CAARD:Spumaretroviridae

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

(EFV:0.238833,(FFV:0.023485,FSV:0.042109)N2:0.306572,(HFV:0.234101,SFV:0.140934)N3:0.179964);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name Father Distance to father Sons
EFVN10.238833-
FFVN20.0234848-
FSVN20.0421088-
HFVN30.234101-
SFVN30.140934-
N1root!-EFV N2 N3
N2N10.306572FFV FSV
N3N10.179964HFV SFV

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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
05.38165e-005360.0163904720.0006095751080.0192524
10.0157724370.0159724735.80535e-0071099.28822e-009
20.000941077380.0159724748.01854e-0051100.0210204
30.000154035394.50382e-005750.04279511110.0159724
40.0185706400.000449852760.0004833471128.46963e-006
58.28536e-006410.00135471770.04279511131.69495e-006
60.000341814420.0210204780.01276561140.0427951
70.0127656430.00191487790.000267071150.00990647
80.0102574446.82761e-006806.8191e-0051160.0122447
90.00197487450.0346535810.0001204621171.32629e-006
100.0219636460.0160012823.26162e-0051180.00990647
114.30465e-007470.00210299832.17262e-0061190.0212073
123.19192e-009480.000119588840.00078961200.00982481
130.00135471495.3135e-006850.0005636051210.0122447
140.0427951500.00163053862.81052e-0051220.0163904
151.96977e-006510.0212073870.0003504861230.0346535
166.0325e-005520.0163904881.95868e-0061240.00617817
170.0212073530.0128442896.54418e-0071250.0160012
182.92775e-006544.60951e-005900.00124681262.30157e-005
190.0219636550.00074352910.04279511270.0128442
200.0025148568.0892e-006924.06985e-0071289.23027e-006
213.00009e-005577.76743e-005932.0497e-0071290.0219636
223.25698e-007580.00176538940.00133691300.00617817
238.88376e-008590.0159724952.83628e-0081314.70692e-006
243.83208e-009600.000108371960.04279511320.0128442
250.0025148610.000674823972.07178e-0051330.0185706
261.20134e-005626.75141e-005981.34233e-0071340.0127656
270.0127656639.33133e-005993.39411e-0071350.0346535
280.0128442640.02196361001.00373e-0071368.58916e-005
290.00617817655.27655e-0051010.02102041371.33635e-006
300.0346535660.01577241021.747e-0051382.20555e-006
312.36026e-006670.0003749181035.68067e-0081390.0219636
321.218e-005680.02196361040.04279511402.08666e-005
331.747e-005690.009906471050.0003604981410.0219636
349.93251e-007703.99612e-0061065.89657e-010  
356.67866e-008712.61721e-0071070.0427951  
Total log likelihood of joint reconstruction: -1170.16

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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="spumaretroviridae" 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
05.39429e-005360.0164673720.0006246671080.0192564
10.0158022370.0159757736.8528e-0071093.001e-008
20.00103337380.0159757748.133e-0051100.0210437
30.000155907396.85118e-005750.04281751110.0159757
40.0186019400.0004647760.0005368861121.14869e-005
51.94975e-005410.00137545770.04281751133.46889e-006
60.000376027420.0210437780.01278351140.0428175
70.0127835430.00205224790.0002824811150.00990647
80.0102575447.26115e-006807.16352e-0051160.0122492
90.00215097450.0346585810.0002911311174.0908e-006
100.0219664460.016018823.41474e-0051180.00990647
111.23857e-006470.00222136832.33433e-0061190.0212479
125.93373e-009480.000248522840.0008068411200.00983248
130.00137545491.31476e-005850.0005829071210.0122492
140.0428175500.00172856863.01171e-0051220.0164673
153.31103e-006510.0212479870.0003663871230.0346585
166.95011e-005520.0164673882.45704e-0061240.00617957
170.0212479530.0128941892.26225e-0061250.016018
184.55511e-006549.71756e-005900.00127951262.60973e-005
190.0219664550.000889906910.04281751270.0128941
200.00272774561.28445e-005927.16817e-0071281.3172e-005
214.91919e-005578.27521e-005939.80248e-0071290.0219664
221.71897e-006580.0018584940.001400471300.00617957
233.20357e-007590.0159757951.14778e-0071318.52544e-006
241.89377e-008600.000163348960.04281751320.0128941
250.00272774610.000765705974.23819e-0051330.0186019
261.93766e-005620.000161294985.76599e-0071340.0127835
270.0127835630.000244769999.28581e-0071350.0346585
280.0128941640.02196641003.34824e-0071368.75251e-005
290.00617957655.81919e-0051010.02104371371.58573e-006
300.0346585660.01580221022.02749e-0051382.36759e-006
314.91344e-006670.0005716421031.28046e-0071390.0219664
321.87707e-005680.02196641040.04281751404.7806e-005
332.02749e-005690.009906471050.0003839441410.0219664
341.18159e-006707.50055e-0061065.32244e-009  
351.16635e-007713.9184e-0071070.0428175  
Total log likelihood of joint reconstruction: -1130.91

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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="spumaretroviridae" 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_spumaretroviridae profile HMM generated consensus sequence
wDsgAditCvPksfLeeEePikkrliktiHGekeenvYYltfKiqGRkveaEvigtpld
YvlisPsDiPWllkkpLeLtikvdlqeqqerlLnktiLskegKeqLksLFvKYdnLWqh
WEnqvGHRrirPHkiAtGtvnPrP

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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 36.8, E = 8.6e-12

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D+GA++ ++++k+   ++                          P+
AP_spumare     1    WDSGADI-TCVPKS--FLEEEE-----------------------PI 21   

                 sktsttaqdtirgagGqs..kiyvSklktsgqirknllslvtikitkGnv
                 +k+       i++++G++++++y+  l++++q rk     v+ ++  G  
AP_spumare    22 KKRL------IKTIHGEKeeNVYY--LTFKIQGRK-----VEAEVI-G-- 55   

                 TevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                       +++ d   +++ +p+d    ++++L   ++    +   +dl   
AP_spumare    56 ------TPL-D--YVLI-SPSD----IPWLLKK-PLELTIK---VDL    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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