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OPENSEQ.org
cIp_5_2_cIV_2_4
Genes: A B A+B
Length: 264 227 437
Sequences: 308 5082 80
Seq/Len: 1.17 22.39 0.18
MirrorTree (Pazo et al. 2001) 0.43
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.01 0.01
20 0.00 0.01 0.01
100 0.00 0.02 0.02
∞ 0.00 0.04 0.16
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
87_C 156_S 1.55 0.32 0.00
62_G 61_M 1.41 0.26 0.00
247_Q 199_I 1.28 0.20 0.00
205_S 111_T 1.23 0.19 0.00
103_H 63_T 1.23 0.18 0.00
176_V 13_T 1.17 0.16 0.00
181_H 12_A 1.17 0.16 0.00
176_V 39_L 1.16 0.16 0.00
64_Y 44_L 1.14 0.15 0.00
93_V 99_S 1.13 0.15 0.00
94_I 16_I 1.13 0.15 0.00
171_W 148_A 1.12 0.15 0.00
93_V 129_E 1.11 0.14 0.00
174_F 189_P 1.11 0.14 0.00
57_Q 156_S 1.10 0.14 0.00
246_R 199_I 1.09 0.14 0.00
170_I 22_T 1.08 0.14 0.00
141_I 64_V 1.08 0.14 0.00
88_I 224_V 1.06 0.13 0.00
127_E 212_E 1.06 0.13 0.00
132_L 77_A 1.06 0.13 0.00
64_Y 40_Y 1.05 0.13 0.00
135_L 163_W 1.04 0.13 0.00
75_Q 142_V 1.03 0.12 0.00
116_A 42_L 1.03 0.12 0.00
150_L 165_V 1.03 0.12 0.00
204_L 18_E 1.02 0.12 0.00
216_V 61_M 1.01 0.12 0.00
180_N 163_W 0.99 0.11 0.00
187_I 63_T 0.99 0.11 0.00
86_V 122_M 0.98 0.11 0.00
148_D 131_G 0.98 0.11 0.00
205_S 181_Q 0.97 0.11 0.00
114_L 205_S 0.97 0.11 0.00
174_F 26_H 0.97 0.11 0.00
170_I 47_T 0.97 0.11 0.00
227_A 32_F 0.96 0.11 0.00
170_I 122_M 0.96 0.11 0.00
243_P 224_V 0.96 0.11 0.00
64_Y 30_I 0.95 0.10 0.00
147_T 26_H 0.95 0.10 0.00
131_N 168_L 0.94 0.10 0.00
174_F 125_P 0.94 0.10 0.00
162_A 119_N 0.94 0.10 0.00
68_I 92_D 0.94 0.10 0.00
180_N 191_V 0.94 0.10 0.00
173_M 74_V 0.93 0.10 0.00
113_D 16_I 0.93 0.10 0.00
67_E 215_P 0.93 0.10 0.00
136_R 172_T 0.93 0.10 0.00
158_S 47_T 0.92 0.10 0.00
173_M 223_P 0.92 0.10 0.00
123_Q 9_L 0.91 0.10 0.00
216_V 125_P 0.90 0.10 0.00
245_Y 217_K 0.90 0.10 0.00
180_N 14_S 0.90 0.09 0.00
158_S 217_K 0.90 0.09 0.00
111_L 97_I 0.90 0.09 0.00
135_L 141_R 0.90 0.09 0.00
204_L 223_P 0.90 0.09 0.00
114_L 142_V 0.89 0.09 0.00
158_S 32_F 0.89 0.09 0.00
194_E 140_N 0.89 0.09 0.00
108_F 13_T 0.88 0.09 0.00
112_V 99_S 0.88 0.09 0.00
94_I 14_S 0.88 0.09 0.00
114_L 192_Y 0.88 0.09 0.00
160_F 156_S 0.87 0.09 0.00
230_F 93_P 0.87 0.09 0.00
245_Y 13_T 0.86 0.09 0.00
208_V 156_S 0.86 0.09 0.00
73_V 125_P 0.86 0.09 0.00
204_L 97_I 0.86 0.09 0.00
156_A 20_L 0.86 0.09 0.00
93_V 174_A 0.86 0.09 0.00
246_R 137_D 0.86 0.09 0.00
177_F 191_V 0.85 0.09 0.00
152_P 120_S 0.85 0.09 0.00
86_V 7_V 0.85 0.09 0.00
81_F 128_L 0.85 0.09 0.00
67_E 44_L 0.85 0.08 0.00
159_V 89_E 0.84 0.08 0.00
243_P 86_M 0.84 0.08 0.00
187_I 86_M 0.84 0.08 0.00
115_T 67_I 0.84 0.08 0.00
164_N 44_L 0.84 0.08 0.00
174_F 89_E 0.83 0.08 0.00
225_E 16_I 0.83 0.08 0.00
91_D 142_V 0.83 0.08 0.00
187_I 187_T 0.83 0.08 0.00
220_V 70_A 0.83 0.08 0.00
105_N 44_L 0.83 0.08 0.00
90_P 156_S 0.82 0.08 0.00
119_V 224_V 0.82 0.08 0.00
115_T 142_V 0.82 0.08 0.00
71_K 96_T 0.82 0.08 0.00
156_A 14_S 0.82 0.08 0.00
123_Q 21_I 0.82 0.08 0.00
176_V 26_H 0.82 0.08 0.00
58_L 17_M 0.81 0.08 0.00
147_T 120_S 0.81 0.08 0.00
182_P 31_I 0.81 0.08 0.00
85_E 203_N 0.81 0.08 0.00
67_E 217_K 0.80 0.08 0.00
71_K 188_R 0.80 0.08 0.00
127_E 33_L 0.80 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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