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OPENSEQ.org
1IAM_A ICAM-1 domain 1-2 1MQ9_A Integrin a-L I domain
Genes: A B A+B
Length: 185 180 350
Sequences: 12704 4026 68
Seq/Len: 68.67 22.37 0.19
MirrorTree (Pazo et al. 2001) 0.27
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 0.16 0.11 0.02
2 0.18 0.11 0.02
5 0.20 0.13 0.08
10 0.21 0.13 0.12
20 0.22 0.13 0.19
100 0.24 0.14 0.40
∞ 0.25 0.17 0.57
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
101_G 169_L 1.85 0.51 0.00
67_S 47_F 1.62 0.37 0.00
67_S 85_A 1.62 0.37 0.00
98_Q 165_T 1.50 0.31 0.00
69_C 70_L 1.43 0.27 0.00
149_R 47_F 1.28 0.21 0.00
130_L 167_E 1.24 0.20 0.00
146_V 116_A 1.24 0.19 0.00
21_C 9_L 1.19 0.18 0.00
84_W 47_F 1.17 0.17 0.00
79_F 135_I 1.16 0.17 0.00
134_P 111_I 1.16 0.17 0.00
36_P 43_A 1.15 0.16 0.00
154_G 8_F 1.15 0.16 0.00
9_V 47_F 1.12 0.15 0.00
100_V 58_S 1.11 0.15 0.00
14_G 15_S 1.11 0.15 0.00
21_C 42_F 1.11 0.15 0.00
28_P 47_F 1.10 0.15 0.00
79_F 56_D 1.09 0.14 0.00
163_L 48_S 1.09 0.14 0.00
153_H 9_L 1.09 0.14 0.00
159_C 6_L 1.08 0.14 0.00
126_G 155_P 1.06 0.14 0.00
17_V 128_I 1.06 0.14 0.00
155_A 131_Y 1.05 0.13 0.00
42_L 70_L 1.04 0.13 0.00
60_D 78_L 1.03 0.13 0.00
81_T 106_K 1.03 0.13 0.00
157_F 23_K 1.03 0.13 0.00
17_V 148_L 1.02 0.13 0.00
157_F 6_L 1.02 0.12 0.00
171_E 70_L 1.01 0.12 0.00
155_A 21_F 1.00 0.12 0.00
62_Q 43_A 0.99 0.12 0.00
159_C 35_L 0.99 0.12 0.00
24_S 73_V 0.99 0.12 0.00
123_L 148_L 0.99 0.12 0.00
80_L 82_T 0.98 0.11 0.00
166_R 116_A 0.98 0.11 0.00
9_V 128_I 0.97 0.11 0.00
31_L 101_R 0.97 0.11 0.00
75_T 133_I 0.97 0.11 0.00
110_V 147_T 0.97 0.11 0.00
129_E 47_F 0.97 0.11 0.00
60_D 152_A 0.96 0.11 0.00
6_P 108_L 0.96 0.11 0.00
159_C 31_V 0.96 0.11 0.00
82_V 9_L 0.95 0.11 0.00
172_L 45_V 0.95 0.11 0.00
98_Q 106_K 0.95 0.11 0.00
63_P 148_L 0.95 0.11 0.00
167_P 45_V 0.95 0.11 0.00
101_G 9_L 0.94 0.11 0.00
108_C 9_L 0.94 0.11 0.00
21_C 110_I 0.94 0.11 0.00
115_P 13_S 0.94 0.11 0.00
25_C 42_F 0.94 0.10 0.00
21_C 13_S 0.94 0.10 0.00
151_D 132_I 0.94 0.10 0.00
57_V 60_Y 0.94 0.10 0.00
21_C 11_D 0.93 0.10 0.00
39_K 147_T 0.93 0.10 0.00
31_L 57_F 0.93 0.10 0.00
78_T 74_K 0.93 0.10 0.00
51_V 148_L 0.92 0.10 0.00
19_V 35_L 0.92 0.10 0.00
163_L 21_F 0.92 0.10 0.00
19_V 127_D 0.91 0.10 0.00
127_E 111_I 0.91 0.10 0.00
123_L 73_V 0.91 0.10 0.00
169_G 27_F 0.91 0.10 0.00
110_V 124_A 0.91 0.10 0.00
19_V 84_G 0.91 0.10 0.00
11_L 91_T 0.91 0.10 0.00
63_P 116_A 0.91 0.10 0.00
103_Q 35_L 0.91 0.10 0.00
166_R 131_Y 0.90 0.10 0.00
151_D 169_L 0.90 0.10 0.00
65_C 9_L 0.90 0.10 0.00
63_P 176_L 0.90 0.10 0.00
141_E 58_S 0.89 0.10 0.00
93_P 160_V 0.89 0.10 0.00
69_C 144_S 0.89 0.10 0.00
23_T 5_D 0.89 0.10 0.00
134_P 171_D 0.89 0.10 0.00
145_T 110_I 0.89 0.10 0.00
54_L 91_T 0.89 0.10 0.00
72_G 103_D 0.87 0.09 0.00
100_V 89_V 0.87 0.09 0.00
165_L 82_T 0.87 0.09 0.00
100_V 7_V 0.87 0.09 0.00
14_G 136_G 0.87 0.09 0.00
27_Q 85_A 0.87 0.09 0.00
54_L 161_C 0.87 0.09 0.00
14_G 11_D 0.87 0.09 0.00
28_P 66_P 0.86 0.09 0.00
160_R 161_C 0.86 0.09 0.00
128_K 94_F 0.86 0.09 0.00
19_V 161_C 0.86 0.09 0.00
161_T 152_A 0.85 0.09 0.00
154_G 135_I 0.85 0.09 0.00
144_T 106_K 0.85 0.09 0.00
25_C 48_S 0.85 0.09 0.00
161_T 131_Y 0.85 0.09 0.00
148_V 149_H 0.85 0.09 0.00
151_D 163_L 0.85 0.09 0.00
161_T 51_Y 0.85 0.09 0.00
161_T 133_I 0.84 0.09 0.00
80_L 80_T 0.84 0.09 0.00
100_V 106_K 0.84 0.09 0.00
43_L 112_T 0.84 0.09 0.00
153_H 6_L 0.84 0.09 0.00
14_G 13_S 0.83 0.08 0.00
36_P 85_A 0.83 0.08 0.00
128_K 45_V 0.83 0.08 0.00
153_H 152_A 0.83 0.08 0.00
146_V 106_K 0.83 0.08 0.00
40_K 72_H 0.83 0.08 0.00
144_T 48_S 0.83 0.08 0.00
166_R 42_F 0.83 0.08 0.00
123_L 15_S 0.83 0.08 0.00
63_P 8_F 0.83 0.08 0.00
73_Q 106_K 0.82 0.08 0.00
63_P 127_D 0.82 0.08 0.00
115_P 9_L 0.82 0.08 0.00
151_D 103_D 0.82 0.08 0.00
61_S 65_D 0.82 0.08 0.00
51_V 10_F 0.82 0.08 0.00
31_L 82_T 0.82 0.08 0.00
36_P 122_I 0.82 0.08 0.00
155_A 116_A 0.82 0.08 0.00
158_S 12_G 0.82 0.08 0.00
27_Q 86_I 0.81 0.08 0.00
47_N 73_V 0.81 0.08 0.00
24_S 48_S 0.81 0.08 0.00
160_R 51_Y 0.81 0.08 0.00
54_L 48_S 0.81 0.08 0.00
111_E 107_V 0.81 0.08 0.00
101_G 73_V 0.81 0.08 0.00
76_A 111_I 0.81 0.08 0.00
31_L 7_V 0.81 0.08 0.00
117_A 116_A 0.81 0.08 0.00
79_F 28_M 0.81 0.08 0.00
149_R 16_L 0.80 0.08 0.00
63_P 123_D 0.80 0.08 0.00
51_V 87_N 0.80 0.08 0.00
151_D 45_V 0.80 0.08 0.00
15_G 107_V 0.80 0.08 0.00
163_L 113_D 0.80 0.08 0.00
54_L 33_K 0.79 0.08 0.00
124_L 137_K 0.79 0.08 0.00
150_R 57_F 0.79 0.08 0.00
56_N 48_S 0.79 0.08 0.00
49_R 177_Q 0.79 0.08 0.00
18_L 76_M 0.79 0.08 0.00
108_C 165_T 0.79 0.07 0.00
108_C 31_V 0.79 0.07 0.00
104_L 161_C 0.78 0.07 0.00
69_C 68_A 0.78 0.07 0.00
60_D 145_Q 0.78 0.07 0.00
69_C 44_A 0.78 0.07 0.00
106_L 110_I 0.78 0.07 0.00
166_R 16_L 0.78 0.07 0.00
31_L 154_K 0.78 0.07 0.00
163_L 73_V 0.78 0.07 0.00
64_M 149_H 0.78 0.07 0.00
5_S 106_K 0.78 0.07 0.00
174_E 4_V 0.78 0.07 0.00
21_C 82_T 0.77 0.07 0.00
28_P 43_A 0.77 0.07 0.00
167_P 35_L 0.77 0.07 0.00
124_L 160_V 0.77 0.07 0.00
140_A 109_I 0.77 0.07 0.00
120_T 74_K 0.77 0.07 0.00
155_A 41_Q 0.77 0.07 0.00
163_L 80_T 0.77 0.07 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)
ID Seq/Len Name Options I_Prob Status
4116 0.19 1IAM_A ICAM-1 domain 1-2 1MQ9_A Integrin a-L I domain Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4080 0.31 1IAM_A ICAM-1 domain 1-2 1MQ9_A Integrin a-L I domain Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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