CAARD:Tat

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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

(B1147A04:0.303325,(Cinful1:0.345617,Retrosor1:0.236405)N2:0.215906,((RIRE2:0.029132,Orizacinfu:0.075526)N4:0.230674,(Grande:0.522943, (Ogre:0.639515,(Tft1:0.337216,(Tat4-1:0.304526,Tft2:0.356348)N8:0.128821)N7:0.076434)N6:0.260180)N5:0.068321)N3:0.061040);

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Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide
Name Father Distance to father Sons
B1147A04N10.303325-
Cinful1N20.345617-
Retrosor1N20.236405-
RIRE2N40.0291318-
OrizacinfuN40.0755262-
GrandeN50.522943-
OgreN60.639515-
Tft1N70.337216-
Tat4-1N80.304526-
Tft2N80.356348-
N1root!-B1147A04 N2 N3
N2N10.215906Cinful1 Retrosor1
N3N10.0610404N4 N5
N4N30.230674RIRE2 Orizacinfu
N5N30.0683211Grande N6
N6N50.26018Ogre N7
N7N60.0764342Tft1 N8
N8N70.128821Tat4-1 Tft2

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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
01.41368e-006294.86429e-018584.66671e-013879.63661e-005
10.000785818303.01313e-008591.6776e-011881.38765e-012
22.27026e-008310.000171151605.89048e-010891.73183e-006
30.00507483321.04585e-008614.28759e-015902.15333e-007
42.01005e-005336.2955e-015624.566e-009916.43821e-015
53.53726e-007341.10903e-005632.09022e-005920.00050763
69.042e-009350.000130426641.2049e-005931.44632e-008
71.6277e-007363.19345e-009651.34854e-012942.46642e-009
81.53342e-006371.6104e-011667.30346e-006953.91563e-006
91.88822e-008381.03722e-006674.68925e-011969.83054e-015
105.7376e-007393.00308e-015680.00291627977.05276e-012
111.97012e-013401.34097e-010699.43145e-011985.91373e-006
126.42366e-014417.82515e-017708.80988e-005993.06561e-008
131.80724e-009420.00975184711.03416e-0091008.17295e-011
141.29388e-006435.14249e-013728.9066e-0051011.48106e-009
154.09213e-012443.81251e-009731.00951e-0111021.89571e-005
162.37299e-012452.91563e-009741.23689e-0151032.97866e-011
176.63906e-010460.00507483752.92218e-0141046.42094e-007
186.28341e-012472.81925e-011765.31879e-0121054.41981e-015
190.0173312482.13087e-005770.0001914141065.95987e-013
207.19865e-011495.66222e-013781.15391e-0061074.05319e-014
219.95909e-015508.3792e-006792.58017e-0081088.94314e-005
221.59868e-014511.15531e-006801.30999e-0051098.15832e-011
237.32091e-016522.38958e-006814.15227e-0071101.57442e-012
248.13337e-016530.00990247820.005074831116.29e-009
257.2796e-008548.82727e-012833.51539e-0061122.70596e-009
261.92834e-014551.15501e-009849.04621e-0071134.44276e-011
271.36162e-010560.00507483852.86482e-0111146.08058e-006
283.05747e-008571.87889e-011866.31577e-006  
Total log likelihood of joint reconstruction: -2231.98

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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="mag" 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
03.6725e-006292.25569e-016586.98006e-012870.000462618
10.000790939301.6841e-007594.21865e-011883.63272e-012
23.64004e-008310.000171607602.02251e-009898.21749e-006
30.00507721324.94875e-008611.81827e-014902.90049e-007
42.06099e-005333.11238e-014621.87911e-008912.24241e-014
59.00976e-007341.1297e-005633.45323e-005920.000510622
62.59392e-008350.000379112641.60915e-005932.8276e-008
72.47309e-007366.71391e-009651.66128e-011947.03625e-009
83.59597e-006374.60679e-011663.48913e-005955.55346e-006
93.01302e-008381.0604e-006673.63827e-010961.47975e-013
105.76851e-007398.01785e-014680.00291829974.07826e-011
117.22958e-013404.95242e-010694.52588e-010988.20857e-006
123.57058e-013418.2508e-016709.82203e-005994.69936e-008
133.0699e-009420.051691711.65234e-0091008.52691e-011
141.6756e-006438.07757e-012729.04857e-0051014.28075e-009
151.89075e-011447.3326e-009737.70404e-0111021.9261e-005
163.32507e-011453.78818e-009743.89697e-0151034.03253e-011
177.06141e-010460.00507721755.55726e-0131046.47817e-007
182.30741e-011471.15373e-010769.9636e-0121054.67254e-014
190.06183482.59197e-005770.0001930331062.33224e-012
201.74411e-010491.5318e-012781.17323e-0061077.7275e-013
214.65163e-014508.94634e-006794.13205e-0081088.99998e-005
224.80621e-014511.18273e-006801.39044e-0051091.8569e-010
231.42906e-015523.27771e-006816.86813e-0071107.55878e-012
248.35835e-015530.053761820.005077211112.13339e-008
251.84309e-007544.56922e-011833.9448e-0061126.78394e-009
266.90828e-014552.21269e-009849.55472e-0071136.82608e-011
271.63109e-010560.00507721851.11599e-0101146.16635e-006
283.50803e-008571.01897e-010861.37113e-005  
Total log likelihood of joint reconstruction: -2121.62

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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="mag" 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_tat profile HMM generated consensus sequence
vDtGSslnvlfaktLqqmgverselqpsqsPliGvfpgetlmplGtItLPVtfGttenf
rTehvsFeVvDleaaYnaILGRPwLhakfkAvpstlhlcmKmpsprGvitvrG

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

       Domain 1 of 1, from 1 to 93: score 65.0, E = 2.8e-20

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTG+s+ +v+ +    +q++g +r++                +qPs
AP_tat         1    VDTGSSL-NVLFAK--TLQQMGVERSE----------------LQPS 28   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   +s++    i ++ G++ +      ++g+        +t+ +t+G+ Te
AP_tat        29 --QSPL----IGVFPGETLM------PLGT--------ITLPVTFGT-TE 57   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                 +++++++s   f vv d+e+   +y++ILGr ++L +++++++     
AP_tat        58 NFRTEHVS---FEVV-DLEA---AYNAILGR-PWL-HAKFKAVPS    93   

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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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