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OPENSEQ.org
cI_4_20_cI_6_10_tt
Genes: A B A+B
Length: 409 181 558
Sequences: 2519 1433 1497
Seq/Len: 6.16 7.92 2.68
MirrorTree (Pazo et al. 2001) 0.95
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 0.84
2 0.00 0.01 2.16
5 0.01 0.02 2.24
10 0.02 0.02 2.27
20 0.02 0.02 2.29
100 0.04 0.04 2.38
∞ 0.10 0.09 2.54
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 1.67 0.98 0.87
69_T 120_N 1.52 0.95 0.80
158_D 57_R 1.50 0.95 0.79
64_T 83_R 1.43 0.93 0.74
41_L 81_A 1.03 0.65 0.35
81_Y 117_M 1.03 0.65 0.35
65_G 120_N 1.00 0.61 0.32
342_V 36_L 0.99 0.60 0.31
146_F 51_M 0.97 0.57 0.29
167_R 49_E 0.92 0.52 0.24
86_D 88_M 0.92 0.51 0.24
40_V 41_F 0.90 0.49 0.23
403_V 43_L 0.90 0.49 0.23
169_H 118_F 0.90 0.49 0.23
32_P 144_P 0.89 0.49 0.22
106_G 56_A 0.89 0.48 0.22
127_A 31_G 0.88 0.47 0.21
107_A 130_V 0.87 0.46 0.20
86_D 43_L 0.86 0.44 0.19
349_A 43_L 0.85 0.44 0.19
87_Y 45_C 0.85 0.43 0.18
96_A 153_Q 0.84 0.43 0.18
67_E 111_C 0.84 0.42 0.18
406_D 45_C 0.83 0.41 0.17
349_A 84_L 0.82 0.40 0.17
67_E 140_C 0.82 0.39 0.16
146_F 55_D 0.81 0.39 0.16
147_F 56_A 0.81 0.39 0.16
167_R 144_P 0.80 0.37 0.15
147_F 53_S 0.79 0.36 0.14
62_L 44_A 0.79 0.36 0.14
79_I 118_F 0.77 0.34 0.14
63_H 121_Y 0.77 0.34 0.13
77_Q 148_I 0.77 0.34 0.13
405_G 47_A 0.76 0.34 0.13
39_G 45_C 0.76 0.33 0.13
40_V 88_M 0.76 0.33 0.13
266_L 21_F 0.76 0.33 0.12
61_Y 94_R 0.75 0.32 0.12
405_G 42_G 0.74 0.31 0.12
336_H 103_K 0.74 0.31 0.12
33_Q 41_F 0.74 0.31 0.12
194_L 156_K 0.74 0.31 0.12
405_G 43_L 0.73 0.30 0.11
119_I 151_V 0.73 0.30 0.11
112_R 132_P 0.73 0.30 0.11
191_K 67_V 0.73 0.30 0.11
194_L 60_L 0.72 0.29 0.11
49_G 73_R 0.72 0.29 0.11
403_V 81_A 0.72 0.29 0.10
140_L 110_A 0.72 0.29 0.10
359_S 103_K 0.72 0.29 0.10
301_P 152_M 0.71 0.28 0.10
41_L 20_L 0.71 0.28 0.10
360_D 41_F 0.71 0.28 0.10
399_S 27_L 0.71 0.28 0.10
58_H 86_K 0.71 0.28 0.10
353_L 60_L 0.71 0.28 0.10
402_P 43_L 0.70 0.27 0.10
128_S 91_V 0.70 0.27 0.10
62_L 47_A 0.70 0.27 0.10
64_T 123_I 0.70 0.27 0.09
138_L 81_A 0.70 0.27 0.09
93_H 45_C 0.69 0.27 0.09
78_N 95_V 0.69 0.27 0.09
325_I 41_F 0.69 0.26 0.09
407_V 70_A 0.69 0.26 0.09
37_T 48_I 0.69 0.26 0.09
357_I 30_W 0.69 0.26 0.09
192_K 130_V 0.69 0.26 0.09
153_R 138_P 0.69 0.26 0.09
40_V 44_A 0.69 0.26 0.09
198_P 118_F 0.69 0.26 0.09
226_P 24_L 0.69 0.26 0.09
295_E 106_I 0.69 0.26 0.09
147_F 61_A 0.69 0.26 0.09
392_D 64_G 0.68 0.26 0.09
80_T 83_R 0.68 0.25 0.09
407_V 43_L 0.68 0.25 0.09
131_V 51_M 0.68 0.25 0.09
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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