CAARD:Pepsins A1b d1

Revision as of 10:51, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (Nepheneshi:0.372257,NM_114992.:1.022165,(CND41_1:0.479291,(AtASP38_1:0.555408,Nucelin_1:0.620928)N3:0.048556)N2:0.043466); |fin_output= <table class="tabdata"> <tr ...)
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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

(Nepheneshi:0.372257,NM_114992.:1.022165,(CND41_1:0.479291,(AtASP38_1:0.555408,Nucelin_1:0.620928)N3:0.048556)N2:0.043466);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
NepheneshiN10.372257-
NM_114992.N11.02217-
CND41_1N20.479291-
AtASP38_1N30.555408-
Nucelin_1N30.620928-
N1root!-Nepheneshi NM_114992. N2
N2N10.0434657CND41_1 N3
N3N20.0485564AtASP38_1 Nucelin_1

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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
08.0937e-007401.83718e-008801.30364e-006120 0.00141425
17.96508e-006415.22093e-009811.05024e-005121 0.0102317
20.00256133424.48241e-005822.19433e-007122 0.00339716
30.0011929430.000404681835.74433e-007123 3.26869e-005
40.0102317440.000866462848.41431e-005124 1.11534e-009
50.00107583452.17095e-005851.9603e-006125 3.43243e-006
61.94063e-005463.91443e-00586 4.72459e-005126 5.96334e-008
70.0127188471.06869e-00587 1.06673e-006127 3.58198e-008
84.04918e-007482.24262e-00588 2.36328e-0071280.000193919
90.00535302495.02363e-00689 3.45778e-0081291.46051e-007
106.95352e-006500.0033971690 0.00015841301.76118e-009
112.21254e-005512.0962e-00791 9.79644e-0071311.53111e-007
120.00339716526.00608e-00792 2.11605e-0061321.64533e-006
134.24714e-007532.33951e-00793 4.09457e-0051337.37841e-007
140.0211041549.84382e-00994 0.0003778941341.41788e-005
151.5393e-006550.0033971695 1.77281e-0061350.00157819
161.57468e-005561.22688e-00896 4.32346e-0051366.1302e-006
174.05652e-006573.73132e-00797 2.12379e-0081373.06715e-007
185.14417e-008581.81482e-00798 8.31931e-0051382.64686e-006
193.02574e-005592.83274e-00799 4.32465e-0091390.000233869
207.67795e-009602.92569e-005100 4.83222e-0061400.00100563
210.0182668611.27261e-006101 2.06245e-0051412.12538e-007
220.0185134626.3242e-007102 2.61833e-0061420.000233869
230.0463971639.95861e-007103 5.0156e-0061431.67091e-006
240.0236971643.99297e-008104 2.64804e-0061445.63293e-006
250.0244633650.034129105 9.12698e-0061451.96141e-007
260.0207248660.000904001106 5.88637e-0071460.00112721
270.0367895672.55153e-007107 8.8342e-0071472.79908e-007
280.0463971686.07288e-007108 0.0003683831487.12754e-005
290.0168121694.13812e-005109 0.001245091494.63107e-005
300.0136403708.21809e-009110 2.39132e-0051505.89455e-005
311.55616e-005710.0281867111 1.56931e-0071518.33417e-007
321.13773e-005720.034129112 1.99203e-0061520.000169736
330.000119982730.0509014113 9.03888e-006153 0.00031041
342.59878e-009740.0509014114 6.91843e-007154 0.0015403
355.44181e-008750.0509014115 5.1244e-006155 0.0138565
363.45672e-006760.0509014116 1.65247e-007156 0.0138565
370.000111897770.0509014117 9.73438e-006  
389.9788e-007780.0509014118 6.25912e-006  
390.00552696790.0509014119 2.28911e-006  
Total log likelihood of joint reconstruction: -1698.83

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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="pepsins_a1b_d1" 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
01.44819e-006408.84727e-008803.81103e-0061200.00141725
11.48728e-005411.94639e-008811.27706e-0051210.0102345
20.00257298424.62054e-005822.46344e-0071220.00339722
30.00119715430.000450611836.30665e-0071233.28885e-005
40.0102345440.000902559848.41818e-0051243.91382e-009
50.00108226452.52308e-005853.05718e-0061254.83463e-006
62.24004e-005465.47497e-005864.74605e-0051268.87774e-008
70.0127329473.57707e-005871.63538e-0061271.15113e-007
86.68257e-007484.57591e-005883.41268e-0071280.000195067
90.00535303495.07502e-006891.35614e-0071293.7541e-007
108.78311e-006500.00339722900.0001586471307.10525e-009
112.2503e-005517.36257e-007911.83686e-0061311.98691e-007
120.00339722529.29883e-007922.17329e-0061322.10034e-006
139.07418e-007532.69018e-007934.17917e-0051332.15888e-006
140.032102542.19084e-008940.0003840711346.17061e-005
151.55537e-006550.00339722952.67291e-0061350.00205962
161.57867e-005562.06831e-008967.1603e-0051362.76055e-005
176.10247e-006575.41705e-007973.31862e-0081374.68006e-007
188.20032e-008582.97737e-007988.34521e-0051383.96523e-006
193.03171e-005599.86034e-007997.9424e-0091390.000234571
202.99516e-008604.23627e-0051006.13905e-0061400.00101938
210.051691612.32953e-0061012.2375e-0051411.15528e-006
220.051544623.56516e-0061023.8739e-0061420.000234571
230.091904633.09907e-0061031.00313e-0051432.12989e-006
240.058676644.07409e-0071043.01664e-0061445.71771e-006
250.06183650.0660051059.29703e-0061452.0461e-007
260.066005660.0009059271061.02901e-0061460.00113441
270.073152674.87752e-0071071.37986e-0061476.56039e-007
280.091904687.48004e-0071080.00111141487.95396e-005
290.068765694.1521e-0051090.003649931496.35825e-005
300.040752702.396e-0081102.45418e-0051506.3369e-005
312.67965e-005710.0585651113.16862e-0071514.61356e-006
321.35652e-005720.0660051122.85513e-0061520.000178385
330.000120108730.0731521131.80595e-0051530.000312563
348.81003e-009740.0731521141.33902e-0061540.0017739
351.28789e-007750.0731521152.81094e-0051551
363.89873e-006760.0731521164.17211e-0071561
370.000118442770.0731521171.03608e-005  
381.92756e-006780.0731521187.18212e-006  
390.00552829790.0731521194.26786e-006  
Total log likelihood of joint reconstruction: -1614.21

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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="pepsins_a1b_d1" folder="mrof"></align>

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Models

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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_pepsins_a1b_d1 profile HMM generated consensus sequence
iiDTGSDLtWLqCnpCSnCnsqPtpLFdPngSssYStvpCssqrCqdlsrdftPssCan
nnqChYtlsYgdGSsSqGvLatdtftfGnssvdsNIaFGCGennrGfnqgnptptaGLl
Gmgrgslslpsql

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

        Domain 1 of 1, from 2 to 131: score 34.6, E = 3.7e-11

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkk.a.fdp..SS.Y..v.C...
                    +DTG++++++   +c + +   +++++++ fdp++SS+Y++v+C+++
AP_pepsins     2    IDTGSDLTWL---QC-NPC-SNCNSQPtPlFDPngSSsYstVpCssq 43   

                 ivt.l..................lsysqPssktsttaqdtirgagGqski
                 ++++l+++ ++++  ++++ + +lsy+++ss ++++a+dt+ ++g+    
AP_pepsins    44 RCQdLsrdftpsscannnqchytLSYGDGSSSQGVLATDTF-TFGN---- 88   

                 yvSklktsgqirknllslvtikitkGnvTevenrslpsdgvflvvtdped
                       +s+          +++ + G       + +   g f +  +p  
AP_pepsins    89 ------SSV---------DSNIAF-G-------CGENNRG-FNQG-NPTP 113  

                 qksrydvILGrldfLrqlnsvhidl<-*
                       ++LG+ ++ +   +   +l   
AP_pepsins   114 ----TAGLLGM-GRGSLSLP--SQL    131  

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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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