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OPENSEQ.org
cIm_H_2_cyt1_2_human
Genes: A B A+B
Length: 318 325 570
Sequences: 6374 747 141
Seq/Len: 20.04 2.3 0.25
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.01
100 0.00 0.02 0.02
∞ 0.03 0.02 0.22
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
157_S 70_G 1.45 0.34 0.00
251_S 282_H 1.35 0.28 0.00
67_T 309_H 1.29 0.25 0.00
220_F 138_V 1.26 0.24 0.00
33_L 236_Y 1.22 0.22 0.00
304_H 115_Q 1.15 0.20 0.00
243_L 209_D 1.14 0.19 0.00
292_N 144_E 1.12 0.18 0.00
27_I 91_P 1.11 0.18 0.00
236_T 259_T 1.08 0.17 0.00
100_L 169_G 1.07 0.16 0.00
292_N 263_M 1.05 0.16 0.00
174_L 242_I 1.04 0.15 0.00
119_S 245_A 1.04 0.15 0.00
252_P 267_A 1.04 0.15 0.00
112_A 114_F 1.04 0.15 0.00
8_L 126_S 1.04 0.15 0.00
233_M 245_A 1.03 0.15 0.00
77_L 267_A 1.02 0.14 0.00
97_N 314_L 1.02 0.14 0.00
164_T 186_R 1.01 0.14 0.00
250_L 314_L 1.01 0.14 0.00
105_I 295_M 1.01 0.14 0.00
20_L 259_T 1.01 0.14 0.00
222_L 197_L 1.01 0.14 0.00
298_L 302_L 1.01 0.14 0.00
211_F 306_I 1.01 0.14 0.00
212_N 307_K 1.01 0.14 0.00
89_L 123_S 1.01 0.14 0.00
15_I 123_S 1.01 0.14 0.00
312_S 248_I 1.00 0.14 0.00
27_I 176_P 1.00 0.14 0.00
118_W 286_K 1.00 0.14 0.00
177_P 235_P 1.00 0.14 0.00
108_T 148_L 0.99 0.14 0.00
5_N 293_L 0.99 0.14 0.00
211_F 213_S 0.99 0.14 0.00
20_L 267_A 0.98 0.14 0.00
263_T 256_D 0.98 0.14 0.00
89_L 114_F 0.98 0.13 0.00
159_S 108_T 0.98 0.13 0.00
233_M 274_L 0.97 0.13 0.00
257_T 126_S 0.97 0.13 0.00
236_T 71_G 0.97 0.13 0.00
237_L 109_S 0.97 0.13 0.00
151_L 152_V 0.97 0.13 0.00
303_W 271_C 0.97 0.13 0.00
265_L 87_L 0.96 0.13 0.00
22_L 221_P 0.96 0.13 0.00
98_L 275_R 0.96 0.13 0.00
22_L 127_M 0.96 0.13 0.00
237_L 116_V 0.96 0.13 0.00
255_Y 160_E 0.96 0.13 0.00
16_A 307_K 0.95 0.13 0.00
130_I 227_L 0.95 0.13 0.00
296_L 128_D 0.95 0.12 0.00
12_P 300_V 0.94 0.12 0.00
72_I 205_H 0.94 0.12 0.00
292_N 130_V 0.93 0.12 0.00
252_P 159_N 0.93 0.12 0.00
163_S 76_M 0.93 0.12 0.00
220_F 139_C 0.93 0.12 0.00
178_S 299_L 0.93 0.12 0.00
243_L 96_W 0.92 0.12 0.00
102_L 190_N 0.92 0.12 0.00
149_I 232_Y 0.91 0.12 0.00
128_A 290_L 0.91 0.12 0.00
178_S 266_I 0.91 0.12 0.00
3_M 127_M 0.91 0.12 0.00
8_L 271_C 0.91 0.12 0.00
159_S 206_G 0.91 0.12 0.00
292_N 298_L 0.91 0.11 0.00
263_T 245_A 0.91 0.11 0.00
132_A 141_T 0.91 0.11 0.00
100_L 83_S 0.90 0.11 0.00
174_L 308_R 0.90 0.11 0.00
212_N 266_I 0.90 0.11 0.00
67_T 127_M 0.90 0.11 0.00
3_M 86_D 0.90 0.11 0.00
61_L 68_A 0.90 0.11 0.00
166_I 122_A 0.90 0.11 0.00
97_N 221_P 0.90 0.11 0.00
32_Q 156_D 0.90 0.11 0.00
164_T 245_A 0.90 0.11 0.00
102_L 314_L 0.90 0.11 0.00
305_V 266_I 0.90 0.11 0.00
151_L 93_S 0.89 0.11 0.00
31_M 138_V 0.89 0.11 0.00
94_P 102_L 0.89 0.11 0.00
236_T 174_Y 0.89 0.11 0.00
105_I 252_V 0.89 0.11 0.00
247_Y 127_M 0.89 0.11 0.00
237_L 154_V 0.89 0.11 0.00
151_L 188_A 0.89 0.11 0.00
312_S 256_D 0.88 0.11 0.00
27_I 275_R 0.88 0.11 0.00
128_A 159_N 0.88 0.11 0.00
261_T 95_P 0.88 0.11 0.00
70_L 146_K 0.88 0.11 0.00
80_T 175_F 0.87 0.11 0.00
251_S 82_V 0.87 0.10 0.00
151_L 242_I 0.87 0.10 0.00
97_N 214_L 0.87 0.10 0.00
255_Y 253_L 0.86 0.10 0.00
212_N 306_I 0.86 0.10 0.00
67_T 145_A 0.86 0.10 0.00
253_E 268_K 0.86 0.10 0.00
237_L 272_T 0.86 0.10 0.00
132_A 134_H 0.86 0.10 0.00
28_L 281_E 0.86 0.10 0.00
212_N 281_E 0.86 0.10 0.00
98_L 131_A 0.86 0.10 0.00
23_T 299_L 0.86 0.10 0.00
60_P 307_K 0.85 0.10 0.00
116_I 138_V 0.85 0.10 0.00
32_Q 309_H 0.85 0.10 0.00
55_L 281_E 0.85 0.10 0.00
263_T 126_S 0.85 0.10 0.00
106_L 219_C 0.85 0.10 0.00
27_I 309_H 0.85 0.10 0.00
105_I 271_C 0.85 0.10 0.00
22_L 199_Y 0.85 0.10 0.00
102_L 238_P 0.85 0.10 0.00
70_L 271_C 0.84 0.10 0.00
62_K 92_P 0.84 0.10 0.00
276_A 114_F 0.84 0.10 0.00
97_N 212_F 0.84 0.10 0.00
257_T 250_T 0.84 0.10 0.00
105_I 91_P 0.84 0.10 0.00
84_L 286_K 0.84 0.10 0.00
58_K 191_G 0.84 0.10 0.00
80_T 115_Q 0.84 0.10 0.00
7_L 215_L 0.84 0.10 0.00
152_S 128_D 0.84 0.10 0.00
222_L 238_P 0.83 0.10 0.00
87_T 270_V 0.83 0.10 0.00
130_I 290_L 0.83 0.10 0.00
140_I 231_L 0.83 0.10 0.00
17_M 240_Q 0.83 0.10 0.00
112_A 310_K 0.83 0.10 0.00
70_L 177_K 0.83 0.10 0.00
182_A 209_D 0.83 0.10 0.00
212_N 213_S 0.82 0.09 0.00
182_A 213_S 0.82 0.09 0.00
116_I 201_V 0.82 0.09 0.00
72_I 132_Y 0.82 0.09 0.00
92_P 117_Y 0.82 0.09 0.00
150_L 73_G 0.82 0.09 0.00
65_T 239_G 0.82 0.09 0.00
43_Y 130_V 0.82 0.09 0.00
53_M 105_L 0.82 0.09 0.00
7_L 132_Y 0.81 0.09 0.00
118_W 68_A 0.81 0.09 0.00
159_S 96_W 0.81 0.09 0.00
182_A 186_R 0.81 0.09 0.00
299_A 179_Y 0.81 0.09 0.00
96_V 313_V 0.81 0.09 0.00
292_N 307_K 0.80 0.09 0.00
57_T 161_D 0.80 0.09 0.00
186_F 148_L 0.80 0.09 0.00
132_A 131_A 0.80 0.09 0.00
76_T 300_V 0.80 0.09 0.00
251_S 127_M 0.80 0.09 0.00
100_L 254_E 0.79 0.09 0.00
148_I 117_Y 0.79 0.09 0.00
56_F 300_V 0.79 0.09 0.00
67_T 177_K 0.79 0.09 0.00
116_I 159_N 0.79 0.09 0.00
112_A 115_Q 0.79 0.09 0.00
27_I 301_P 0.79 0.09 0.00
78_A 146_K 0.79 0.09 0.00
10_I 281_E 0.79 0.09 0.00
184_M 221_P 0.78 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
5776 0.23 cIm_H_40_cyt1_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5775 0.25 cIm_H_2_cyt1_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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