Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100152
Name   oriT_pPMA4326A in_silico
Organism   Pseudomonas syringae pv. maculicola
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_005918 (39285..39370 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      IR1: 1..12, 16..27  (GTTCCAAAGGGG..CCCCTTTGGCAC)
  IR2: 30..47, 56..73  (CGATTGGCTACGAAAAAG..CTTTTTTGTAGACAATCG)
Location of nic site      81..82nt
Conserved sequence flanking the
  nic site    		  TAACGTG|C
Note   _

  oriT sequence  


Download         Length: 86 nt

>oriT_pPMA4326A
GTTCCAAAGGGGTATCCCCTTTGGCACGTCGATTGGCTACGAAAAAGGCGAAGCTCTTTTTTGTAGACAATCGGTAACGTGCCTGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Stavrinides J et al. (2004) Nucleotide sequence and evolution of the five-plasmid complement of the phytopathogen Pseudomonas syringae pv. maculicola ES4326. J Bacteriol. 186(15):5101-15. [PMID:15262947]


Relaxase

ID   146 GenBank   YP_025665
Name   A47_pPMA4326A insolico UniProt ID   Q6J2F7
Length   1245 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 1245 a.a.        Molecular weight: 137980.56 Da        Isoelectric Point: 9.5673

>YP_025665.1 relaxase (plasmid) [Pseudomonas syringae pv. maculicola]
MLIRVSGYNTGAQEYLEKGNKSGREFTRDELDHRLIIEGQLSLTRAIYESIPDYGQDRYLTFTLSFKEDT
VSPELLKSITTDFKNFFMHAYKPEEFNLYAEAHLPKMKTVTDRKTGEVIDRKPHIHIIIPRINLLSGNEA
NPVDVYKNHEKYFEAIQEHINQKYGLSSPRENVRADITDAASVLSRYKGDDFYGKNRQFKQELVKQVIER
GVTSRADFYALVAEHGETRIRNEGKDTEYISVKLPGDAKGTNLKDTIFQDDFIVRRELKKPPLEASVIQE
RLLAWPQRAREIKYVNKATPKFRKTYSEASPEDRVRLLADREAKFYQVHGEHNDNVHTGQRQRDHQRSPA
ETAGRRTAAPADGVQDLSVSDVADHRQAGSARSRDGALLLPSDAHVHLGQSQPGGDSGLRPPVPGGGRGR
RNGSTAERGRGGSGPAAVSQEATGTATPAGATGRRRAGAGKPRNARVRAGRIVPPYAKNPHRVATIADIE
ERGRRLFDPLKKPSDNALVFYRTPSTPSNTPATATTTSGRSSAGRKPRTSGKPRPPRQWRPGSVVPPYAK
NPHRVATVADIEQRARMLFDPLKRPADKALVFKRASIKALTVNRQASTVAAYFTREAQHNRIAPAHRQAI
RRIDQQYFALRRAVFSDQRLTRQDKAQLVSVLTFERLKAREQFHKPQPNTEVNFMGSAAIRNLLEDEKED
PGFSISGARGPGPEGVRDRVKRVMDRFAKQVDPAAASQRARDLSAKDLYTRKAKFSQNVHYLDKQTDKTL
FVDTGKTISMRRTGITESGVSVALQLARERFGSTLTITGTADFKKLVIEAVAKNGLDVHFTDKAMNHSLA
ARRAELDIERGGQSIGPATDLPRHVDDSTRDVRDQADRLAVTVPIEALYGEGKTAEQVSQALAAQLDTVP
EPERIAFVELVAITLGIPERGEPKGDQAFAQWQAQRAQPAADVAATATSEAQANVPTPSDAAPEPVSPEA
AKPARVNDPDLQSPSELVRREAQWRRDFPMSEADVRASDTVMGLRGEDHAIWIIATDDKTPEAAAMLTAY
MENDSYREAFKSSLETAYRQVENWPQAVQDLDQITEMAVKIVQQVEARLYPAPQAASGQATPSRNKVIEG
ELLDHGPAPYQHKDDKQMSYFVTLKPEGGKPRTVWGVGLEDAMKDSNLKQGDQVRLEDLGTQPVVVQVIE
EDGTVTDKTVNRREWSAQPTAPEREVAETTPKGQAAAAGTPELSSPDEEDGMSVD

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(40-255)

Large polyvalent protein-associated domain 7 (LPD7)

(756-843)


  Protein structure


Source ID Structure
AlphaFold DB Q6J2F7

  Reference


[1] Stavrinides J et al. (2004) Nucleotide sequence and evolution of the five-plasmid complement of the phytopathogen Pseudomonas syringae pv. maculicola ES4326. J Bacteriol. 186(15):5101-15. [PMID:15262947]


Auxiliary protein

ID   212 GenBank   YP_025664
Name   A46_pPMA4326A insolico UniProt ID   Q6J2F8
Length   241 a.a. PDB ID   _
Note   relaxosome component

  Auxiliary protein sequence


Download         Length: 241 a.a.        Molecular weight: 27256.38 Da        Isoelectric Point: 10.3492

>YP_025664.1 relaxosome component (plasmid) [Pseudomonas syringae pv. maculicola]
MAKKVTKSCPVSCRFTDEQFARFAEPIAQSGLKPARFFHDLVMSRSPTFEQSAIDKQRMQQVFEKSGHAL
NRVAYSANSAPYNGTLYQKQYLHWLNKLNAIQQLLLTVLPETDPPKPARPVHNGNRGSPNVSGKKVHIIR
FRLTQDEMAQFNDMIKRAGCSASAFFRELILNKTPVFREFAGFRKRIVFIVNKAGNNISQLAYIAKSASD
RGLIADSVRDKWYESLVVIETILLAGIEYAD

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q6J2F8

  Reference


[1] Stavrinides J et al. (2004) Nucleotide sequence and evolution of the five-plasmid complement of the phytopathogen Pseudomonas syringae pv. maculicola ES4326. J Bacteriol. 186(15):5101-15. [PMID:15262947]


T4CP

ID   146 GenBank   YP_025656
Name   VirD4_pPMA4326A insolico UniProt ID   Q6J2G6
Length   557 a.a. PDB ID   _
Note   similar to Pseudomonas syringae pv. syringae A2 plasmid pPSR1 VirD4 encoded by GenBank Accession Number AY342395

  T4CP protein sequence


Download         Length: 557 a.a.        Molecular weight: 61679.29 Da        Isoelectric Point: 6.2665

>YP_025656.1 VirD4 (plasmid) [Pseudomonas syringae pv. maculicola]
MGKAKQQPISPDNPQERIEEHPAILIGKHPTKDTFLASYGQTFVMLAAPPGTGKTVGVVTPNLLSYPDSV
VVNDPKFENWRDTAGFRAAAGHKVYRFSPELLETHRWNPLSALSRDPLYRLGQIRTLAGVLFVSDNPKNQ
EWYNKAANVFAAILLYLMEMEGMKLNGMKLTLPQAYEVASLGTGLGVWAQQAIEQHSTGPNALSVETLRE
LNGVFEASKNKSSGWSTTVDILRGALSMYAEKTVAWAVSDTDIDFTKLRKEKISIYFCVTGNAIKKYGPL
MNLFFTQAIQQNTDVMPEQGGHCADGTLILKYQVLFVIDEIAVMGRIEIMEMAPALTRGAGLRYIIIFQG
KDQLRSERTYGREAGNGIMQAFHIEIVYGTGNVELAKEYSTRLGNTTVRVHNQSLNRQKHEIGARGQTDS
YSEQPRPLLLPQEVSALPYGEELIFVEATKTTPAANIRARKIFWYEEPVFKERAGMPTPDVPIGDASKID
ALTVPVRTVEAKVAVADTKPMQAEQRQRWNPKDKASEVAQAEAAKAQPPEVEPDPEPAQADDTPETM

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(26-477)

  Protein structure


Source ID Structure
AlphaFold DB Q6J2G6

  Reference


[1] Stavrinides J et al. (2004) Nucleotide sequence and evolution of the five-plasmid complement of the phytopathogen Pseudomonas syringae pv. maculicola ES4326. J Bacteriol. 186(15):5101-15. [PMID:15262947]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17976..28483

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS318_RS00090 (PMA4326A16) 13496..13807 + 312 WP_004666658 hypothetical protein -
HS318_RS00095 (PMA4326A17) 14012..14989 + 978 WP_007247761 IS5 family transposase -
HS318_RS00100 (PMA4326A18) 15338..15724 - 387 WP_011178577 hypothetical protein -
HS318_RS00105 (PMA4326A19) 15966..16436 - 471 WP_007253332 DUF6392 family protein -
HS318_RS00110 (PMA4326A20) 16524..16874 - 351 WP_004666693 helix-turn-helix transcriptional regulator -
HS318_RS00115 (PMA4326A21) 17139..17666 + 528 WP_007253333 transcription termination/antitermination NusG family protein -
HS318_RS00120 (PMA4326A22) 17681..17947 + 267 WP_228409371 hypothetical protein -
HS318_RS00125 (PMA4326A23) 17976..18674 + 699 WP_007253334 lytic transglycosylase domain-containing protein virB1
HS318_RS00130 (PMA4326A24) 18674..19009 + 336 WP_007253335 hypothetical protein -
HS318_RS00135 (PMA4326A25) 19022..19498 + 477 WP_011178579 VirB3 family type IV secretion system protein virB3
HS318_RS00140 (PMA4326A26) 19413..21911 + 2499 WP_228409372 conjugal transfer protein virb4
HS318_RS00145 (PMA4326A27) 21908..22594 + 687 WP_011178580 P-type DNA transfer protein VirB5 -
HS318_RS00150 (PMA4326A28) 22864..23130 + 267 WP_228409373 hypothetical protein -
HS318_RS00155 (PMA4326A29) 23141..24073 + 933 WP_007253341 type IV secretion system protein virB6
HS318_RS00160 (PMA4326A31) 24492..25280 + 789 WP_007253342 type IV secretion system protein virB8
HS318_RS00165 (PMA4326A32) 25270..26079 + 810 WP_011178583 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS318_RS00170 (PMA4326A33) 26066..27415 + 1350 WP_007253344 TrbI/VirB10 family protein virB10
HS318_RS00175 (PMA4326A34) 27425..28483 + 1059 WP_007253345 P-type DNA transfer ATPase VirB11 virB11
HS318_RS00180 (PMA4326A35) 28493..28858 + 366 WP_007253346 hypothetical protein -
HS318_RS00185 28932..29222 + 291 WP_007253347 hypothetical protein -
HS318_RS00190 (PMA4326A36) 29219..29485 + 267 WP_007253348 hypothetical protein -
HS318_RS00195 29605..29838 + 234 WP_057421666 hypothetical protein -
HS318_RS00200 29838..30011 + 174 Protein_39 type IV secretory system conjugative DNA transfer family protein -
HS318_RS00205 (PMA4326A37) 30074..31090 + 1017 WP_007253350 hypothetical protein -
HS318_RS00210 31138..31281 + 144 WP_007253351 hypothetical protein -
HS318_RS00215 31393..31626 + 234 WP_159372490 hypothetical protein -
HS318_RS00220 (PMA4326A38) 31626..33299 + 1674 WP_007253352 type IV secretory system conjugative DNA transfer family protein -

Host bacterium

ID   146 GenBank   NC_005918
Plasmid name   pPMA4326A Incompatibility group   IncI
Plasmid size   46697 bp Coordinate of oriT [Strand]   39285..39370 [-]
Host baterium   Pseudomonas syringae pv. maculicola

Cargo genes

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