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OPENSEQ.org
cI_4_20_cI_6_20_tt
Genes: A B A+B
Length: 409 181 556
Sequences: 2519 1141 1284
Seq/Len: 6.16 6.3 2.31
MirrorTree (Pazo et al. 2001) 0.89
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 0.01 0.53
2 0.00 0.01 1.85
5 0.01 0.01 1.93
10 0.02 0.02 1.95
20 0.02 0.02 1.98
100 0.04 0.03 2.06
∞ 0.10 0.08 2.18
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
66_F 118_F 1.91 0.99 0.95
158_D 57_R 1.83 0.98 0.94
69_T 120_N 1.60 0.96 0.86
64_T 83_R 1.40 0.89 0.74
65_G 120_N 1.29 0.83 0.65
81_Y 117_M 1.26 0.81 0.62
146_F 51_M 1.12 0.70 0.48
41_L 81_A 0.99 0.56 0.33
123_L 103_K 0.99 0.56 0.33
74_T 101_D 0.96 0.52 0.30
169_H 118_F 0.96 0.52 0.30
107_A 130_V 0.95 0.51 0.29
33_Q 41_F 0.93 0.49 0.27
147_F 61_A 0.90 0.45 0.24
127_A 31_G 0.90 0.45 0.24
62_L 44_A 0.88 0.43 0.23
33_Q 39_A 0.88 0.43 0.22
134_G 58_N 0.88 0.43 0.22
147_F 56_A 0.87 0.41 0.21
198_P 118_F 0.87 0.41 0.21
64_T 123_I 0.86 0.40 0.20
399_S 27_L 0.85 0.39 0.20
146_F 55_D 0.84 0.39 0.19
37_T 48_I 0.83 0.37 0.18
202_D 153_Q 0.83 0.37 0.18
161_E 143_R 0.82 0.37 0.18
266_L 21_F 0.82 0.36 0.18
64_T 85_S 0.82 0.36 0.17
40_V 88_M 0.81 0.35 0.17
63_H 121_Y 0.81 0.35 0.17
194_L 60_L 0.81 0.35 0.17
86_D 88_M 0.81 0.35 0.17
69_T 110_A 0.80 0.34 0.16
65_G 122_A 0.80 0.34 0.16
80_T 83_R 0.80 0.34 0.16
62_L 47_A 0.80 0.34 0.16
276_M 55_D 0.80 0.34 0.16
349_A 43_L 0.79 0.33 0.15
39_G 45_C 0.79 0.33 0.15
349_A 84_L 0.78 0.32 0.14
407_V 70_A 0.77 0.31 0.14
147_F 54_T 0.76 0.30 0.13
79_I 118_F 0.76 0.30 0.13
87_Y 69_R 0.76 0.29 0.13
147_F 66_E 0.76 0.29 0.13
65_G 149_Y 0.75 0.29 0.12
270_G 137_V 0.75 0.29 0.12
154_E 100_P 0.74 0.29 0.12
40_V 41_F 0.74 0.28 0.12
77_Q 148_I 0.74 0.28 0.12
61_Y 94_R 0.74 0.28 0.12
69_T 146_A 0.74 0.28 0.12
346_T 130_V 0.74 0.28 0.12
220_G 131_V 0.74 0.28 0.12
77_Q 80_V 0.74 0.28 0.12
325_I 117_M 0.74 0.28 0.12
68_K 121_Y 0.74 0.28 0.12
403_V 47_A 0.74 0.28 0.12
83_P 126_N 0.74 0.28 0.12
33_Q 98_Q 0.74 0.28 0.12
405_G 47_A 0.73 0.27 0.12
313_P 135_V 0.72 0.26 0.11
180_E 97_E 0.72 0.26 0.11
192_K 130_V 0.72 0.26 0.11
88_L 48_I 0.72 0.26 0.11
403_V 43_L 0.72 0.26 0.11
405_G 44_A 0.71 0.25 0.10
58_H 86_K 0.71 0.25 0.10
150_F 51_M 0.71 0.25 0.10
380_S 148_I 0.70 0.25 0.10
52_V 159_R 0.70 0.25 0.10
95_L 147_L 0.70 0.24 0.10
377_N 110_A 0.70 0.24 0.10
248_V 158_V 0.70 0.24 0.10
401_D 146_A 0.70 0.24 0.10
304_D 96_W 0.69 0.24 0.10
50_E 72_P 0.69 0.24 0.10
81_Y 118_F 0.69 0.24 0.09
147_F 67_V 0.69 0.24 0.09
157_L 70_A 0.69 0.23 0.09
251_A 137_V 0.69 0.23 0.09
385_C 150_A 0.69 0.23 0.09
261_T 103_K 0.69 0.23 0.09
383_Y 70_A 0.68 0.23 0.09
235_T 154_L 0.68 0.23 0.09
149_A 100_P 0.68 0.23 0.09
342_V 84_L 0.68 0.23 0.09
295_E 147_L 0.68 0.23 0.09
49_G 73_R 0.68 0.23 0.09
29_N 45_C 0.68 0.23 0.09
223_V 106_I 0.68 0.23 0.09
403_V 81_A 0.67 0.22 0.09
402_P 56_A 0.67 0.22 0.09
139_D 108_M 0.67 0.22 0.09
178_V 97_E 0.67 0.22 0.09
206_A 153_Q 0.67 0.22 0.09
188_P 36_L 0.67 0.22 0.09
26_M 155_Q 0.67 0.22 0.09
235_T 80_V 0.67 0.22 0.08
211_S 87_K 0.66 0.21 0.08
36_S 48_I 0.66 0.21 0.08
25_V 103_K 0.66 0.21 0.08
106_G 56_A 0.66 0.21 0.08
369_K 94_R 0.66 0.21 0.08
350_R 92_M 0.66 0.21 0.08
179_K 146_A 0.65 0.21 0.08
86_D 43_L 0.65 0.21 0.08
57_P 108_M 0.65 0.20 0.08
228_V 155_Q 0.65 0.20 0.08
64_T 110_A 0.65 0.20 0.08
164_T 152_M 0.65 0.20 0.08
403_V 40_T 0.64 0.20 0.07
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
6517 1.93 4 and 6 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.94 Done - Shared
4887 2.68 cI_4_20_cI_6_10_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4885 2.35 cI_4_10_cI_6_20_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
4884 2.04 cI_4_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4883 2.31 cI_4_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4882 2.93 cI_4_10_cI_6_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.91 Done - Shared
4881 3.18 cI_4_6_cI_6_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
4866 3.43 cI_4_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.80 Done - Shared
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