Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100261
Name   oriT_pA1 in_silico
Organism   Sphingomonas sp. A1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_007353 (16444..17034 [+], 591 nt)
oriT length   591 nt
IRs (inverted repeats)      148..159, 167..178  (AGGCGCTGCCGG..CCGGCAGCGCCT)
 250..254, 259..263  (CCGGC..GCCGG)
 317..334, 340..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_pA1
TGTCGTTACCCCTTGAGCGCGTGCGCCGTGTGCCGCGCGTAGGTCGCCACGGCTCGCCAGTAGGCGGCCATCGGCCCCTTGCGGCGTGCCCATGCCTTTTCGGCTTCGTCGTTGGCCTGCGTGCGCAGCTCGCGCAGCACGCGGGCGAGGCGCTGCCGGTCGGCCGCCGGCAGCGCCTGGAGTTCGCGGCCTGCTGGAAGCTCCAGCAGCGGATTGATGTAGCCCATGTCGTTCGTCTCTCGCTTCTTGCCGGCGGTAGCCGGTCGCCTCGCAGAGCAGGATGCCCGTTGAGTGCCGCAGGCGCGAATAAGGGACAGCGAAGATAGATAACCGGCTCGCCCGGTTAGCTAACTTCGCACATCCTGCCCGCCTTACGGCGTTGATAACACCAAGGAAAGTCTATACCGAAACCTTCGCATCTGTCTGCATTTAGCGCGAAAAGATGGCGGATATATCGAATGAAGGCGTACAATGCCCGGAAAGCGCGCTAGATGCAGCGGTGTCAAGCTGCTATCCACGCGCTTTACATAGACTTTCCACGGGTCGATACATGAAAATGACGGCTATTTACAAACCACGGAAGCGAGGCGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   332 GenBank   YP_302615
Name   TraI_pA1 insolico UniProt ID   Q4AC74
Length   755 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 755 a.a.        Molecular weight: 83463.24 Da        Isoelectric Point: 10.7762

>YP_302615.1 TraI (plasmid) [Sphingomonas sp. A1]
MIAKHVPMRSLGKSDFAGLVNYVTDAQSKDHRLGQVQITNCDAVSVQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICAGLGYGEHQRVSAVHNDTDNLHIHIAINKIHPTRRTMHEPYYSHRA
LAELCTALERDYGLERDNHEPRQRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GLELRERANGLVIEAGDGTMVKASTLARDLSKPKLEVRLGPFEPSPERQTRTKAKRQYQKDPIRLRVNTV
ELYARYKAEQQTLTATRGQALEQARRRKDRLVEAAKRSNRLRRATIKVVGESRTNKKLLYAQASKALRDE
IQAINKQYQQDRQALYDSHSRRTWADWLKKEATHGNAEALAALRAREAAQGLQGNTIQGRGDARPGHAPV
TDNITKKGTIIFRAGLSAVRDDGDKLQVSREATREGLQEALRLAMERYGSRITVNGTTQFKAQVIRAAVD
SQLPITFADPALESRRLALLKKENTHERPDRTDRTERADQRPAEHRGRAGRGPGGPGQRAAAHDDAARPV
AIARAGFGRPGAGRTDAAGVHAGAVHRKPDIGRIGRVPPPQSQHRLRTLSQLGVVRIAGGSEVLLPRDVP
RHLEQQGTQPDHQLRRGISRPGTGVATAPPGLAAADKYIAEREAKRSKGFDIPKHARYTDGDGALAFQGV
RNIEGQALALLKRGDEVMVMPIDQATARRLSRIAVGDAVTITPKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(420-507)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure


Source ID Structure
AlphaFold DB Q4AC74


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 33696..44330

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXB82_RS00170 (pA1_31) 28802..29233 - 432 WP_011304112 antirestriction protein -
HXB82_RS00175 29405..29668 + 264 WP_011114070 type II toxin-antitoxin system RelB/DinJ family antitoxin -
HXB82_RS00180 29655..29934 + 280 Protein_35 type II toxin-antitoxin system YafQ family toxin -
HXB82_RS00185 31141..31341 - 201 WP_176705365 hypothetical protein -
HXB82_RS00295 31316..32041 - 726 WP_281042235 plasmid replication initiator TrfA -
HXB82_RS00300 32017..32103 - 87 Protein_38 plasmid replication initiator TrfA -
HXB82_RS00205 (pA1_33) 32590..32928 - 339 WP_011304114 single-stranded DNA-binding protein -
HXB82_RS00210 (pA1_34) 33037..33396 + 360 WP_015063362 transcriptional regulator -
HXB82_RS00215 (pA1_35) 33696..34661 + 966 WP_011304116 P-type conjugative transfer ATPase TrbB virB11
HXB82_RS00220 (pA1_36) 34683..35147 + 465 WP_011304117 conjugal transfer system pilin TrbC virB2
HXB82_RS00225 (pA1_37) 35151..35462 + 312 WP_011304118 conjugal transfer protein TrbD virB3
HXB82_RS00230 (pA1_38) 35459..38017 + 2559 WP_011304119 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXB82_RS00235 (pA1_39) 38014..38802 + 789 WP_011304120 conjugal transfer protein TrbF virB8
HXB82_RS00240 (pA1_40) 38820..39713 + 894 WP_176705367 P-type conjugative transfer protein TrbG virB9
HXB82_RS00245 (pA1_41) 39716..40177 + 462 WP_011304122 lipoprotein -
HXB82_RS00250 (pA1_42) 40182..41561 + 1380 WP_011304123 TrbI/VirB10 family protein virB10
HXB82_RS00255 (pA1_43) 41578..42351 + 774 WP_011304124 P-type conjugative transfer protein TrbJ virB5
HXB82_RS00260 (pA1_44) 42361..42582 + 222 WP_011304125 entry exclusion lipoprotein TrbK -
HXB82_RS00265 (pA1_45) 42594..44330 + 1737 WP_011304126 P-type conjugative transfer protein TrbL virB6
HXB82_RS00270 (pA1_46) 44348..44926 + 579 WP_011013272 TrbM/KikA/MpfK family conjugal transfer protein -
HXB82_RS00275 (pA1_47) 44928..45563 + 636 WP_011304127 transglycosylase SLT domain-containing protein -
HXB82_RS00280 (pA1_48) 45593..45862 + 270 WP_011304128 hypothetical protein -
HXB82_RS00285 (pA1_49) 45859..46557 + 699 WP_011304129 TraX family protein -

Host bacterium

ID   723 GenBank   NC_007353
Plasmid name   pA1 Incompatibility group   IncP1
Plasmid size   46557 bp Coordinate of oriT [Strand]   16444..17034 [+]
Host baterium   Sphingomonas sp. A1

Cargo genes

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