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OPENSEQ.org
l5_mad (A, 15-205) (B, 1-265)
Genes: A B A+B
Length: 191 265 401
Sequences: 3043 2341 99
Seq/Len: 15.93 8.83 0.25
MirrorTree (Pazo et al. 2001) 0.22
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 0.08 0.00
2 0.11 0.11 0.00
5 0.11 0.15 0.01
10 0.11 0.16 0.01
20 0.11 0.17 0.04
100 0.13 0.19 0.11
∞ 0.16 0.22 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
29_L 85_A 1.34 0.28 0.00
117_A 169_L 1.23 0.23 0.00
52_S 14_V 1.20 0.21 0.00
115_I 212_I 1.18 0.21 0.00
169_I 40_M 1.18 0.20 0.00
171_S 156_G 1.11 0.18 0.00
160_T 62_T 1.07 0.16 0.00
112_V 110_Q 1.05 0.16 0.00
174_D 125_I 1.05 0.16 0.00
25_L 60_T 1.05 0.15 0.00
179_S 203_Q 1.04 0.15 0.00
107_C 126_E 1.03 0.15 0.00
117_A 5_F 1.03 0.15 0.00
165_F 94_S 1.02 0.15 0.00
35_W 3_P 1.02 0.15 0.00
100_C 7_K 1.01 0.14 0.00
138_W 40_M 1.00 0.14 0.00
35_W 16_E 1.00 0.14 0.00
177_I 32_R 1.00 0.14 0.00
115_I 65_I 0.98 0.14 0.00
35_W 29_A 0.98 0.14 0.00
22_F 169_L 0.98 0.14 0.00
22_F 157_D 0.98 0.13 0.00
16_G 171_V 0.96 0.13 0.00
183_F 99_V 0.96 0.13 0.00
134_Y 121_V 0.96 0.13 0.00
90_A 154_R 0.96 0.13 0.00
172_I 171_V 0.95 0.13 0.00
40_V 193_G 0.95 0.12 0.00
69_P 55_G 0.95 0.12 0.00
174_D 24_V 0.94 0.12 0.00
82_T 44_L 0.94 0.12 0.00
171_S 126_E 0.94 0.12 0.00
134_Y 187_L 0.94 0.12 0.00
117_A 215_I 0.94 0.12 0.00
122_A 215_I 0.94 0.12 0.00
35_W 42_Y 0.94 0.12 0.00
83_A 84_I 0.94 0.12 0.00
35_W 138_E 0.93 0.12 0.00
40_V 215_I 0.92 0.12 0.00
117_A 14_V 0.92 0.12 0.00
140_S 134_R 0.92 0.12 0.00
170_L 1_H 0.92 0.12 0.00
125_T 217_T 0.90 0.11 0.00
126_G 208_E 0.90 0.11 0.00
172_I 58_V 0.90 0.11 0.00
24_V 65_I 0.90 0.11 0.00
129_I 97_A 0.90 0.11 0.00
51_F 167_C 0.90 0.11 0.00
69_P 19_R 0.89 0.11 0.00
90_A 152_A 0.89 0.11 0.00
100_C 213_L 0.88 0.11 0.00
126_G 187_L 0.88 0.11 0.00
97_S 150_I 0.88 0.11 0.00
35_W 105_N 0.88 0.11 0.00
63_L 65_I 0.88 0.11 0.00
22_F 103_V 0.87 0.10 0.00
134_Y 5_F 0.87 0.10 0.00
50_L 204_P 0.87 0.10 0.00
29_L 171_V 0.87 0.10 0.00
49_G 31_D 0.87 0.10 0.00
96_G 92_G 0.86 0.10 0.00
92_F 99_V 0.86 0.10 0.00
167_L 136_V 0.86 0.10 0.00
29_L 111_V 0.85 0.10 0.00
22_F 61_Y 0.85 0.10 0.00
29_L 1_H 0.85 0.10 0.00
125_T 187_L 0.84 0.10 0.00
93_L 59_E 0.84 0.10 0.00
103_L 22_A 0.83 0.10 0.00
160_T 30_T 0.83 0.10 0.00
93_L 80_K 0.83 0.10 0.00
171_S 67_T 0.83 0.10 0.00
165_F 135_Y 0.83 0.10 0.00
177_I 80_K 0.82 0.09 0.00
165_F 68_A 0.81 0.09 0.00
25_L 76_R 0.81 0.09 0.00
154_Y 121_V 0.81 0.09 0.00
110_A 171_V 0.81 0.09 0.00
16_G 79_F 0.81 0.09 0.00
128_M 208_E 0.80 0.09 0.00
129_I 18_A 0.80 0.09 0.00
17_T 65_I 0.80 0.09 0.00
118_W 58_V 0.80 0.09 0.00
126_G 166_K 0.80 0.09 0.00
36_I 187_L 0.80 0.09 0.00
128_M 153_R 0.80 0.09 0.00
125_T 153_R 0.79 0.09 0.00
72_F 29_A 0.79 0.09 0.00
97_S 158_A 0.79 0.09 0.00
65_C 193_G 0.79 0.09 0.00
85_F 196_L 0.79 0.09 0.00
110_A 137_Q 0.79 0.09 0.00
161_I 65_I 0.79 0.09 0.00
177_I 157_D 0.79 0.09 0.00
92_F 12_G 0.79 0.09 0.00
170_L 150_I 0.79 0.09 0.00
33_P 41_A 0.78 0.09 0.00
97_S 195_L 0.78 0.09 0.00
130_G 6_Q 0.78 0.09 0.00
21_C 97_A 0.78 0.09 0.00
115_I 101_V 0.78 0.09 0.00
102_S 44_L 0.78 0.08 0.00
121_L 10_Y 0.77 0.08 0.00
171_S 83_V 0.77 0.08 0.00
170_L 127_D 0.77 0.08 0.00
117_A 154_R 0.77 0.08 0.00
29_L 79_F 0.77 0.08 0.00
65_C 140_I 0.77 0.08 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
12890 0.07 l5_mad (A, 15-205) (B, 1-265) Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
12889 0.25 l5_mad (A, 15-205) (B, 1-265) Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
12888 0.06 l5_mad (A, 15-205) (B, 1-265) Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
12887 0 l5_mad (A, 15-205) (B, 1-265) Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
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