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OPENSEQ.org
4 and 6
Genes: A B A+B
Length: 409 181 541
Sequences: 3257 986 1043
Seq/Len: 7.96 5.45 1.93
MirrorTree (Pazo et al. 2001) 0.89
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.10 0.45
2 0.06 0.10 1.66
5 0.06 0.10 1.73
10 0.07 0.10 1.75
20 0.08 0.10 1.77
100 0.09 0.11 1.84
∞ 0.17 0.13 2.00
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
158_D 57_R 1.94 0.98 0.94
66_F 118_F 1.81 0.97 0.91
64_T 83_R 1.71 0.96 0.87
65_G 120_N 1.56 0.93 0.80
81_Y 117_M 1.42 0.87 0.70
69_T 120_N 1.26 0.77 0.54
146_F 51_M 1.25 0.76 0.53
80_T 83_R 1.23 0.74 0.51
41_L 81_A 1.18 0.70 0.46
350_R 92_M 1.10 0.63 0.38
146_F 55_D 1.08 0.60 0.36
64_T 123_I 1.01 0.53 0.29
62_L 44_A 1.01 0.52 0.28
157_L 70_A 1.00 0.52 0.28
40_V 88_M 1.00 0.51 0.27
81_Y 118_F 0.95 0.46 0.23
342_V 84_L 0.95 0.46 0.23
266_L 21_F 0.95 0.45 0.23
33_Q 41_F 0.92 0.43 0.21
81_Y 107_S 0.91 0.42 0.20
140_L 103_K 0.91 0.41 0.19
62_L 47_A 0.89 0.40 0.18
40_V 41_F 0.89 0.39 0.18
150_F 68_F 0.89 0.39 0.18
349_A 84_L 0.88 0.39 0.18
87_Y 69_R 0.88 0.38 0.17
400_L 124_V 0.87 0.38 0.17
65_G 122_A 0.87 0.38 0.17
61_Y 94_R 0.87 0.37 0.17
147_F 66_E 0.85 0.35 0.15
405_G 47_A 0.85 0.35 0.15
37_T 48_I 0.84 0.35 0.15
342_V 36_L 0.84 0.34 0.15
86_D 88_M 0.84 0.34 0.15
407_V 70_A 0.83 0.34 0.14
33_Q 39_A 0.83 0.33 0.14
41_L 48_I 0.83 0.33 0.14
123_L 103_K 0.83 0.33 0.14
161_E 143_R 0.83 0.33 0.14
223_V 131_V 0.82 0.33 0.14
77_Q 148_I 0.82 0.32 0.13
352_E 92_M 0.81 0.31 0.13
225_P 28_V 0.81 0.31 0.13
147_F 54_T 0.80 0.31 0.12
83_P 126_N 0.80 0.30 0.12
154_E 100_P 0.80 0.30 0.12
406_D 155_Q 0.80 0.30 0.12
342_V 71_S 0.79 0.29 0.12
63_H 121_Y 0.78 0.28 0.11
35_P 98_Q 0.78 0.28 0.11
232_L 97_E 0.78 0.28 0.11
169_H 118_F 0.78 0.28 0.11
86_D 42_G 0.77 0.28 0.11
147_F 56_A 0.77 0.28 0.11
64_T 120_N 0.77 0.28 0.11
139_D 42_G 0.77 0.27 0.11
61_Y 144_P 0.77 0.27 0.10
134_G 152_M 0.77 0.27 0.10
138_L 68_F 0.76 0.27 0.10
401_D 146_A 0.76 0.27 0.10
106_G 56_A 0.76 0.27 0.10
104_L 84_L 0.76 0.26 0.10
161_E 145_E 0.75 0.26 0.10
372_A 75_A 0.75 0.26 0.10
79_I 118_F 0.75 0.26 0.10
36_S 19_I 0.75 0.26 0.10
135_T 70_A 0.75 0.26 0.10
250_K 154_L 0.75 0.26 0.10
197_L 137_V 0.74 0.25 0.09
248_V 158_V 0.74 0.25 0.09
147_F 61_A 0.74 0.25 0.09
147_F 67_V 0.74 0.25 0.09
403_V 42_G 0.74 0.25 0.09
88_L 48_I 0.74 0.25 0.09
360_D 41_F 0.74 0.25 0.09
95_L 149_Y 0.74 0.25 0.09
300_G 92_M 0.74 0.25 0.09
87_Y 42_G 0.74 0.25 0.09
149_A 100_P 0.73 0.24 0.09
183_P 104_W 0.73 0.24 0.09
404_M 117_M 0.73 0.24 0.09
130_L 100_P 0.73 0.24 0.09
394_V 61_A 0.73 0.24 0.09
349_A 43_L 0.73 0.24 0.09
377_N 118_F 0.72 0.24 0.09
130_L 55_D 0.72 0.23 0.08
369_K 118_F 0.72 0.23 0.08
287_V 21_F 0.72 0.23 0.08
64_T 85_S 0.72 0.23 0.08
260_Y 146_A 0.71 0.23 0.08
329_K 92_M 0.71 0.23 0.08
198_P 118_F 0.71 0.23 0.08
150_F 51_M 0.71 0.22 0.08
83_P 155_Q 0.70 0.22 0.08
57_P 108_M 0.70 0.22 0.08
381_L 81_A 0.70 0.22 0.08
195_E 19_I 0.70 0.22 0.08
28_L 156_K 0.70 0.22 0.08
350_R 110_A 0.70 0.22 0.07
62_L 85_S 0.70 0.22 0.07
69_T 83_R 0.70 0.22 0.07
86_D 43_L 0.70 0.21 0.07
360_D 101_D 0.69 0.21 0.07
41_L 20_L 0.69 0.21 0.07
403_V 40_T 0.69 0.21 0.07
346_T 130_V 0.69 0.21 0.07
225_P 19_I 0.69 0.21 0.07
405_G 43_L 0.69 0.21 0.07
137_L 151_V 0.69 0.21 0.07
179_K 67_V 0.69 0.21 0.07
145_P 47_A 0.69 0.21 0.07
89_H 92_M 0.69 0.21 0.07
331_Y 137_V 0.68 0.21 0.07
283_M 137_V 0.68 0.21 0.07
157_L 52_A 0.68 0.20 0.07
343_Y 44_A 0.68 0.20 0.07
50_E 72_P 0.68 0.20 0.07
222_G 124_V 0.68 0.20 0.07
65_G 125_Q 0.68 0.20 0.07
137_L 110_A 0.68 0.20 0.07
337_P 44_A 0.68 0.20 0.07
259_T 100_P 0.68 0.20 0.07
398_A 78_M 0.68 0.20 0.07
396_I 129_S 0.68 0.20 0.07
52_V 27_L 0.68 0.20 0.07
314_R 135_V 0.68 0.20 0.07
87_Y 46_C 0.67 0.20 0.07
69_T 123_I 0.67 0.20 0.07
260_Y 129_S 0.67 0.20 0.07
350_R 127_V 0.67 0.20 0.07
390_V 57_R 0.67 0.20 0.07
36_S 95_V 0.67 0.20 0.06
354_G 32_R 0.67 0.20 0.06
369_K 29_A 0.67 0.19 0.06
174_R 104_W 0.67 0.19 0.06
127_A 31_G 0.67 0.19 0.06
405_G 44_A 0.66 0.19 0.06
150_F 43_L 0.66 0.19 0.06
403_V 47_A 0.66 0.19 0.06
49_G 73_R 0.66 0.19 0.06
403_V 43_L 0.66 0.19 0.06
48_S 92_M 0.66 0.19 0.06
325_I 41_F 0.66 0.19 0.06
116_I 63_F 0.66 0.19 0.06
38_H 42_G 0.66 0.19 0.06
402_P 56_A 0.66 0.19 0.06
398_A 77_V 0.66 0.19 0.06
142_A 74_Q 0.66 0.19 0.06
274_D 81_A 0.66 0.19 0.06
362_G 114_S 0.65 0.18 0.06
87_Y 51_M 0.65 0.18 0.06
197_L 56_A 0.65 0.18 0.06
178_V 97_E 0.65 0.18 0.06
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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