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OPENSEQ.org
cI_A_2_isp_2_human
Genes: A B A+B
Length: 115 274 322
Sequences: 6709 609 105
Seq/Len: 58.34 2.22 0.33
MirrorTree (Pazo et al. 2001) 0.36
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 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.01
100 0.00 0.00 0.02
∞ 0.01 0.00 0.27
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
20_I 126_A 1.40 0.37 0.00
8_M 88_F 1.28 0.30 0.00
57_L 220_L 1.26 0.29 0.00
104_Y 247_G 1.25 0.28 0.00
12_L 156_L 1.17 0.24 0.00
91_S 64_L 1.15 0.23 0.00
103_A 93_R 1.15 0.23 0.00
105_E 64_L 1.15 0.23 0.00
57_L 134_T 1.15 0.23 0.00
7_L 119_G 1.09 0.20 0.00
15_L 206_K 1.08 0.20 0.00
66_D 221_G 1.08 0.20 0.00
89_M 234_Y 1.07 0.20 0.00
64_L 114_S 1.06 0.19 0.00
8_M 127_Y 1.04 0.18 0.00
76_P 222_C 1.03 0.18 0.00
76_P 238_C 1.03 0.18 0.00
47_A 78_Y 1.03 0.18 0.00
107_L 70_L 1.01 0.17 0.00
64_L 211_V 0.99 0.16 0.00
15_L 272_I 0.99 0.16 0.00
103_A 66_A 0.99 0.16 0.00
17_L 191_E 0.98 0.16 0.00
88_V 92_R 0.98 0.16 0.00
103_A 250_R 0.96 0.15 0.00
44_M 79_S 0.96 0.15 0.00
86_L 66_A 0.95 0.15 0.00
89_M 216_V 0.95 0.15 0.00
23_W 104_R 0.95 0.15 0.00
100_L 255_P 0.94 0.15 0.00
5_L 117_V 0.94 0.15 0.00
112_D 112_G 0.94 0.14 0.00
49_V 108_E 0.93 0.14 0.00
99_A 224_P 0.92 0.14 0.00
95_I 132_A 0.92 0.14 0.00
64_L 169_W 0.92 0.14 0.00
76_P 241_S 0.91 0.14 0.00
69_I 68_V 0.91 0.14 0.00
56_F 126_A 0.91 0.14 0.00
64_L 195_L 0.91 0.13 0.00
8_M 126_A 0.91 0.13 0.00
92_L 103_S 0.90 0.13 0.00
19_I 230_D 0.89 0.13 0.00
86_L 175_F 0.88 0.12 0.00
19_I 96_V 0.86 0.12 0.00
19_I 184_I 0.86 0.12 0.00
96_I 200_H 0.86 0.12 0.00
114_A 104_R 0.86 0.12 0.00
51_F 126_A 0.86 0.12 0.00
21_T 247_G 0.86 0.12 0.00
101_S 64_L 0.86 0.12 0.00
112_D 115_Y 0.86 0.12 0.00
8_M 125_V 0.85 0.12 0.00
105_E 204_R 0.85 0.12 0.00
46_P 99_S 0.84 0.11 0.00
83_N 234_Y 0.84 0.11 0.00
8_M 95_E 0.84 0.11 0.00
40_G 217_C 0.84 0.11 0.00
40_G 219_H 0.84 0.11 0.00
40_G 236_C 0.84 0.11 0.00
40_G 239_H 0.84 0.11 0.00
99_A 142_A 0.83 0.11 0.00
92_L 211_V 0.83 0.11 0.00
51_F 128_A 0.83 0.11 0.00
12_L 117_V 0.83 0.11 0.00
83_N 116_L 0.83 0.11 0.00
105_E 68_V 0.82 0.11 0.00
12_L 257_N 0.82 0.11 0.00
35_T 259_E 0.82 0.11 0.00
7_L 206_K 0.82 0.11 0.00
64_L 103_S 0.82 0.11 0.00
11_T 262_T 0.81 0.11 0.00
80_Q 172_K 0.81 0.10 0.00
25_P 72_V 0.81 0.10 0.00
88_V 118_T 0.81 0.10 0.00
100_L 83_I 0.80 0.10 0.00
57_L 207_K 0.80 0.10 0.00
49_V 220_L 0.80 0.10 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
5579 0.33 cI_A_2_isp_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5578 0 cI_A_40_isp_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5577 0.39 cI_A_4_isp_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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