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OPENSEQ.org
T1 and 3
Genes: A B A+B
Length: 269 299 503
Sequences: 2722 48602 201
Seq/Len: 10.12 162.55 0.4
MirrorTree (Pazo et al. 2001) 0.18
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.12 0.08 0.02
2 0.12 0.09 0.05
5 0.13 0.11 0.09
10 0.13 0.13 0.18
20 0.14 0.16 0.35
100 0.15 0.24 1.58
∞ 0.22 0.27 3.34
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
146_T 244_L 1.32 0.37 0.00
242_S 268_I 1.19 0.29 0.00
109_V 59_F 1.12 0.25 0.00
154_L 133_E 1.11 0.24 0.00
138_A 95_V 1.08 0.23 0.00
111_G 185_A 0.98 0.18 0.00
149_V 67_V 0.98 0.18 0.00
242_S 184_L 0.98 0.18 0.00
256_F 257_V 0.94 0.16 0.00
203_M 130_S 0.93 0.16 0.00
174_L 59_F 0.93 0.16 0.00
121_L 263_L 0.92 0.15 0.00
116_A 221_D 0.92 0.15 0.00
107_I 243_Y 0.90 0.15 0.00
252_V 182_V 0.90 0.14 0.00
109_V 43_D 0.90 0.14 0.00
209_F 211_L 0.89 0.14 0.00
162_M 156_Q 0.89 0.14 0.00
145_I 68_G 0.88 0.14 0.00
188_D 131_V 0.88 0.14 0.00
141_I 101_K 0.88 0.14 0.00
149_V 148_N 0.88 0.14 0.00
257_F 61_I 0.88 0.14 0.00
121_L 95_V 0.87 0.14 0.00
250_D 138_L 0.87 0.14 0.00
205_K 206_E 0.86 0.13 0.00
224_T 96_Y 0.85 0.13 0.00
211_A 61_I 0.85 0.13 0.00
205_K 248_H 0.85 0.13 0.00
67_V 84_M 0.85 0.13 0.00
234_S 263_L 0.84 0.13 0.00
162_M 133_E 0.83 0.12 0.00
154_L 203_L 0.83 0.12 0.00
155_A 290_T 0.83 0.12 0.00
169_A 201_V 0.83 0.12 0.00
222_V 69_V 0.83 0.12 0.00
210_G 153_L 0.81 0.12 0.00
26_I 60_K 0.81 0.12 0.00
154_L 59_F 0.81 0.12 0.00
136_L 269_V 0.81 0.12 0.00
35_I 58_S 0.81 0.12 0.00
203_M 89_A 0.81 0.12 0.00
187_M 95_V 0.81 0.12 0.00
149_V 131_V 0.80 0.12 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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