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OPENSEQ.org
cI_4_6_cI_6_6_tt
Genes: A B A+B
Length: 409 181 556
Sequences: 3489 1588 1769
Seq/Len: 8.53 8.77 3.18
MirrorTree (Pazo et al. 2001) 0.92
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 1.20
2 0.01 0.01 2.54
5 0.03 0.02 2.72
10 0.04 0.02 2.73
20 0.05 0.03 2.77
100 0.06 0.04 2.85
∞ 0.13 0.10 3.00
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 1.62 0.98 0.88
158_D 57_R 1.49 0.96 0.81
64_T 83_R 1.42 0.94 0.77
69_T 120_N 1.38 0.93 0.74
41_L 81_A 1.08 0.75 0.46
123_L 103_K 1.08 0.75 0.45
81_Y 117_M 1.08 0.75 0.45
146_F 51_M 1.07 0.74 0.44
88_L 48_I 1.02 0.68 0.38
106_G 56_A 0.93 0.58 0.29
178_V 127_V 0.92 0.56 0.28
32_P 144_P 0.92 0.56 0.28
65_G 120_N 0.91 0.55 0.27
154_E 49_E 0.90 0.54 0.26
403_V 43_L 0.90 0.54 0.26
62_L 47_A 0.89 0.53 0.25
86_D 43_L 0.88 0.52 0.24
167_R 49_E 0.87 0.51 0.24
402_P 43_L 0.84 0.47 0.21
37_T 48_I 0.83 0.45 0.20
36_S 40_T 0.83 0.45 0.20
346_T 130_V 0.82 0.44 0.19
40_V 41_F 0.82 0.44 0.19
115_T 24_L 0.81 0.44 0.19
50_E 64_G 0.81 0.43 0.18
404_M 110_A 0.80 0.42 0.18
136_G 122_A 0.80 0.42 0.18
240_R 73_R 0.79 0.41 0.17
63_H 121_Y 0.79 0.41 0.17
82_T 69_R 0.79 0.41 0.17
194_L 60_L 0.79 0.40 0.17
349_A 43_L 0.77 0.38 0.16
392_D 59_D 0.76 0.37 0.15
153_R 138_P 0.76 0.37 0.15
405_G 47_A 0.75 0.36 0.14
147_F 67_V 0.75 0.35 0.14
166_Q 39_A 0.74 0.35 0.14
51_E 113_S 0.74 0.34 0.13
146_F 55_D 0.73 0.34 0.13
128_S 91_V 0.73 0.34 0.13
179_K 146_A 0.72 0.33 0.13
344_V 159_R 0.72 0.33 0.13
236_G 132_P 0.71 0.32 0.12
126_L 108_M 0.71 0.32 0.12
169_H 118_F 0.71 0.31 0.12
181_D 64_G 0.71 0.31 0.12
40_V 44_A 0.70 0.31 0.12
223_V 106_I 0.70 0.30 0.11
119_I 151_V 0.70 0.30 0.11
147_F 54_T 0.70 0.30 0.11
172_Y 45_C 0.70 0.30 0.11
140_L 110_A 0.70 0.30 0.11
406_D 155_Q 0.69 0.29 0.11
96_A 153_Q 0.69 0.29 0.11
157_L 52_A 0.69 0.29 0.11
154_E 106_I 0.69 0.29 0.11
64_T 122_A 0.69 0.29 0.11
373_P 112_A 0.69 0.29 0.11
402_P 56_A 0.69 0.29 0.11
89_H 43_L 0.68 0.29 0.10
342_V 84_L 0.68 0.28 0.10
150_F 51_M 0.68 0.28 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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