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OPENSEQ.org
DOG1_AHG1 (A, 5-260) (B, 105-410)
Genes: A B A+B
Length: 256 306 536
Sequences: 166 4619 61
Seq/Len: 0.65 15.09 0.11
MirrorTree (Pazo et al. 2001) 0.12
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.04 0.00
2 0.10 0.05 0.00
5 0.12 0.05 0.00
10 0.12 0.06 0.01
20 0.12 0.06 0.01
100 0.12 0.08 0.02
∞ 0.17 0.15 0.11
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
247_W 176_I 1.89 0.38 0.00
161_K 134_V 1.53 0.23 0.00
244_M 42_A 1.29 0.15 0.00
11_Y 5_Y 1.20 0.13 0.00
219_A 42_A 1.18 0.12 0.00
160_T 135_L 1.18 0.12 0.00
217_T 165_H 1.09 0.11 0.00
195_A 142_V 1.08 0.10 0.00
137_L 181_G 1.08 0.10 0.00
148_L 231_A 1.06 0.10 0.00
4_I 42_A 1.06 0.10 0.00
213_L 287_L 1.04 0.10 0.00
163_V 130_A 1.01 0.09 0.00
103_A 292_L 1.01 0.09 0.00
148_L 135_L 1.00 0.09 0.00
101_V 191_V 1.00 0.09 0.00
75_A 11_M 0.99 0.09 0.00
24_E 134_V 0.99 0.09 0.00
227_P 42_A 0.99 0.09 0.00
160_T 176_I 0.97 0.09 0.00
217_T 207_K 0.97 0.09 0.00
206_L 135_L 0.97 0.08 0.00
24_E 217_T 0.96 0.08 0.00
82_L 167_P 0.96 0.08 0.00
84_N 229_V 0.96 0.08 0.00
247_W 198_S 0.95 0.08 0.00
112_R 176_I 0.95 0.08 0.00
223_G 240_S 0.94 0.08 0.00
9_D 53_S 0.94 0.08 0.00
230_G 179_A 0.94 0.08 0.00
217_T 18_E 0.94 0.08 0.00
213_L 236_W 0.93 0.08 0.00
210_A 18_E 0.93 0.08 0.00
145_I 216_V 0.93 0.08 0.00
15_M 242_Q 0.92 0.08 0.00
178_V 303_V 0.92 0.08 0.00
76_P 153_C 0.92 0.08 0.00
204_A 176_I 0.92 0.08 0.00
213_L 237_D 0.91 0.07 0.00
240_L 206_L 0.90 0.07 0.00
63_A 177_E 0.90 0.07 0.00
237_G 289_R 0.90 0.07 0.00
217_T 19_D 0.90 0.07 0.00
12_L 294_R 0.89 0.07 0.00
43_K 64_V 0.89 0.07 0.00
206_L 284_A 0.89 0.07 0.00
203_M 68_L 0.89 0.07 0.00
85_A 252_L 0.88 0.07 0.00
210_A 175_R 0.88 0.07 0.00
82_L 158_A 0.87 0.07 0.00
244_M 303_V 0.87 0.07 0.00
155_E 148_S 0.87 0.07 0.00
208_V 42_A 0.87 0.07 0.00
161_K 194_I 0.86 0.07 0.00
50_K 211_A 0.86 0.07 0.00
224_I 280_S 0.86 0.07 0.00
174_P 305_I 0.86 0.07 0.00
53_G 135_L 0.86 0.07 0.00
221_I 140_I 0.85 0.07 0.00
154_D 176_I 0.85 0.07 0.00
26_K 159_I 0.85 0.07 0.00
88_W 172_E 0.85 0.07 0.00
88_W 203_D 0.85 0.07 0.00
88_W 214_P 0.85 0.07 0.00
88_W 233_D 0.85 0.07 0.00
88_W 234_G 0.85 0.07 0.00
88_W 298_D 0.85 0.07 0.00
94_P 172_E 0.85 0.07 0.00
94_P 203_D 0.85 0.07 0.00
94_P 214_P 0.85 0.07 0.00
94_P 233_D 0.85 0.07 0.00
94_P 234_G 0.85 0.07 0.00
94_P 298_D 0.85 0.07 0.00
141_Q 172_E 0.85 0.07 0.00
141_Q 203_D 0.85 0.07 0.00
141_Q 214_P 0.85 0.07 0.00
141_Q 233_D 0.85 0.07 0.00
141_Q 234_G 0.85 0.07 0.00
141_Q 298_D 0.85 0.07 0.00
156_E 172_E 0.85 0.07 0.00
156_E 203_D 0.85 0.07 0.00
156_E 214_P 0.85 0.07 0.00
156_E 233_D 0.85 0.07 0.00
156_E 234_G 0.85 0.07 0.00
156_E 298_D 0.85 0.07 0.00
214_R 172_E 0.85 0.07 0.00
214_R 203_D 0.85 0.07 0.00
214_R 214_P 0.85 0.07 0.00
214_R 233_D 0.85 0.07 0.00
214_R 234_G 0.85 0.07 0.00
214_R 298_D 0.85 0.07 0.00
229_Q 172_E 0.85 0.07 0.00
229_Q 203_D 0.85 0.07 0.00
229_Q 214_P 0.85 0.07 0.00
229_Q 233_D 0.85 0.07 0.00
229_Q 234_G 0.85 0.07 0.00
229_Q 298_D 0.85 0.07 0.00
16_S 55_L 0.84 0.07 0.00
235_L 131_V 0.84 0.07 0.00
47_L 49_G 0.84 0.07 0.00
217_T 45_D 0.84 0.07 0.00
217_T 47_H 0.84 0.07 0.00
190_V 240_S 0.84 0.07 0.00
41_D 177_E 0.84 0.07 0.00
167_Q 144_N 0.84 0.07 0.00
226_S 162_S 0.84 0.07 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
10605 0.11 DOG1_AHG1 (A, 5-260) (B, 105-410) Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10604 0.29 DOG1_AHG1 (A, 5-260) (B, 105-410) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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