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OPENSEQ.org
cI_4_4_cI_6_4_tt
Genes: A B A+B
Length: 409 181 556
Sequences: 3475 1709 1905
Seq/Len: 8.5 9.44 3.43
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 1.46
2 0.01 0.01 2.75
5 0.03 0.02 2.94
10 0.04 0.02 2.96
20 0.05 0.03 2.99
100 0.06 0.04 3.07
∞ 0.13 0.10 3.23
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 1.52 0.97 0.80
158_D 57_R 1.44 0.95 0.75
81_Y 117_M 1.34 0.93 0.67
64_T 83_R 1.33 0.92 0.66
69_T 120_N 1.15 0.83 0.48
146_F 51_M 1.01 0.70 0.34
88_L 48_I 1.00 0.69 0.33
404_M 110_A 0.99 0.68 0.32
41_L 81_A 0.98 0.67 0.31
86_D 43_L 0.90 0.56 0.23
154_E 49_E 0.89 0.55 0.22
403_V 43_L 0.88 0.55 0.22
106_G 56_A 0.88 0.54 0.21
65_G 120_N 0.87 0.53 0.21
32_P 144_P 0.86 0.52 0.20
123_L 103_K 0.84 0.50 0.19
260_Y 97_E 0.84 0.49 0.19
167_R 49_E 0.83 0.47 0.18
358_V 148_I 0.82 0.46 0.17
40_V 41_F 0.81 0.45 0.16
37_T 48_I 0.80 0.43 0.16
36_S 40_T 0.78 0.41 0.15
211_S 83_R 0.78 0.41 0.14
62_L 47_A 0.77 0.40 0.14
402_P 43_L 0.77 0.40 0.14
137_L 106_I 0.77 0.40 0.14
146_F 55_D 0.76 0.39 0.13
349_A 43_L 0.76 0.38 0.13
405_G 47_A 0.74 0.36 0.12
114_E 63_F 0.74 0.36 0.12
404_M 40_T 0.73 0.35 0.12
217_R 62_R 0.73 0.35 0.12
140_L 110_A 0.73 0.35 0.12
178_V 127_V 0.73 0.35 0.12
89_H 43_L 0.72 0.34 0.11
228_V 65_S 0.72 0.34 0.11
119_I 151_V 0.72 0.34 0.11
261_T 103_K 0.72 0.34 0.11
344_V 159_R 0.72 0.34 0.11
199_H 155_Q 0.71 0.33 0.11
402_P 56_A 0.70 0.32 0.10
399_S 27_L 0.70 0.32 0.10
172_Y 45_C 0.70 0.32 0.10
407_V 43_L 0.70 0.32 0.10
153_R 138_P 0.69 0.31 0.10
372_A 83_R 0.69 0.31 0.10
147_F 54_T 0.69 0.31 0.10
403_V 81_A 0.69 0.31 0.10
210_E 131_V 0.69 0.31 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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