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OPENSEQ.org
1efv
Genes: A B A+B
Length: 312 252 563
Sequences: 3091 2665 2431
Seq/Len: 9.91 10.58 4.32
MirrorTree (Pazo et al. 2001) 0.90
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 0.01 4.27
2 0.01 0.01 4.27
5 0.01 0.01 4.31
10 0.01 0.01 4.31
20 0.02 0.02 4.31
100 0.03 0.03 4.33
∞ 0.09 0.08 4.39
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
179_E 171_R 4.32 1.00 1.00
107_K 137_G 3.25 1.00 1.00
139_K 220_S 3.15 1.00 1.00
103_R 137_G 2.87 1.00 1.00
310_I 240_E 2.34 1.00 1.00
109_E 103_R 2.01 1.00 0.99
112_P 130_Q 1.80 1.00 0.97
278_V 242_L 1.78 0.99 0.97
126_V 225_E 1.73 0.99 0.97
103_R 143_Q 1.73 0.99 0.96
137_T 223_S 1.72 0.99 0.96
106_A 134_M 1.71 0.99 0.96
183_Q 168_E 1.71 0.99 0.96
310_I 243_V 1.60 0.99 0.95
177_I 140_D 1.51 0.98 0.93
182_D 169_T 1.50 0.98 0.92
70_P 143_Q 1.35 0.95 0.87
177_I 142_P 1.34 0.95 0.86
294_Y 242_L 1.27 0.93 0.82
181_L 169_T 1.19 0.90 0.76
296_I 236_V 1.19 0.90 0.76
181_L 171_R 1.19 0.90 0.76
106_A 138_F 1.12 0.85 0.70
296_I 239_T 1.09 0.83 0.67
111_A 97_G 1.09 0.83 0.67
141_D 220_S 1.08 0.83 0.66
178_S 170_L 1.06 0.81 0.64
75_P 140_D 1.05 0.80 0.63
134_A 224_V 1.03 0.79 0.61
99_N 143_Q 1.01 0.77 0.58
134_A 19_V 1.01 0.76 0.58
107_K 140_D 0.99 0.74 0.56
102_P 129_N 0.95 0.69 0.50
139_K 222_I 0.94 0.68 0.49
114_S 130_Q 0.92 0.67 0.47
114_S 128_C 0.90 0.64 0.45
276_T 249_I 0.89 0.63 0.43
109_E 138_F 0.89 0.62 0.43
99_N 145_T 0.84 0.55 0.36
205_G 58_V 0.82 0.54 0.35
181_L 158_K 0.82 0.53 0.34
198_V 211_L 0.82 0.53 0.34
298_A 116_L 0.81 0.52 0.34
177_I 173_K 0.80 0.51 0.32
307_M 243_V 0.80 0.50 0.32
102_P 36_N 0.80 0.50 0.32
179_E 173_K 0.80 0.50 0.32
130_Y 25_G 0.79 0.49 0.31
124_T 222_I 0.79 0.48 0.30
184_K 169_T 0.78 0.47 0.29
111_A 219_L 0.76 0.45 0.28
215_L 17_I 0.76 0.45 0.28
112_P 128_C 0.75 0.43 0.26
150_R 36_N 0.75 0.43 0.26
70_P 170_L 0.74 0.42 0.25
102_P 144_G 0.74 0.42 0.25
247_T 180_A 0.74 0.42 0.25
174_P 142_P 0.73 0.41 0.24
74_T 137_G 0.71 0.39 0.22
233_V 127_D 0.71 0.38 0.22
97_G 42_A 0.70 0.38 0.21
295_G 198_A 0.70 0.38 0.21
176_E 140_D 0.70 0.37 0.21
96_F 170_L 0.70 0.37 0.21
277_I 230_R 0.69 0.36 0.20
148_S 24_T 0.69 0.36 0.20
135_L 225_E 0.69 0.36 0.20
275_K 249_I 0.69 0.36 0.20
283_D 199_K 0.68 0.35 0.19
304_V 105_L 0.68 0.35 0.19
199_V 244_A 0.68 0.34 0.19
137_T 225_E 0.66 0.32 0.17
104_V 220_S 0.66 0.32 0.17
247_T 14_A 0.66 0.32 0.17
278_V 160_E 0.65 0.31 0.17
98_K 146_F 0.65 0.31 0.16
149_V 6_A 0.65 0.30 0.16
234_D 188_R 0.64 0.30 0.16
155_D 251_R 0.64 0.30 0.16
136_C 224_V 0.64 0.30 0.16
137_T 222_I 0.64 0.29 0.15
275_K 202_K 0.64 0.29 0.15
268_L 77_A 0.63 0.28 0.15
199_V 118_L 0.63 0.28 0.15
70_P 137_G 0.63 0.28 0.15
165_S 141_W 0.63 0.28 0.15
237_F 6_A 0.62 0.28 0.14
127_R 127_D 0.62 0.28 0.14
111_A 218_K 0.62 0.27 0.14
199_V 131_T 0.61 0.27 0.14
184_K 160_E 0.61 0.27 0.14
63_D 247_K 0.61 0.26 0.13
109_E 99_L 0.61 0.26 0.13
240_N 135_T 0.61 0.26 0.13
191_P 164_D 0.60 0.26 0.13
142_E 220_S 0.60 0.26 0.13
280_I 61_V 0.60 0.26 0.13
154_F 162_E 0.60 0.25 0.13
304_V 73_R 0.60 0.25 0.13
4_L 43_V 0.60 0.25 0.13
230_R 44_E 0.60 0.25 0.13
102_P 130_Q 0.60 0.25 0.12
128_T 127_D 0.60 0.25 0.12
3_T 210_D 0.60 0.25 0.12
278_V 245_K 0.60 0.25 0.12
75_P 101_V 0.59 0.25 0.12
282_K 199_K 0.59 0.25 0.12
50_K 140_D 0.59 0.24 0.12
77_I 249_I 0.59 0.24 0.12
130_Y 126_D 0.59 0.24 0.12
283_D 86_V 0.59 0.24 0.12
18_T 47_V 0.59 0.24 0.12
229_S 195_I 0.59 0.24 0.12
244_V 182_L 0.59 0.24 0.12
214_L 71_T 0.58 0.24 0.12
221_Q 243_V 0.58 0.23 0.11
311_L 247_K 0.58 0.23 0.11
246_Q 124_I 0.58 0.23 0.11
220_D 61_V 0.57 0.23 0.11
8_E 166_G 0.57 0.23 0.11
93_A 28_T 0.57 0.23 0.11
227_G 109_A 0.57 0.22 0.11
93_A 127_D 0.57 0.22 0.11
54_I 101_V 0.57 0.22 0.11
21_T 88_V 0.57 0.22 0.11
290_Q 190_A 0.57 0.22 0.11
152_T 224_V 0.57 0.22 0.11
148_S 130_Q 0.57 0.22 0.11
232_A 86_V 0.57 0.22 0.10
309_E 178_V 0.56 0.22 0.10
147_F 4_L 0.56 0.22 0.10
284_P 118_L 0.56 0.22 0.10
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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