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OPENSEQ.org
cI_F_cIII_isp_10
Genes: A B A+B
Length: 184 190 366
Sequences: 2037 1442 462
Seq/Len: 11.07 7.59 1.26
MirrorTree (Pazo et al. 2001) 0.71
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 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.01 0.01 0.09
∞ 0.02 0.02 1.24
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
13_I 61_V 1.52 0.84 0.09
57_I 78_I 1.31 0.69 0.05
147_L 186_T 1.28 0.66 0.05
57_I 63_T 1.28 0.66 0.05
96_P 78_I 1.22 0.61 0.04
16_T 91_E 1.21 0.60 0.04
102_I 184_D 1.19 0.58 0.04
173_D 183_D 1.15 0.55 0.03
107_I 29_V 1.15 0.55 0.03
19_V 19_L 1.14 0.53 0.03
138_V 172_Q 1.12 0.52 0.03
97_A 61_V 1.10 0.49 0.03
52_G 12_G 1.10 0.49 0.03
15_A 91_E 1.09 0.48 0.03
57_I 77_F 1.06 0.45 0.02
37_L 148_G 1.05 0.45 0.02
86_Q 189_L 1.05 0.44 0.02
118_G 9_G 1.05 0.44 0.02
21_T 32_G 1.05 0.44 0.02
145_S 141_G 1.04 0.43 0.02
56_I 55_Q 1.04 0.43 0.02
120_D 84_D 1.04 0.43 0.02
79_S 28_T 1.03 0.42 0.02
145_S 47_D 1.03 0.42 0.02
66_L 160_D 1.02 0.42 0.02
120_D 66_Q 1.02 0.42 0.02
35_S 58_V 1.01 0.41 0.02
53_A 27_G 1.00 0.40 0.02
141_V 18_F 0.99 0.39 0.02
52_G 186_T 0.98 0.38 0.02
155_A 27_G 0.97 0.37 0.02
33_I 150_W 0.97 0.36 0.02
175_S 72_L 0.97 0.36 0.02
40_S 22_A 0.96 0.36 0.02
128_A 145_G 0.95 0.35 0.02
179_K 24_A 0.95 0.35 0.02
22_H 33_A 0.95 0.34 0.02
121_G 189_L 0.94 0.34 0.02
41_G 168_G 0.93 0.33 0.01
166_E 189_L 0.93 0.33 0.01
26_V 18_F 0.93 0.33 0.01
95_G 115_E 0.92 0.32 0.01
46_L 42_M 0.92 0.32 0.01
19_V 73_G 0.92 0.32 0.01
14_L 78_I 0.92 0.32 0.01
140_A 98_I 0.91 0.31 0.01
10_L 131_V 0.90 0.31 0.01
73_M 99_D 0.89 0.30 0.01
37_L 28_T 0.89 0.30 0.01
27_H 19_L 0.89 0.29 0.01
139_L 76_V 0.88 0.29 0.01
140_A 188_K 0.88 0.29 0.01
51_A 19_L 0.88 0.29 0.01
83_Q 65_T 0.88 0.29 0.01
36_L 135_L 0.88 0.29 0.01
73_M 177_P 0.88 0.29 0.01
169_S 30_A 0.88 0.28 0.01
27_H 126_L 0.87 0.28 0.01
147_L 166_R 0.87 0.28 0.01
130_G 91_E 0.87 0.28 0.01
128_A 39_V 0.86 0.28 0.01
104_L 131_V 0.86 0.28 0.01
141_V 168_G 0.86 0.27 0.01
138_V 90_R 0.86 0.27 0.01
156_F 59_S 0.85 0.27 0.01
31_Y 25_G 0.85 0.27 0.01
124_I 127_V 0.85 0.27 0.01
3_F 26_A 0.85 0.27 0.01
172_K 34_A 0.85 0.27 0.01
112_L 28_T 0.85 0.26 0.01
176_A 30_A 0.85 0.26 0.01
40_S 10_D 0.85 0.26 0.01
180_T 10_D 0.84 0.26 0.01
56_I 178_V 0.84 0.26 0.01
51_A 178_V 0.84 0.26 0.01
120_D 175_H 0.84 0.26 0.01
179_K 128_M 0.84 0.26 0.01
35_S 182_L 0.84 0.26 0.01
94_I 29_V 0.84 0.26 0.01
64_M 138_V 0.84 0.26 0.01
10_L 121_E 0.84 0.26 0.01
21_T 98_I 0.83 0.25 0.01
138_V 12_G 0.83 0.25 0.01
26_V 64_G 0.82 0.25 0.01
38_A 15_R 0.82 0.24 0.01
146_M 159_Y 0.82 0.24 0.01
17_L 31_A 0.82 0.24 0.01
3_F 105_S 0.82 0.24 0.01
44_F 39_V 0.81 0.24 0.01
16_T 41_Q 0.81 0.24 0.01
124_I 189_L 0.81 0.23 0.01
28_A 63_T 0.81 0.23 0.01
46_L 74_K 0.80 0.23 0.01
136_P 60_G 0.80 0.23 0.01
130_G 14_T 0.80 0.23 0.01
14_L 30_A 0.79 0.22 0.01
4_A 62_E 0.79 0.22 0.01
150_A 68_T 0.79 0.22 0.01
18_R 30_A 0.79 0.22 0.01
171_R 84_D 0.79 0.22 0.01
129_V 159_Y 0.79 0.22 0.01
38_A 184_D 0.79 0.22 0.01
54_L 58_V 0.79 0.22 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)
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