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OPENSEQ.org
1W85_A_B
Genes: A B A+B
Length: 368 324 635
Sequences: 2837 10927 1390
Seq/Len: 7.71 33.73 2.19
MirrorTree (Pazo et al. 2001) 0.73
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 0.01 0.03 1.94
2 0.01 0.03 1.97
5 0.02 0.03 1.99
10 0.02 0.05 1.99
20 0.02 0.07 2.01
100 0.03 0.12 2.10
∞ 0.11 0.22 2.40
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_G 72_Q 3.32 1.00 1.00
160_M 74_F 2.29 1.00 0.99
161_R 22_N 2.21 1.00 0.99
159_K 53_F 1.56 0.94 0.88
156_L 65_L 1.54 0.94 0.88
161_R 74_F 1.50 0.92 0.86
337_K 301_A 1.48 0.92 0.84
343_L 307_W 1.42 0.89 0.81
159_K 50_D 1.27 0.81 0.69
191_F 53_F 1.25 0.80 0.68
346_I 101_R 1.24 0.79 0.67
154_V 72_Q 1.21 0.76 0.63
129_N 102_Y 1.17 0.73 0.60
206_I 36_V 1.11 0.67 0.53
178_Q 88_E 1.07 0.63 0.48
187_F 65_L 1.05 0.60 0.45
156_L 53_F 0.98 0.52 0.37
127_H 105_G 0.97 0.51 0.36
343_L 306_V 0.96 0.50 0.35
160_M 53_F 0.93 0.47 0.32
206_I 81_Q 0.93 0.47 0.31
141_Q 96_Q 0.92 0.46 0.31
160_M 50_D 0.90 0.43 0.28
348_F 239_Q 0.89 0.43 0.28
207_S 81_Q 0.86 0.40 0.25
340_V 306_V 0.86 0.39 0.24
212_K 49_E 0.83 0.36 0.22
273_M 124_T 0.82 0.35 0.21
207_S 82_F 0.81 0.34 0.20
144_I 127_L 0.80 0.33 0.19
117_Q 107_R 0.80 0.33 0.19
152_A 65_L 0.79 0.32 0.18
81_Q 25_I 0.77 0.30 0.17
74_F 124_T 0.77 0.30 0.17
273_M 82_F 0.77 0.30 0.17
349_E 164_N 0.77 0.29 0.16
247_A 258_V 0.76 0.29 0.16
130_Q 103_R 0.75 0.28 0.15
77_P 130_D 0.75 0.28 0.15
206_I 29_D 0.75 0.28 0.15
156_L 24_L 0.75 0.28 0.15
276_D 79_E 0.74 0.28 0.15
187_F 53_F 0.74 0.27 0.15
99_L 96_Q 0.74 0.27 0.14
346_I 105_G 0.74 0.27 0.14
272_T 300_F 0.73 0.26 0.14
74_F 82_F 0.73 0.26 0.14
303_L 17_L 0.73 0.26 0.14
143_I 127_L 0.72 0.25 0.13
137_V 104_T 0.71 0.25 0.13
348_F 274_A 0.71 0.24 0.12
286_L 219_A 0.71 0.24 0.12
196_I 114_I 0.71 0.24 0.12
344_I 294_P 0.71 0.24 0.12
270_P 57_L 0.70 0.24 0.12
62_R 165_D 0.70 0.24 0.12
319_E 244_E 0.70 0.23 0.12
140_P 96_Q 0.69 0.23 0.11
154_V 71_L 0.69 0.22 0.11
193_A 69_L 0.69 0.22 0.11
206_I 295_D 0.68 0.22 0.11
233_V 233_V 0.68 0.22 0.10
270_P 267_G 0.68 0.22 0.10
208_T 57_L 0.67 0.22 0.10
323_E 229_S 0.67 0.21 0.10
177_S 126_E 0.67 0.21 0.10
97_F 72_Q 0.67 0.21 0.10
207_S 29_D 0.67 0.21 0.10
142_I 57_L 0.66 0.21 0.10
276_D 261_E 0.66 0.21 0.10
306_K 230_A 0.66 0.21 0.10
74_F 83_F 0.66 0.20 0.10
81_Q 33_N 0.66 0.20 0.09
280_R 41_E 0.66 0.20 0.09
160_M 67_I 0.65 0.20 0.09
146_A 96_Q 0.65 0.20 0.09
142_I 103_R 0.65 0.20 0.09
313_E 272_V 0.65 0.20 0.09
192_K 206_I 0.65 0.19 0.09
346_I 102_Y 0.64 0.19 0.09
160_M 24_L 0.64 0.19 0.09
186_N 58_A 0.64 0.19 0.09
207_S 117_P 0.64 0.19 0.08
337_K 302_Q 0.63 0.18 0.08
317_V 75_R 0.63 0.18 0.08
274_S 300_F 0.63 0.18 0.08
140_P 84_G 0.63 0.18 0.08
119_F 17_L 0.62 0.18 0.08
180_D 88_E 0.62 0.18 0.08
105_V 54_D 0.62 0.18 0.08
133_E 127_L 0.62 0.18 0.08
240_A 136_V 0.62 0.18 0.08
304_E 200_E 0.61 0.17 0.07
222_K 126_E 0.61 0.17 0.07
231_I 139_Q 0.61 0.17 0.07
121_F 127_L 0.61 0.17 0.07
295_P 264_R 0.61 0.17 0.07
147_Q 132_L 0.61 0.17 0.07
331_K 252_K 0.61 0.17 0.07
228_I 168_I 0.61 0.17 0.07
63_S 246_I 0.60 0.17 0.07
156_L 69_L 0.60 0.17 0.07
102_Y 173_L 0.60 0.17 0.07
145_G 52_V 0.60 0.16 0.07
229_P 45_A 0.60 0.16 0.07
51_R 77_V 0.60 0.16 0.07
144_I 28_E 0.59 0.16 0.07
176_T 58_A 0.59 0.16 0.07
207_S 122_V 0.59 0.16 0.07
207_S 37_F 0.59 0.16 0.07
257_G 191_P 0.59 0.16 0.06
242_Y 252_K 0.59 0.15 0.06
260_L 230_A 0.58 0.15 0.06
226_A 269_A 0.58 0.15 0.06
349_E 109_H 0.58 0.15 0.06
162_G 50_D 0.58 0.15 0.06
152_A 131_S 0.58 0.15 0.06
76_A 126_E 0.57 0.15 0.06
102_Y 82_F 0.57 0.15 0.06
284_K 21_P 0.57 0.15 0.06
301_K 109_H 0.57 0.15 0.06
254_N 233_V 0.57 0.15 0.06
54_V 205_T 0.57 0.15 0.06
174_G 270_A 0.57 0.15 0.06
78_T 84_G 0.57 0.15 0.06
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)
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