Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105529
Name   oriT_NMC25|unnamed1 in_silico
Organism   Pseudomonas fragi strain NMC25
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021133 (21664..21771 [+], 108 nt)
oriT length   108 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 108 nt

>oriT_NMC25|unnamed1
CCGGCGCCTCGCAGAGCAAGATCCCCCGTTGAGCACGAAGTGCGAATAAGGGGAAGTGAAGGAGGAGCCGCCCGGAACGGGTGGGCCTACTTCACCTATCTTGCCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3769 GenBank   WP_086799743
Name   Relaxase_B6D87_RS23090_NMC25|unnamed1 insolico UniProt ID   _
Length   838 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 838 a.a.        Molecular weight: 91264.71 Da        Isoelectric Point: 11.0115

>WP_086799743.1 TraI/MobA(P) family conjugative relaxase [Pseudomonas fragi]
MIARHVPMKEAKLSSFAGLAKYITNSQEKQERVGEVRLTNFQSESLDWAVTEALHVQQRNQRAEGDKTYH
LLISFAPGEQPSAEVLRDVENRICAAIGFGEHQRISAVHHDTDNLHIHIAINKIHPERHTIHEPYRAYQT
MGDMAAILEREHGLQVTNHTGRKRGSENRADDMEQHAGIESLLGWIKRECADQLTQAHTWNDLHEVMRKN
GLELQERGNGLIITDGRGVGVKASSVSRNLSKPSLEKRLGAFEGDTKKKASAKRGPGLHNRKAPPVVAVG
GKPPPMRKGRLSTLSQLGAMEGEPGKRYEGRPIHSAGSAATTELYARYKAEQGIKVHARATAWGAAKNRK
DKAVEAAKRTGRLKRAAIKMLSGPGVNKKLLYALVSKALHAEIQKANTQYLAERQSIHGEFSKRAWADWL
QAKATEGDQQALKALRARKPAKPRAGDTVAGSGPAKRSSPMPLKVDSVTKDGTVIHRFAGSPIRDDGEAL
QVARGSNRAGLEAVLRMAVHRYGQNIAVNGSDEFKEKIARVAATSNLNITFNDAALEARRQELVRLTSKE
SGNDRSNRPSRSADERRRSASSSDGGSRTKRGGRTARTGIRRGPGQTNKSGLGGVGPKPPALSGNGLREL
SQLGVVRLPERSEVLLPRDVPHNVQHEGAEHAGGMRRGVSGAGRRVGTKPRGPGATNKPGVIPVGGKPPA
MLRERLQPMSKIRELPVDGPISVPGMPRPPMPKPAPEITMPAQPKSAADKYIAERTSKRAKGFDIPNHRR
YTQDDKGAALFAGTRQIEGETLALLKRDEEIIVLSVDAATARRIKRYSLGDAVTLNDKGAVTKKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(14-250)

Large polyvalent protein-associated domain 7 (LPD7)

(467-552)


  Protein structure



No available structure.




T4CP

ID   3761 GenBank   WP_086799741
Name   t4cp2_B6D87_RS23085_NMC25|unnamed1 insolico UniProt ID   _
Length   647 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 647 a.a.        Molecular weight: 71599.78 Da        Isoelectric Point: 8.0156

>WP_086799741.1 type IV secretory system conjugative DNA transfer family protein [Pseudomonas fragi]
MSKANNAVGPQTRGKKPGKSKVVPALGLASLVAGSAAATQFFAWKFEYQAILGANYNHLYAPWAIFDWWH
KWNGIYPDALTAAGSVGTLVAAGGLIVTAAAKVIASNSSKANEHLHGSARWADKKDIEDASLLGNDGRDG
GVYVGAWRDKSGKLQYLRHNGPEHVLCYAPTRSGKGVGLVVPTLLSWPHSCVVTDLKGELWAMTAGWRKE
HAGNKVIRFEPASLTGCAYWNPLDEIRLETEYEVGDVQNLATLIVDPDGKGLESHWQKTSQALLVGMILH
VLYKAKHEGTPATLPYVDTMLADPNRDVGELWMEMTLYSHVNGENHPVIGSAGRDMMDRPEEEAGSVLST
AKSYLALYRDPVVARNVSKSQWRIKDLMNHDSPVSLYIVTQPNDKARLRPLVRVLVNMIVRLLADKMEFE
RVNAEMPAWPRFLDRLGFKQQALSYVRSKKNYKHRLLGMIDEFPSLGKLEILQESLAFVAGYGIKFYLIC
QDINQLKSRETGYGPDETITSNCHVQNAYPPNRIETAQHLSKLTGVTTVVKEQITTSGKRAGVFMGQVSR
TIQEVQRPLLTDDECLRMPGPKKDSEGQITQAGDMVVYVAGFPAIYGEQPLYFQDPTFTARAAVEEPKDT
DRLRLQNEPTAKEAIAI

  Protein domains


Predicted by InterproScan.

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

(447-626)

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

(112-420)

  Protein structure



No available structure.



ID   3762 GenBank   WP_086799784
Name   t4cp2_B6D87_RS23215_NMC25|unnamed1 insolico UniProt ID   _
Length   850 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 850 a.a.        Molecular weight: 94976.08 Da        Isoelectric Point: 6.2471

>WP_086799784.1 conjugal transfer protein TrbE [Pseudomonas fragi]
MIESLLIAIAVVGVLLVLFLLSQVRKVNEDLRLKKHQSTEAGLADLLNYAAVVDDGVIVGKNGSFMAAWL
YKGSDNASATDVEREMNSFRINQALANMGSGWMVHVDAVRRPAPNYSHPSQSNFPDPVSAAIDEERRRTF
EGLGNLYEGFFIITVTWFPPMLAERKFVELMFHDDSDKPNNKARTHHLIDFFKKEVKNIESRMSSAVSME
RLRGQKIMNEDGSTVTHDEFLQWLQFCVTGINHAVMLPTNPIYIDNLIGGKELYTGVTPKLGRKFIQVVA
IEGFPLESSPGILTRLAELPVEYRWSNRFIFMDHHEAVSHLEKFRKKWKQKIRGFFDQVFNTNGGTVDED
AVSMVADAASAIAETNSGMVAQGFYTSVVVLMDESRSVVEAAALQLEKAINAMAFTARVETINTMDAFMG
SLPGHGVENVRRPLINTMNLADLIPTSTIWTGENFAPNPLMPPNSPPLMHGLTSGNSPFRVNIDVRDLGH
TIMFGPTRAGKSTHLAILAMSWRRYSNARLFTFDKGMSMYPSCKAAGGAHYVVAGAGEKLAFAPLSNLVT
RSRRAWAMGWIDDLLALNGLKTTPEQRNLIAETIIEMGTVEEKEGRPGTLSEFTAKVQDIDIRVALKDYT
IDGLMGHLLDAEEDQLSISDFITFEIEHLMDLGDRYALPVLLYLFMRIQEALDGRPTLIILDEAWLMLGH
DVFREKIREWLKTLAKKNCRVLMATQNLSDASQSGILDVIVESTATKIYLPNMYARDEAATALYLRMGLN
LRQIEIIATAQQKRDYYLVSEKGRRLYSLALGPLALSFVGATGPDDIAIIKKLEEQHGDSWVHVWLRDRG
LSLDNYRSAA

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(221-431)

TraG P-loop domain (P-loop_TraG)

(621-751)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35200..45554

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
B6D87_RS23175 (B6D87_23150) 30498..30929 - 432 WP_086799767 hypothetical protein -
B6D87_RS23180 (B6D87_23155) 31195..31893 + 699 WP_240518109 hypothetical protein -
B6D87_RS23190 (B6D87_23165) 33123..34307 - 1185 WP_086799771 plasmid replication initiator TrfA -
B6D87_RS23195 (B6D87_23170) 34561..34935 + 375 WP_086799773 transcriptional regulator -
B6D87_RS23200 (B6D87_23175) 35200..36162 + 963 WP_086799777 P-type conjugative transfer ATPase TrbB virB11
B6D87_RS23205 (B6D87_23180) 36174..36608 + 435 WP_086799779 TrbC/VirB2 family protein virB2
B6D87_RS23210 (B6D87_23185) 36614..36925 + 312 WP_086799782 conjugal transfer protein TrbD virB3
B6D87_RS23215 (B6D87_23190) 36922..39474 + 2553 WP_086799784 conjugal transfer protein TrbE virb4
B6D87_RS23220 (B6D87_23195) 39471..40202 + 732 WP_086799789 VirB8/TrbF family protein virB8
B6D87_RS23225 (B6D87_23200) 40223..41119 + 897 WP_086799791 P-type conjugative transfer protein TrbG virB9
B6D87_RS23230 (B6D87_23205) 41119..41580 + 462 WP_086799793 hypothetical protein -
B6D87_RS23235 (B6D87_23210) 41586..42995 + 1410 WP_086799795 TrbI/VirB10 family protein virB10
B6D87_RS23240 (B6D87_23215) 43011..43814 + 804 WP_086799797 P-type conjugative transfer protein TrbJ virB5
B6D87_RS23925 43828..44031 + 204 WP_157665717 hypothetical protein -
B6D87_RS23245 (B6D87_23220) 44031..45554 + 1524 WP_086799811 P-type conjugative transfer protein TrbL virB6
B6D87_RS23250 (B6D87_23225) 45565..45864 + 300 WP_086799799 TrbM/KikA/MpfK family conjugal transfer protein -
B6D87_RS23255 (B6D87_23230) 45875..46531 + 657 WP_086799801 conjugal transfer protein TrbN -
B6D87_RS23260 (B6D87_23235) 46542..47272 + 731 Protein_49 TraX family protein -
B6D87_RS23265 (B6D87_23240) 47301..47774 + 474 WP_086799802 hypothetical protein -
B6D87_RS23270 (B6D87_23245) 47963..49539 - 1577 Protein_51 PAS domain-containing methyl-accepting chemotaxis protein -
B6D87_RS23280 (B6D87_23255) 49849..50409 + 561 WP_001161490 recombinase family protein -

Host bacterium

ID   5967 GenBank   NZ_CP021133
Plasmid name   NMC25|unnamed1 Incompatibility group   -
Plasmid size   79891 bp Coordinate of oriT [Strand]   21664..21771 [+]
Host baterium   Pseudomonas fragi strain NMC25

Cargo genes

Drug resistance gene   -
Virulence gene   mrkF, mrkD, mrkC, mrkB, mrkA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -