-turn-helix domain-containing protein -
A2G96_RS31905 (A2G96_31905) 17491..18165 - 675 WP_062804243 hypothetical protein -
A2G96_RS31910 (A2G96_31910) 18294..18710 - 417 WP_012478195 hypothetical protein -
A2G96_RS31915 (A2G96_31915) 18813..19256 - 444 WP_011255142 OmpA family protein -
A2G96_RS31920 (A2G96_31920) 19272..19970 - 699 WP_012478194 TraX family protein -
A2G96_RS31925 (A2G96_31925) 19967..20236 - 270 WP_011255140 hypothetical protein -
A2G96_RS31930 (A2G96_31930) 20266..20901 - 636 WP_011255139 transglycosylase SLT domain-containing protein -
A2G96_RS31935 (A2G96_31935) 20903..21481 - 579 WP_011255138 TrbM/KikA/MpfK family conjugal transfer protein -
A2G96_RS31940 (A2G96_31940) 21500..23218 - 1719 WP_012478193 P-type conjugative transfer protein TrbL virB6
A2G96_RS31945 (A2G96_31945) 23230..23451 - 222 WP_011255136 entry exclusion lipoprotein TrbK -
A2G96_RS31950 (A2G96_31950) 23461..24234 - 774 WP_011255135 P-type conjugative transfer protein TrbJ virB5
A2G96_RS31955 (A2G96_31955) 24251..25630 - 1380 WP_012478192 TrbI/VirB10 family protein virB10
A2G96_RS31960 (A2G96_31960) 25634..26095 - 462 WP_011013267 lipoprotein -
A2G96_RS31965 (A2G96_31965) 26098..26991 - 894 WP_014386236 P-type conjugative transfer protein TrbG virB9
A2G96_RS31970 (A2G96_31970) 27009..27797 - 789 WP_062804244 conjugal transfer protein TrbF virB8
A2G96_RS31975 (A2G96_31975) 27794..30352 - 2559 WP_011013264 VirB4 family type IV secretion/conjugal transfer ATPase virb4
A2G96_RS31980 (A2G96_31980) 30349..30660 - 312 WP_011013263 conjugal transfer protein TrbD virB3
A2G96_RS31985 (A2G96_31985) 30664..31128 - 465 WP_011013262 conjugal transfer system pilin TrbC virB2
A2G96_RS31990 (A2G96_31990) 31158..32123 - 966 WP_011013261 P-type conjugative transfer ATPase TrbB virB11
A2G96_RS31995 (A2G96_31995) 32438..32797 - 360 WP_011013260 transcriptional regulator -
A2G96_RS32000 (A2G96_32000) 32907..33245 + 339 WP_011013259 single-stranded DNA-binding protein -
A2G96_RS32005 (A2G96_32005) 33294..34517 + 1224 WP_011013257 plasmid replication initiator TrfA -
A2G96_RS32010 (A2G96_32010) 35903..36184 - 282 WP_011114071 type II toxin-antitoxin system YafQ family toxin -
A2G96_RS32015 (A2G96_32015) 36171..36434 - 264 WP_011114070 type II toxin-antitoxin system RelB/DinJ family antitoxin -
A2G96_RS32020 (A2G96_32020) 36607..37035 + 429 WP_011114069 antirestriction protein -

Host bacterium

ID   1246 GenBank   NZ_CP014846
Plasmid name   pX1 Incompatibility group   IncP(Beta)
Plasmid size   60711 bp Coordinate of oriT [Strand]   46565..47155 [-]
Host baterium   Cupriavidus nantongensis strain X1

Cargo genes

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