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OPENSEQ.org
cIm_J_2_isp_2_human
Genes: A B A+B
Length: 174 274 378
Sequences: 8320 609 149
Seq/Len: 47.82 2.22 0.39
MirrorTree (Pazo et al. 2001) 0.21
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 0.00 0.00 0.01
∞ 0.01 0.00 0.33
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
9_S 96_V 1.20 0.29 0.00
40_C 199_Q 1.19 0.28 0.00
17_V 86_P 1.19 0.28 0.00
11_G 171_G 1.13 0.25 0.00
14_M 104_R 1.08 0.22 0.00
128_E 88_F 1.05 0.21 0.00
151_W 78_Y 1.04 0.20 0.00
171_A 72_V 1.01 0.19 0.00
94_V 176_V 1.00 0.18 0.00
95_G 264_E 1.00 0.18 0.00
151_W 105_E 0.99 0.18 0.00
27_Y 216_V 0.99 0.18 0.00
151_W 272_I 0.98 0.18 0.00
135_I 117_V 0.98 0.18 0.00
101_G 257_N 0.96 0.17 0.00
100_V 114_S 0.95 0.16 0.00
34_V 244_D 0.92 0.15 0.00
123_S 218_T 0.92 0.15 0.00
17_V 265_F 0.90 0.14 0.00
150_R 214_I 0.90 0.14 0.00
151_W 66_A 0.90 0.14 0.00
150_R 247_G 0.90 0.14 0.00
102_L 173_P 0.90 0.14 0.00
91_S 112_G 0.90 0.14 0.00
22_K 108_E 0.89 0.14 0.00
100_V 89_S 0.88 0.14 0.00
90_V 234_Y 0.87 0.14 0.00
13_V 144_A 0.86 0.13 0.00
162_V 137_V 0.86 0.13 0.00
129_G 270_M 0.86 0.13 0.00
100_V 92_R 0.86 0.13 0.00
30_L 150_A 0.86 0.13 0.00
171_A 64_L 0.86 0.13 0.00
30_L 161_E 0.85 0.13 0.00
40_C 64_L 0.85 0.13 0.00
128_E 250_R 0.84 0.12 0.00
96_L 123_V 0.84 0.12 0.00
53_L 79_S 0.84 0.12 0.00
33_I 96_V 0.84 0.12 0.00
151_W 135_Q 0.84 0.12 0.00
91_S 108_E 0.83 0.12 0.00
28_G 95_E 0.83 0.12 0.00
3_Y 191_E 0.82 0.12 0.00
162_V 229_G 0.82 0.12 0.00
157_G 142_A 0.82 0.12 0.00
144_A 87_D 0.82 0.12 0.00
21_S 64_L 0.82 0.12 0.00
94_V 162_G 0.82 0.12 0.00
68_G 163_K 0.81 0.12 0.00
30_L 78_Y 0.81 0.12 0.00
103_V 159_I 0.81 0.12 0.00
28_G 185_E 0.81 0.11 0.00
65_V 229_G 0.81 0.11 0.00
3_Y 182_K 0.81 0.11 0.00
102_L 128_A 0.81 0.11 0.00
106_V 174_L 0.81 0.11 0.00
106_V 272_I 0.80 0.11 0.00
7_L 167_F 0.80 0.11 0.00
30_L 216_V 0.80 0.11 0.00
92_V 78_Y 0.80 0.11 0.00
139_P 199_Q 0.80 0.11 0.00
102_L 68_V 0.80 0.11 0.00
41_V 250_R 0.80 0.11 0.00
173_G 257_N 0.80 0.11 0.00
12_L 67_S 0.80 0.11 0.00
103_V 79_S 0.79 0.11 0.00
45_N 268_D 0.79 0.11 0.00
29_G 121_T 0.79 0.11 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
5765 0 cIm_J_20_isp_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5764 0.39 cIm_J_2_isp_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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