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OPENSEQ.org
cIp_6_2_cIV_3_4
Genes: A B A+B
Length: 213 261 436
Sequences: 424 2963 95
Seq/Len: 1.99 11.35 0.22
MirrorTree (Pazo et al. 2001) 0.42
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.00 0.00
20 0.01 0.00 0.01
100 0.01 0.00 0.04
∞ 0.01 0.01 0.20
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
81_P 97_F 1.44 0.31 0.00
180_I 144_I 1.43 0.30 0.00
146_Y 7_A 1.42 0.30 0.00
104_D 97_F 1.25 0.22 0.00
178_I 49_T 1.19 0.19 0.00
148_V 52_L 1.15 0.18 0.00
178_I 256_I 1.14 0.17 0.00
80_W 97_F 1.14 0.17 0.00
199_R 10_M 1.12 0.17 0.00
50_R 168_L 1.10 0.16 0.00
80_W 83_M 1.07 0.15 0.00
71_V 191_G 1.06 0.15 0.00
180_I 198_F 1.06 0.15 0.00
109_V 97_F 1.06 0.15 0.00
119_V 121_I 1.04 0.14 0.00
94_M 123_P 1.03 0.14 0.00
71_V 97_F 1.03 0.14 0.00
191_L 96_G 1.02 0.14 0.00
99_P 97_F 1.02 0.14 0.00
180_I 230_K 1.01 0.13 0.00
80_W 166_T 1.01 0.13 0.00
68_D 27_M 1.01 0.13 0.00
191_L 194_G 1.01 0.13 0.00
106_F 147_A 0.99 0.13 0.00
119_V 222_Q 0.99 0.13 0.00
131_A 152_M 0.99 0.13 0.00
117_S 259_W 0.98 0.12 0.00
106_F 248_V 0.96 0.12 0.00
167_V 219_F 0.96 0.12 0.00
131_A 83_M 0.96 0.12 0.00
68_D 135_S 0.95 0.12 0.00
148_V 178_A 0.95 0.12 0.00
70_L 68_Q 0.95 0.12 0.00
101_Y 218_C 0.95 0.12 0.00
68_D 168_L 0.95 0.12 0.00
178_I 195_S 0.95 0.12 0.00
72_N 26_L 0.94 0.12 0.00
104_D 195_S 0.94 0.12 0.00
69_D 222_Q 0.94 0.11 0.00
193_G 195_S 0.94 0.11 0.00
178_I 194_G 0.93 0.11 0.00
94_M 226_H 0.93 0.11 0.00
53_A 220_I 0.93 0.11 0.00
65_A 15_P 0.92 0.11 0.00
86_L 145_T 0.92 0.11 0.00
186_T 19_T 0.92 0.11 0.00
173_I 153_E 0.92 0.11 0.00
86_L 199_V 0.92 0.11 0.00
170_C 6_H 0.92 0.11 0.00
126_L 6_H 0.91 0.11 0.00
199_R 84_I 0.91 0.11 0.00
178_I 21_A 0.91 0.11 0.00
141_M 118_P 0.91 0.11 0.00
99_P 152_M 0.90 0.10 0.00
99_P 194_G 0.90 0.10 0.00
134_L 106_L 0.90 0.10 0.00
72_N 14_S 0.89 0.10 0.00
191_L 164_L 0.89 0.10 0.00
136_K 174_T 0.89 0.10 0.00
176_V 215_L 0.87 0.10 0.00
194_I 233_F 0.87 0.10 0.00
95_H 79_L 0.87 0.10 0.00
194_I 128_E 0.86 0.10 0.00
109_V 7_A 0.86 0.10 0.00
188_E 154_N 0.85 0.09 0.00
145_R 154_N 0.85 0.09 0.00
142_P 198_F 0.85 0.09 0.00
106_F 83_M 0.84 0.09 0.00
110_F 127_L 0.84 0.09 0.00
191_L 56_Q 0.84 0.09 0.00
120_M 38_H 0.84 0.09 0.00
99_P 45_L 0.84 0.09 0.00
172_R 13_P 0.84 0.09 0.00
148_V 37_F 0.84 0.09 0.00
110_F 147_A 0.84 0.09 0.00
149_S 71_H 0.83 0.09 0.00
136_K 189_S 0.83 0.09 0.00
171_D 203_F 0.83 0.09 0.00
66_K 22_L 0.83 0.09 0.00
71_V 41_A 0.83 0.09 0.00
146_Y 258_W 0.83 0.09 0.00
152_S 144_I 0.83 0.09 0.00
80_W 28_T 0.83 0.09 0.00
46_L 254_V 0.82 0.09 0.00
117_S 35_F 0.82 0.09 0.00
106_F 86_F 0.82 0.09 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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