CAARD:Ty1 Copia

Welcome to the CAARD
The Clan AA Reference Database (CAARD), an in-progress database developed to investigate the major consensus and the phylogeny of clan AA to typify the different protein families according to prior (and further) estimations of their relationships using phylogenies, ancestral reconstructions, sequence logos and HMMs.

Ancestral Maximum Likelihood (ML) Joint Reconstruction

Comments

Ancestral ML reconstructions were performed using FastML 2.02 (Pupko et al. 2000). The tool generates six outputs:

  • Pin; reconstructed ancestral NJ tree in newick format.
  • Fin; parental relationship among reconstructed nodes and contemporary sequences.
  • Jrof; multiple alignment of contemporary sequences and nodes reconstructed with the Joint method.
  • Jpf; joint probability per position and total log likelihood.
  • Mrof; multiple alignment of contemporary sequences and nodes reconstructed with the marginal method
  • Mpf; marginal probability and total log likelihood

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Pin output : Ancestral tree

(N1:0.0,CsRN1:0.300000);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
CsRN1N10.3-
KabukiN10.3-
N1root!-CsRN1 Kabuki

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Jpf output: Joint probability per amino acid position and total Log Likelihood

Position Joint probability Position Joint probability Position Joint probability Position Joint probability
00.032548230.0224481460.000318314690.0275402
10.028196240.000465707470.0621819700.0621819
20.0269084250.0621819480.0283934710.0269084
30.0498761269.8643e-005490.0283934720.000234719
40.0372241270.0372241500.0372241730.000219649
50.000394280.0372241510.0275402740.0201276
60.00496762290.0201276520.003304750.0621819
70.0297219300.0498761530.0118237760.000631961
80.032548310.0269084540.000193889770.032548
90.0621819320.000270872550.000501149780.028196
100.0330756330.0259827560.00197359790.000870203
114.60464e-005340.0372241570.0621819800.000944084
120.0410315350.0269084580.0372241810.000394
130.0347441360.00143919590.028196820.003304
140.0373745370.0498761600.000388376830.003304
150.00277478380.0358474610.0347441840.0621819
160.000184753390.003304620.000253439850.00197082
170.00189948400.00277478630.00149859860.028196
184.74821e-005410.0621819640.0259827870.0001602
190.000260032420.000832469650.00197082880.00197359
200.00210886430.0621819660.0498761  
210.00149859440.028196670.0372241  
220.00210886450.0621819680.028196  
Total log likelihood of joint reconstruction: -444.947

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Jrof output: Ancestral ML Reconstruction Alignment

There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. <align id="csrn1" folder="jrof"></align>

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Mpf output: Marginal probability per amino acid position and total Log Likelihood

Position Joint probability Position Joint probability Position Joint probability Position Joint probability
00.0338425230.0225776460.000903596690.0277081
10.028886240.00120941470.0628339700.0628339
20.0276271250.0628339480.0288953710.0276271
30.050169260.000259589490.0288953720.00060996
40.0382672270.0382672500.0382672730.000477705
50.00122284280.0382672510.0277081740.0205182
60.0102288290.0205182520.00686751750.0628339
70.0307625300.050169530.0118267760.00170555
80.0338425310.0276271540.000508665770.0338425
90.0628339320.000821553550.000994096780.028886
100.0332631330.0269992560.00486276790.00202297
110.000151071340.0382672570.0628339800.00213116
120.050901350.0276271580.0382672810.00122284
130.0353273360.00288774590.028886820.00686751
140.053761370.050169600.000889856830.00686751
150.00596595380.0366289610.0353273840.0628339
160.00051148390.00686751620.000652718850.00479559
170.0038781400.00596595630.00308282860.028886
180.000143592410.0628339640.0269992870.000389225
190.000821372420.00224015650.00479559880.00486276
200.00437808430.0628339660.050169  
210.00308282440.028886670.0382672  
220.00437808450.0628339680.028886  
Total log likelihood of joint reconstruction: -409.852

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Mrof output: Ancestral ML Reconstruction Alignment

There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. <align id="csrn1" folder="mrof"></align>

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Models

Logo csrn1.png

Sequence logo constructed from the input of the processed Jrof alignment. In every position, each residue is a letter whose height is proportional to its frequency multiplied by the information content of each position measured in bits. Letters are placed such that the most common is at the top.

  • Basic residues are represented in red
  • Hydrophobic residues in black
  • Amino acids frequent in β-turns (G and P) in dark grey
  • Small nucleophiles in violet
  • Acidic residues in orange
  • Acidic-relative amides in green

The logo was constructed using ChekAlign server with the Shannon's algorithm (Shannon 1997) and options "include gaps" and "Correction factor". Gaps are not represented by any symbol but occupy a blank also proportional to its frequency and, for aesthetic reasons, always at the top. Maximum entropy is log221. The alignment gap is considered to be another state or amino acid species.

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HMMs

>AP_csrn1 profile HMM generated consensus sequence
VDTGAevSVLPvPKisklidsasYkLyAANGTrIATyGEksLvLDLkLRRAFkWiflLA
DvKtaIlGADFLTsyNLlVDvrekkLlDkl

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Pairwise alignment between the MRC sequence and the DTG/ILG template HMM-profile

      Domain 1 of 1, from 1 to 80: score 29.5, E = 1.3e-09

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTGA+v sv++     + kl                        ++
AP_csrn1       1    VDTGAEV-SVLPVP--KISKL------------------------ID 20   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 s +s++    + +a+G  ++      t+g          ++ ++     +
AP_csrn1      21 S-ASYK----LYAANGTRIA------TYGE--------KSLVLD-----L 46   

                 venrsl.psdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                 +++r++++    fl++ d         +ILG  dfL+ +n   +d+   
AP_csrn1      47 KLRRAFkW-I--FLLA-DV------KTAILGA-DFLTSYNLL-VDV    80   

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Cite this site

Llorens, C. Futami, R. Renaud, G. and A. Moya (2009). Bioinformatic Flowchart and Database to Investigate the Diversity of Clan AA Peptidases.Biology Direct, 4:3.




Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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