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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: 185 180 354
Sequences: 12032 9320 111
Seq/Len: 65.04 51.78 0.31
MirrorTree (Pazo et al. 2001) 0.34
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 0.12 0.03
2 0.18 0.13 0.04
5 0.20 0.15 0.13
10 0.22 0.15 0.21
20 0.23 0.16 0.30
100 0.25 0.18 0.65
∞ 0.26 0.23 1.01
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
35_T 85_A 1.60 0.49 0.00
63_P 45_V 1.47 0.40 0.00
23_T 47_F 1.43 0.38 0.00
52_Y 112_T 1.33 0.32 0.00
161_T 9_L 1.30 0.30 0.00
149_R 47_F 1.28 0.29 0.00
144_T 116_A 1.19 0.24 0.00
111_E 44_A 1.19 0.24 0.00
17_V 98_L 1.18 0.23 0.00
36_P 85_A 1.17 0.23 0.00
20_T 7_V 1.16 0.23 0.00
30_L 65_D 1.13 0.21 0.00
161_T 43_A 1.08 0.19 0.00
67_S 47_F 1.08 0.19 0.00
28_P 112_T 1.04 0.18 0.00
146_V 66_P 1.03 0.17 0.00
155_A 6_L 1.03 0.17 0.00
54_L 110_I 1.02 0.17 0.00
72_G 85_A 1.00 0.16 0.00
10_I 6_L 0.99 0.16 0.00
75_T 29_K 0.99 0.16 0.00
54_L 12_G 0.99 0.16 0.00
54_L 45_V 0.98 0.15 0.00
121_V 148_L 0.98 0.15 0.00
127_E 95_R 0.98 0.15 0.00
86_P 50_S 0.97 0.15 0.00
51_V 119_S 0.96 0.15 0.00
176_T 42_F 0.96 0.15 0.00
47_N 73_V 0.96 0.14 0.00
22_S 6_L 0.96 0.14 0.00
105_T 130_R 0.95 0.14 0.00
44_L 90_A 0.95 0.14 0.00
40_K 73_V 0.95 0.14 0.00
121_V 66_P 0.95 0.14 0.00
85_T 88_Y 0.95 0.14 0.00
108_C 9_L 0.94 0.14 0.00
12_P 109_I 0.94 0.14 0.00
80_L 87_N 0.93 0.14 0.00
146_V 68_A 0.93 0.14 0.00
15_G 47_F 0.92 0.13 0.00
127_E 109_I 0.92 0.13 0.00
172_L 124_A 0.92 0.13 0.00
46_G 55_F 0.92 0.13 0.00
129_E 85_A 0.92 0.13 0.00
82_V 92_E 0.91 0.13 0.00
107_R 9_L 0.91 0.13 0.00
48_N 25_L 0.91 0.13 0.00
19_V 161_C 0.91 0.13 0.00
54_L 153_S 0.91 0.13 0.00
22_S 134_G 0.91 0.13 0.00
38_P 73_V 0.91 0.13 0.00
157_F 152_A 0.91 0.13 0.00
106_L 35_L 0.90 0.13 0.00
121_V 166_F 0.90 0.13 0.00
24_S 31_V 0.90 0.13 0.00
41_E 89_V 0.89 0.12 0.00
163_L 47_F 0.89 0.12 0.00
130_L 133_I 0.89 0.12 0.00
52_Y 33_K 0.88 0.12 0.00
110_V 45_V 0.88 0.12 0.00
80_L 46_Q 0.88 0.12 0.00
57_V 12_G 0.88 0.12 0.00
110_V 31_V 0.88 0.12 0.00
144_T 108_L 0.88 0.12 0.00
126_G 150_K 0.88 0.12 0.00
170_L 169_L 0.88 0.12 0.00
18_L 65_D 0.87 0.12 0.00
121_V 145_Q 0.87 0.12 0.00
80_L 48_S 0.86 0.12 0.00
100_V 84_G 0.86 0.12 0.00
19_V 6_L 0.86 0.11 0.00
21_C 13_S 0.85 0.11 0.00
41_E 10_F 0.85 0.11 0.00
153_H 56_D 0.85 0.11 0.00
100_V 127_D 0.85 0.11 0.00
125_R 138_H 0.85 0.11 0.00
126_G 106_K 0.85 0.11 0.00
67_S 134_G 0.85 0.11 0.00
142_V 122_I 0.84 0.11 0.00
150_R 34_K 0.84 0.11 0.00
34_E 89_V 0.84 0.11 0.00
49_R 10_F 0.84 0.11 0.00
111_E 133_I 0.84 0.11 0.00
6_P 128_I 0.84 0.11 0.00
102_K 74_K 0.84 0.11 0.00
74_S 131_Y 0.83 0.11 0.00
86_P 40_Y 0.83 0.11 0.00
30_L 130_R 0.83 0.11 0.00
100_V 100_A 0.83 0.11 0.00
54_L 78_L 0.83 0.11 0.00
80_L 8_F 0.82 0.10 0.00
66_Y 74_K 0.82 0.10 0.00
153_H 131_Y 0.82 0.10 0.00
21_C 82_T 0.81 0.10 0.00
95_P 151_F 0.81 0.10 0.00
157_F 62_K 0.81 0.10 0.00
54_L 126_K 0.81 0.10 0.00
106_L 74_K 0.81 0.10 0.00
32_G 136_G 0.81 0.10 0.00
130_L 77_L 0.81 0.10 0.00
119_L 85_A 0.81 0.10 0.00
161_T 155_P 0.81 0.10 0.00
8_K 7_V 0.81 0.10 0.00
104_L 126_K 0.81 0.10 0.00
7_S 42_F 0.81 0.10 0.00
68_N 132_I 0.81 0.10 0.00
174_E 24_I 0.81 0.10 0.00
110_V 106_K 0.81 0.10 0.00
27_Q 151_F 0.81 0.10 0.00
63_P 85_A 0.80 0.10 0.00
161_T 31_V 0.80 0.10 0.00
180_Y 113_D 0.80 0.10 0.00
142_V 32_M 0.80 0.10 0.00
10_I 56_D 0.80 0.10 0.00
67_S 79_L 0.80 0.10 0.00
126_G 45_V 0.79 0.10 0.00
153_H 116_A 0.79 0.10 0.00
152_H 16_L 0.79 0.10 0.00
101_G 47_F 0.79 0.10 0.00
29_K 101_R 0.78 0.10 0.00
11_L 58_S 0.78 0.09 0.00
132_R 161_C 0.78 0.09 0.00
115_P 86_I 0.78 0.09 0.00
110_V 163_L 0.78 0.09 0.00
112_G 35_L 0.77 0.09 0.00
52_Y 62_K 0.77 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)
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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