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OPENSEQ.org
1tco
Genes: A B A+B
Length: 352 169 457
Sequences: 1517 5652 84
Seq/Len: 4.31 33.44 0.18
MirrorTree (Pazo et al. 2001) 0.05
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 0.04 0.06 0.01
2 0.04 0.07 0.02
5 0.04 0.07 0.04
10 0.05 0.08 0.10
20 0.05 0.08 0.16
100 0.09 0.11 0.44
∞ 0.15 0.16 1.02
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
170_L 15_D 1.32 0.22 0.00
171_M 105_Y 1.31 0.21 0.00
268_Y 57_V 1.22 0.18 0.00
301_V 107_S 1.13 0.15 0.00
195_L 32_D 1.13 0.15 0.00
109_C 71_F 1.11 0.14 0.00
71_I 22_L 1.09 0.14 0.00
53_R 150_E 1.06 0.13 0.00
162_F 62_D 1.05 0.13 0.00
240_Y 145_G 1.01 0.12 0.00
253_N 53_L 1.00 0.12 0.00
157_A 47_E 0.97 0.11 0.00
156_D 94_A 0.96 0.11 0.00
250_Q 137_I 0.94 0.10 0.00
192_I 105_Y 0.94 0.10 0.00
182_L 139_A 0.94 0.10 0.00
145_E 35_G 0.94 0.10 0.00
247_E 34_S 0.93 0.10 0.00
257_I 36_S 0.93 0.10 0.00
260_A 106_I 0.92 0.10 0.00
127_L 97_I 0.92 0.10 0.00
245_V 59_D 0.92 0.10 0.00
254_L 69_V 0.91 0.10 0.00
44_I 106_I 0.91 0.10 0.00
160_D 57_V 0.91 0.10 0.00
58_L 89_Q 0.91 0.10 0.00
240_Y 104_G 0.90 0.09 0.00
300_A 148_S 0.88 0.09 0.00
165_L 13_H 0.86 0.09 0.00
210_I 105_Y 0.85 0.09 0.00
166_P 23_G 0.85 0.09 0.00
291_Y 111_L 0.85 0.09 0.00
234_R 74_F 0.84 0.08 0.00
162_F 67_G 0.84 0.08 0.00
106_S 19_I 0.83 0.08 0.00
52_L 53_L 0.83 0.08 0.00
133_C 143_G 0.82 0.08 0.00
250_Q 39_V 0.82 0.08 0.00
31_M 150_E 0.82 0.08 0.00
32_K 128_L 0.82 0.08 0.00
192_I 19_I 0.82 0.08 0.00
36_L 20_K 0.81 0.08 0.00
189_L 125_D 0.81 0.08 0.00
106_S 31_L 0.81 0.08 0.00
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)
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