CAARD:Betaretroviridae

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

((SERV:0.083916,(MPMV:0.005850,SRV-1:0.005850)N3:0.086036)N2:0.183677, (MMTV:0.485878,(RTVL-H3:0.724208,HERV-K10:0.488442)N5:0.110959)N4:0.060627,(SMRV-H:0.239491,JSRV:0.359773)N6:0.031609);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
SERVN20.0839156-
MPMVN30.00584983-
SRV-1N30.00584983-
MMTVN40.485878-
RTVL-H3N50.724208-
HERV-K10N50.488442-
SMRV-HN60.239491-
JSRVN60.359773-
N1root!-N2 N4 N6
N2N10.183677SERV N3
N3N20.0860362MPMV SRV-1
N4N10.0606267MMTV N5
N5N40.110959RTVL-H3 HERV-K10
N6N10.0316087SMRV-H JSRV

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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
01.71239e-006232.37951e-006461.53929e-008693.06092e-006
10.00304456246.65944e-009470.0115193703.31159e-006
20.00151293253.25017e-005480.000135832710.0145443
30.0118904262.814e-010491.97911e-011720.000202726
40.00257428270.001378501.85621e-007730.0118904
50.000109893281.30865e-008512.01843e-010740.00307066
61.41809e-009290.0118904521.39693e-006750.000469603
78.65925e-006300.000246553532.77061e-009761.19715e-005
84.01624e-008310.015944541.19421e-008770.000613426
90.000410954320.0118904557.98552e-006781.72681e-007
104.28268e-008333.42962e-007560.000333466796.16299e-007
111.29917e-014341.27089e-005571.45847e-010801.21593e-007
125.30984e-011356.63916e-009581.74301e-008814.91465e-008
139.63425e-010363.4956e-007595.86821e-008820.00017905
140.000170846370.0123011600.0135052835.21427e-008
150.00657246381.20254e-006617.16586e-005849.36887e-006
161.05064e-011392.96432e-009625.03373e-008859.09886e-007
171.39281e-007401.3197e-005634.85524e-006862.67906e-005
180.000202726417.34695e-005643.03363e-005873.42796e-011
190.000742579422.07106e-007650.000266521883.05605e-015
201.86975e-012431.11753e-008662.00038e-010892.30648e-012
211.6247e-008443.86644e-011675.01929e-006  
223.78952e-011450.0145443680.00657246  
Total log likelihood of joint reconstruction: -1231.29

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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="betaretroviridae" 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
04.80258e-006236.19938e-006465.3106e-008696.55895e-006
10.00305919241.19586e-008470.019803703.52991e-006
20.0015189253.35436e-005480.000136001710.0145634
30.0118946261.29281e-009497.76362e-011720.000202842
40.00258627270.00140306502.53036e-007730.0118946
50.000112604282.95329e-008515.79879e-010740.0030792
61.7481e-009290.0118946522.21796e-006750.000480443
71.68596e-005300.000251009531.40242e-008761.33051e-005
81.10503e-007310.051544541.77564e-008770.00061957
90.000425625320.0118946559.18254e-006783.00394e-007
101.11153e-007333.58359e-007560.000453486796.39003e-007
113.0013e-013341.39955e-005576.38798e-010801.95249e-007
121.33671e-010351.70167e-008582.7485e-008811.04134e-007
133.91664e-009366.38944e-007591.17943e-007820.000645016
140.000170955371600.068765837.92491e-007
150.00657451381.35694e-006617.22384e-005842.38657e-005
165.43591e-011398.51044e-009621.66824e-007855.63591e-006
171.4724e-007401.34171e-005638.81887e-006867.08554e-005
180.000202842417.61922e-005645.56483e-005876.22788e-011
190.000748945423.91918e-007650.00027154882.54817e-014
207.64614e-012431.28463e-008665.82461e-010893.63151e-012
214.05446e-008448.27136e-011676.64935e-006  
222.91652e-010450.0145634680.00657451  
Total log likelihood of joint reconstruction: -1172.67

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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="betaretroviridae" 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

>betaretroviridae profile HMM generated consensus sequence
lDTGADvtvIsskqWPtnWPiqktvThLrGIGqAsnPqqSsqlLtWrdkeqnSglikPf
ViPtLPlNLWGRDILsqmkismmslvm

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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 42.8, E = 1.3e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA+v +vis    ++ +                        +P+
  AP_betaret     1    LDTGADV-TVISSK--QWPT-----------------------NWPI 21   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   +kt t     +rg+ Gq ++       + q+ + ll++   + ++G    
  AP_betaret    22 QKTVTH----LRGI-GQ-AS------NPQQSSQ-LLTWRDKEQNSG---- 54   

                   venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                        l     ++v++ +      +  ++Gr d+L+q++ +++ l   
  AP_betaret    55 -----LIK---PFVIPTL------PLNLWGR-DILSQMKISMMSL    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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