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OPENSEQ.org
cI_4_10_cI_6_10_tt
Genes: A B A+B
Length: 409 181 557
Sequences: 3490 1433 1630
Seq/Len: 8.53 7.92 2.93
MirrorTree (Pazo et al. 2001) 0.91
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 0.01 0.01 1.01
2 0.01 0.01 2.32
5 0.03 0.02 2.46
10 0.04 0.02 2.47
20 0.05 0.02 2.51
100 0.06 0.04 2.60
∞ 0.13 0.09 2.76
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 1.70 0.98 0.91
69_T 120_N 1.60 0.97 0.87
158_D 57_R 1.53 0.96 0.84
64_T 83_R 1.50 0.95 0.82
41_L 81_A 1.23 0.85 0.62
154_E 49_E 1.16 0.80 0.55
81_Y 117_M 1.11 0.75 0.49
146_F 51_M 1.08 0.73 0.46
65_G 120_N 1.05 0.69 0.42
88_L 48_I 1.02 0.66 0.39
86_D 88_M 0.94 0.56 0.30
167_R 49_E 0.93 0.56 0.30
107_A 130_V 0.93 0.56 0.30
32_P 144_P 0.92 0.55 0.29
146_F 55_D 0.91 0.53 0.28
86_D 43_L 0.91 0.53 0.28
40_V 41_F 0.91 0.53 0.27
403_V 43_L 0.90 0.52 0.26
106_G 56_A 0.89 0.51 0.26
128_S 91_V 0.85 0.46 0.22
342_V 36_L 0.85 0.45 0.22
67_E 111_C 0.84 0.45 0.22
191_K 67_V 0.84 0.44 0.21
37_T 48_I 0.83 0.44 0.20
67_E 140_C 0.82 0.43 0.20
169_H 118_F 0.82 0.42 0.19
360_D 97_E 0.82 0.42 0.19
63_H 121_Y 0.81 0.40 0.18
405_G 47_A 0.79 0.39 0.17
147_F 67_V 0.79 0.38 0.17
49_G 73_R 0.78 0.38 0.17
402_P 43_L 0.78 0.38 0.17
150_F 68_F 0.78 0.38 0.17
217_R 64_G 0.78 0.37 0.16
292_Q 35_S 0.78 0.37 0.16
140_L 110_A 0.78 0.37 0.16
179_K 67_V 0.78 0.37 0.16
58_H 86_K 0.77 0.37 0.16
266_L 21_F 0.77 0.37 0.16
198_P 118_F 0.77 0.37 0.16
40_V 44_A 0.77 0.36 0.16
138_L 68_F 0.77 0.36 0.16
349_A 43_L 0.77 0.36 0.16
64_T 110_A 0.76 0.35 0.15
128_S 42_G 0.76 0.34 0.15
192_K 130_V 0.75 0.34 0.15
301_P 152_M 0.75 0.34 0.14
235_T 154_L 0.75 0.34 0.14
47_L 151_V 0.74 0.33 0.14
62_L 47_A 0.74 0.33 0.14
61_Y 94_R 0.74 0.33 0.14
404_M 110_A 0.74 0.33 0.14
33_Q 39_A 0.74 0.32 0.14
42_R 46_C 0.73 0.32 0.13
40_V 88_M 0.73 0.32 0.13
147_F 56_A 0.73 0.32 0.13
52_V 159_R 0.72 0.31 0.13
153_R 138_P 0.72 0.31 0.13
80_T 83_R 0.72 0.31 0.13
123_L 103_K 0.72 0.31 0.13
287_V 20_L 0.72 0.31 0.13
350_R 34_N 0.72 0.31 0.12
127_A 31_G 0.72 0.31 0.12
161_E 143_R 0.72 0.30 0.12
64_T 123_I 0.72 0.30 0.12
121_N 20_L 0.72 0.30 0.12
39_G 45_C 0.71 0.30 0.12
62_L 44_A 0.71 0.30 0.12
407_V 70_A 0.71 0.30 0.12
77_Q 148_I 0.71 0.30 0.12
80_T 45_C 0.71 0.29 0.12
350_R 110_A 0.71 0.29 0.12
406_D 155_Q 0.71 0.29 0.12
101_V 143_R 0.70 0.29 0.12
223_V 106_I 0.70 0.29 0.11
172_Y 45_C 0.70 0.29 0.11
112_R 132_P 0.70 0.28 0.11
342_V 84_L 0.70 0.28 0.11
370_V 122_A 0.70 0.28 0.11
96_A 29_A 0.69 0.28 0.11
407_V 43_L 0.69 0.28 0.11
403_V 81_A 0.69 0.28 0.11
28_L 23_T 0.68 0.27 0.10
405_G 43_L 0.68 0.27 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)
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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