CAARD:COG5550

Revision as of 11:39, 8 May 2009 by imported>Gydbwiki (New page: {{CAARD |pin_output= (RB280:0.746085,(SSO1395:0.457434,ST0709:0.380994)N2:0.217651,((all7265:0.579096, (PAE0993:0.413358,PAE0531:0.412493)N5:0.382074)N4:0.146186,(AF0612:0.797852, (SSO2164...)
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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

(RB280:0.746085,(SSO1395:0.457434,ST0709:0.380994)N2:0.217651,((all7265:0.579096, (PAE0993:0.413358,PAE0531:0.412493)N5:0.382074)N4:0.146186,(AF0612:0.797852, (SSO2164:0.412159,(SS01929:0.196241,SS01523:0.000589)N8:0.548989)N7:0.144960)N6:0.129051)N3:0.058060);

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Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide
Name Father Distance to father Sons
RB280N10.746085-
SSO1395N20.457434-
ST0709N20.380994-
all7265N40.579096-
PAE0993N50.413358-
PAE0531N50.412493-
AF0612N60.797852-
SSO2164N70.412159-
SS01929N80.196241-
SS01523N80.000589257-
N1root!--
N2N10.217651-
N3N10.0580597-
N4N30.146186-
N5N40.382074-
N6N30.129051-
N7N60.14496-
N8N70.548989-

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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
02.07755e-007320.0114254641.12465e-010963.41864e-011
16.16028e-006330.00633147654.6863e-007970.000126396
22.84179e-005345.99032e-005666.26756e-014980.00503064
30.00162644355.73143e-013674.16281e-010991.16824e-012
45.7979e-007364.87795e-010688.52815e-0141000.00269989
51.17327e-010370.000215497699.18399e-0111011.05534e-009
60.00274713381.10747e-009701.77576e-0121021.14876e-008
71.63818e-011393.22146e-013718.2412e-0101033.33415e-006
80.0221475402.29634e-013720.009464781046.58553e-012
91.16265e-009411.16653e-014730.004432331053.18635e-011
104.36039e-010423.00558e-014740.004013311061.1147e-009
117.79227e-010438.0983e-013751.46555e-0111075.35543e-007
123.48535e-009444.56434e-011768.94946e-0151084.38763e-010
135.96252e-016453.7383e-010773.18603e-0061095.35656e-012
142.81093e-011465.02626e-014783.37571e-0101109.44788e-013
150.00389872472.66827e-007791.11485e-0091114.54911e-010
162.83014e-009481.74806e-006808.27156e-0141120.00276597
177.85328e-010496.62296e-015810.005429961135.74397e-011
187.93748e-013502.06042e-008820.004060871143.69354e-011
191.07462e-007512.1064e-009831.66109e-0071151.38784e-005
200.000977573523.14138e-010842.00264e-0101164.35012e-007
215.70249e-005535.08745e-012852.39273e-0121176.2004e-009
224.65245e-010548.00885e-012861.85687e-0151188.63412e-011
239.09187e-005553.866e-009873.50557e-0111192.58201e-010
241.5792e-009562.57977e-006881.78112e-0061209.63224e-006
250.0114254573.3233e-011891.59469e-0121211.88822e-010
260.0120658581.19256e-010901.9257e-0061223.12042e-014
271.0173e-006591.49794e-009916.15001e-0071231.74136e-014
287.64498e-010602.16886e-009921.02648e-0061249.66364e-015
291.31444e-007611.22629e-011930.001626441252.83992e-016
300.000187558625.0934e-007948.81775e-011  
310.0203703636.34388e-007954.276e-010  
Total log likelihood of joint reconstruction: -2384.59

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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="cog5550" 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
03.26027e-007320.040126641.75613e-010961.1148e-010
16.2885e-006330.066005653.39123e-006970.000132659
22.88831e-005340.00036467663.87814e-013980.051691
30.00162883351.804e-012677.52485e-010995.88923e-012
46.68679e-007369.85517e-010681.1913e-0121000.068765
55.31867e-010370.00180356692.92944e-0101012.15313e-009
60.00352469383.47166e-008703.84059e-0111023.62088e-008
72.68261e-011391.3709e-011711.2703e-0081036.49747e-005
80.091904406.25959e-012720.061831042.93241e-010
96.79276e-009411.11971e-013730.0537611059.21871e-011
103.09825e-009423.45282e-013740.0585651067.11178e-009
113.42832e-009431.06651e-011752.61063e-0101079.20531e-007
129.54289e-009449.10074e-011763.9142e-0141081.305e-009
135.53359e-015452.36183e-009778.57053e-0051091.90838e-011
143.88989e-011461.25477e-013788.71339e-0101107.8035e-012
150.053761472.72383e-007794.77677e-0091113.30683e-009
161.04919e-008487.58499e-006809.5676e-0131120.042645
171.6877e-009494.73034e-014810.05203841131.5211e-010
183.55651e-012509.93123e-008820.0687651145.39737e-011
191.19602e-007517.19671e-009835.88856e-0061150.00034091
200.00584221521.20571e-009843.12541e-0101162.97634e-006
210.000555916532.32515e-011856.80113e-0121175.27331e-008
221.58166e-009543.61172e-011861.82965e-0141184.06358e-010
230.00219016552.26234e-008876.13497e-0111193.1414e-010
243.7401e-009569.68935e-006884.66399e-0061201.31871e-005
250.040126576.03357e-010891.12967e-0111218.67366e-010
260.050901583.8868e-010905.48459e-0061225.78527e-013
277.4096e-006591.00293e-008917.05281e-0071232.83184e-013
281.34019e-009601.47587e-008921.8015e-0061243.47157e-014
299.23977e-007613.13167e-011930.001628831259.77076e-016
300.0026529626.51112e-007941.89476e-010  
310.073152631.54459e-005959.02772e-010  
Total log likelihood of joint reconstruction: -2184.87

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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="cog5550" 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_cog5550 profile HMM generated consensus sequence
IDTGFnGylliPqeifdklpsleltdnreyttanGkikstvfatieIgnklnrdaarvl
afspviepnLLGtelLkklglridykdgklEKivldp

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

        Domain 1 of 1, from 1 to 84: score 42.9, E = 1.2e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTG + + +i++e  +++kl+                     ++ +
  AP_cog5550     1    IDTGFNGYLLIPQE--IFDKLPS--------------------LELT 25   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    ++        ++a+G  ki     k+++          ti+i  G    
  AP_cog5550    26 DNRE------YTTANG--KI-----KSTV-F-------ATIEI--G---- 48   

                   venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                       +l +d+  +v+  +p++     + +LG   +L++l+   id+   
  AP_cog5550    49 ---NKLNRDA-ARVLaFSPVI----EPNLLGT-ELLKKLGLR-IDY    84   

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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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