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OPENSEQ.org
Bccp-PII of Selongatus PCC7942_eternal
Genes: A B A+B
Length: 158 112 260
Sequences: 2418 2537 764
Seq/Len: 15.3 22.65 2.94
MirrorTree (Pazo et al. 2001) 0.32
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.04 0.00
2 0.01 0.06 0.01
5 0.02 0.06 0.02
10 0.02 0.06 0.04
20 0.02 0.06 0.09
100 0.03 0.07 0.39
∞ 0.04 0.19 2.83
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
34_V 100_I 1.12 0.77 0.04
118_L 31_S 1.00 0.64 0.03
91_F 65_V 0.99 0.63 0.03
118_L 50_E 0.94 0.57 0.02
126_E 100_I 0.93 0.56 0.02
77_G 67_D 0.92 0.54 0.02
67_A 71_D 0.91 0.53 0.02
150_Q 26_V 0.84 0.45 0.02
150_Q 78_V 0.84 0.44 0.01
74_P 63_I 0.83 0.43 0.01
113_Q 63_I 0.82 0.43 0.01
102_F 107_K 0.81 0.41 0.01
151_P 4_I 0.79 0.39 0.01
14_V 17_K 0.79 0.39 0.01
124_M 59_L 0.78 0.38 0.01
123_L 21_V 0.77 0.36 0.01
142_N 107_K 0.76 0.35 0.01
135_V 93_V 0.76 0.35 0.01
81_L 96_V 0.73 0.32 0.01
15_L 52_T 0.73 0.32 0.01
129_S 94_S 0.73 0.31 0.01
156_R 4_I 0.72 0.31 0.01
15_L 59_L 0.71 0.30 0.01
9_Q 33_V 0.70 0.29 0.01
138_I 94_S 0.70 0.29 0.01
64_P 53_V 0.70 0.29 0.01
10_E 3_K 0.70 0.29 0.01
31_E 110_D 0.70 0.29 0.01
108_R 25_I 0.70 0.28 0.01
69_A 93_V 0.69 0.28 0.01
101_P 105_G 0.69 0.28 0.01
72_A 74_I 0.69 0.28 0.01
52_V 7_I 0.69 0.28 0.01
94_A 25_I 0.69 0.27 0.01
123_L 28_M 0.68 0.27 0.01
110_Q 61_L 0.68 0.27 0.01
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
12876 2.94 Bccp-PII of Selongatus PCC7942_eternal Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.04 Done - Shared
12875 0.09 Bccp-PII of Selongatus PCC7942 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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