Example

This document lists the results of the job (Example) submitted to Leri Analytics webserver.
Sequence:
--------10--------20--------30--------40--------50--------60
123456789|123456789|123456789|123456789|123456789|123456789|
NERSRQIDDILEKTYYNVDTHPAESLDWFNVLIGQTIQQLREEAWKKDNIVYSLNAFIER
KAQELPSYLDSIKITELDIGHDFPIFSNCRIQYSPNSNGRKLEAKIDIDLNDRLAVGIET
RLLLNYPKPLTASLPINVTVSIIRFQACLTVSLTFLMFSFAPEYRMEFETQSLIGAENIP
KIGSLVEYQIKKWFVERCVEPRFQFIKLPSVWPRSKNTREG
MSA: 5644 sequences of 221 sites
MSA (trimmed): 5644 sequences of 221 sites
MSA (effective): 1606.887 samples (80% identical neighborhood = 1.0 sample)
MSA (very good quality): 7.270 (> 5: very good; > 1 && < 5: good; < 1: bad)

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Figure 1: Multiple sequence alignment

Figure 1: Figure: Multiple sequence alignment. Small nonpolar: G, A, S, T, hydrophobic: C, V, I, L, P, F, Y, M, W, polar: N, Q, H, negatively charged: D, E, and positively charged: K, R.

Figure 2: Sequence similarity

Figure 2: Figure: Distribution of similarities between pairwise sequences (the first 1000 sequences in the MSA, similarities among all sequences can be downloaded).

Figure 3: Degree of conservation

Figure 3: Figure: Degree of conservation at each single site. The symbol before each amino acid is illustrated as follows, +: charged (side chains often form salt bridges), >: polar (form hydrogen bonds as proton donors or acceptors), *: hydrophobic (normally buried inside the protein core), and #: amphipathic (often found at the surface of proteins or lipid membranes, sometimes also classified as polar).

Figure 4: Evolutionary couplings of amino acids

Figure 4: Figure: Inferred evolutionary couplings between pairwise amino acids. The symbol before each amino acid is illustrated as follows, +: charged (side chains often form salt bridges), >: polar (form hydrogen bonds as proton donors or acceptors), *: hydrophobic (normally buried inside the protein core), and #: amphipathic (often found at the surface of proteins or lipid membranes, sometimes also classified as polar).

Figure 5: Evolutionary networks of amino acids

Figure 5: Figure: Evolutionary networks of amino acids. (if not shown online, please download the figure) The symbol before each amino acid is illustrated as follows, +: charged (side chains often form salt bridges), >: polar (form hydrogen bonds as proton donors or acceptors), *: hydrophobic (normally buried inside the protein core), and #: amphipathic (often found at the surface of proteins or lipid membranes, sometimes also classified as polar).

Figure 6: Evolutionary networks in chord plotting

Figure 6: Figure: Evolutionary networks of amino acids. The symbol before each amino acid is illustrated as follows, +: charged (side chains often form salt bridges), >: polar (form hydrogen bonds as proton donors or acceptors), *: hydrophobic (normally buried inside the protein core), and #: amphipathic (often found at the surface of proteins or lipid membranes, sometimes also classified as polar).

Figure 7: Evolutionary networks on the structure

Figure 7: Figure: Evolutionary networks of amino acids that are mapped to the tertiary structure.

Figure 8: Inferred contacts

Figure 8: Figure: Inferred contacts between pairwise amino acids from the multiple sequnece alignment.

Figure 9: Coupled mutations

Figure 9: Figure: Changes in evolutionary energy estimated for the rational protein design in silico.

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