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OPENSEQ.org
cIm_H_2_isp_2_human
Genes: A B A+B
Length: 318 274 520
Sequences: 6316 609 107
Seq/Len: 19.86 2.22 0.21
MirrorTree (Pazo et al. 2001) 0.15
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
∞ 0.03 0.00 0.18
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
3_M 88_F 1.60 0.38 0.00
160_F 116_L 1.40 0.28 0.00
288_L 89_S 1.26 0.22 0.00
83_L 123_V 1.26 0.21 0.00
29_G 108_E 1.25 0.21 0.00
299_A 130_K 1.22 0.20 0.00
83_L 133_V 1.20 0.19 0.00
236_T 87_D 1.19 0.19 0.00
159_S 199_Q 1.19 0.19 0.00
76_T 114_S 1.19 0.19 0.00
57_T 204_R 1.18 0.18 0.00
52_A 139_S 1.18 0.18 0.00
122_A 234_Y 1.14 0.17 0.00
183_M 66_A 1.12 0.16 0.00
105_I 90_E 1.12 0.16 0.00
61_L 268_D 1.12 0.16 0.00
152_S 65_V 1.11 0.16 0.00
176_L 250_R 1.11 0.16 0.00
183_M 65_V 1.10 0.16 0.00
11_V 108_E 1.09 0.15 0.00
222_L 113_F 1.08 0.15 0.00
269_L 90_E 1.08 0.15 0.00
306_S 93_R 1.07 0.15 0.00
20_L 113_F 1.06 0.14 0.00
253_E 123_V 1.06 0.14 0.00
271_L 133_V 1.06 0.14 0.00
155_L 117_V 1.05 0.14 0.00
60_P 218_T 1.05 0.14 0.00
87_T 267_S 1.04 0.14 0.00
187_I 71_N 1.03 0.14 0.00
96_V 81_T 1.03 0.14 0.00
303_W 122_T 1.03 0.14 0.00
7_L 255_P 1.01 0.13 0.00
222_L 140_M 1.01 0.13 0.00
248_D 106_S 1.01 0.13 0.00
166_I 250_R 0.99 0.12 0.00
183_M 71_N 0.99 0.12 0.00
250_L 112_G 0.99 0.12 0.00
97_N 87_D 0.99 0.12 0.00
183_M 262_T 0.99 0.12 0.00
104_F 118_T 0.99 0.12 0.00
122_A 79_S 0.98 0.12 0.00
16_A 234_Y 0.98 0.12 0.00
266_L 182_K 0.97 0.12 0.00
229_T 133_V 0.96 0.12 0.00
60_P 259_E 0.96 0.12 0.00
70_L 66_A 0.95 0.11 0.00
70_L 270_M 0.94 0.11 0.00
187_I 66_A 0.94 0.11 0.00
149_I 115_Y 0.93 0.11 0.00
187_I 177_R 0.93 0.11 0.00
224_F 112_G 0.93 0.11 0.00
29_G 257_N 0.93 0.11 0.00
11_V 154_I 0.93 0.11 0.00
269_L 200_H 0.92 0.11 0.00
226_A 78_Y 0.92 0.11 0.00
160_F 119_G 0.92 0.11 0.00
62_K 70_L 0.91 0.10 0.00
236_T 89_S 0.89 0.10 0.00
152_S 250_R 0.89 0.10 0.00
261_T 129_A 0.89 0.10 0.00
299_A 116_L 0.88 0.10 0.00
101_G 132_A 0.86 0.09 0.00
65_T 162_G 0.86 0.09 0.00
171_H 264_E 0.86 0.09 0.00
201_A 243_Y 0.86 0.09 0.00
297_T 247_G 0.86 0.09 0.00
65_T 83_I 0.86 0.09 0.00
305_V 127_Y 0.85 0.09 0.00
280_F 127_Y 0.85 0.09 0.00
151_L 108_E 0.85 0.09 0.00
11_V 122_T 0.85 0.09 0.00
239_T 272_I 0.85 0.09 0.00
158_G 257_N 0.84 0.09 0.00
224_F 234_Y 0.84 0.09 0.00
271_L 117_V 0.84 0.09 0.00
109_S 199_Q 0.84 0.09 0.00
186_F 108_E 0.84 0.09 0.00
305_V 87_D 0.83 0.09 0.00
95_L 162_G 0.83 0.09 0.00
4_A 211_V 0.83 0.09 0.00
104_F 138_S 0.83 0.09 0.00
299_A 145_D 0.83 0.09 0.00
239_T 216_V 0.83 0.09 0.00
117_L 71_N 0.83 0.09 0.00
275_T 216_V 0.83 0.09 0.00
102_L 87_D 0.83 0.09 0.00
6_L 108_E 0.83 0.09 0.00
288_L 95_E 0.82 0.09 0.00
157_S 118_T 0.82 0.09 0.00
107_A 133_V 0.82 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
5773 0.2 cIm_H_2_isp_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5772 0.21 cIm_H_2_isp_2_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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