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OPENSEQ.org
cIV_C_40_cI_A_20_human
Genes: A B A+B
Length: 261 115 375
Sequences: 2457 4326 2300
Seq/Len: 9.41 37.62 6.13
MirrorTree (Pazo et al. 2001) 0.71
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 0.00 4.32
2 0.00 0.00 4.54
5 0.00 0.00 4.91
10 0.00 0.00 5.18
20 0.00 0.00 5.32
100 0.00 0.01 5.49
∞ 0.00 0.02 6.12
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
80_R 108_Q 1.74 1.00 0.96
22_L 72_L 1.47 0.99 0.89
184_S 24_L 1.25 0.96 0.78
46_G 60_I 1.09 0.90 0.63
13_P 76_P 1.09 0.90 0.63
73_P 79_X 1.08 0.90 0.62
127_L 54_K 1.06 0.89 0.60
13_P 70_A 1.06 0.88 0.60
26_L 110_G 1.02 0.85 0.55
149_H 56_F 0.97 0.82 0.50
91_V 57_L 0.97 0.82 0.50
6_H 58_V 0.97 0.81 0.49
128_E 53_M 0.91 0.76 0.42
100_A 54_K 0.91 0.75 0.42
92_L 58_V 0.91 0.75 0.42
18_L 70_A 0.91 0.75 0.41
77_K 9_I 0.90 0.74 0.41
21_A 71_L 0.89 0.73 0.40
48_L 15_L 0.89 0.73 0.40
178_A 59_A 0.87 0.71 0.37
223_L 16_L 0.86 0.69 0.36
110_P 76_P 0.84 0.66 0.33
144_I 35_T 0.83 0.66 0.33
147_A 104_Y 0.83 0.65 0.32
230_K 47_A 0.82 0.63 0.31
46_G 70_A 0.81 0.62 0.30
80_R 106_W 0.80 0.61 0.29
47_L 9_I 0.80 0.61 0.29
95_A 78_A 0.80 0.61 0.29
142_V 54_K 0.80 0.61 0.29
228_T 67_L 0.79 0.59 0.28
68_Q 56_F 0.79 0.59 0.28
114_G 54_K 0.78 0.59 0.27
240_W 113_W 0.78 0.58 0.27
132_L 97_I 0.78 0.58 0.27
92_L 71_L 0.77 0.57 0.26
135_S 54_K 0.77 0.56 0.26
39_S 19_I 0.76 0.55 0.25
104_S 56_F 0.76 0.55 0.24
170_G 113_W 0.76 0.55 0.24
19_T 5_L 0.75 0.54 0.24
20_G 13_L 0.75 0.54 0.24
217_I 16_L 0.75 0.54 0.24
193_Y 98_L 0.75 0.53 0.23
165_I 8_M 0.74 0.53 0.23
228_T 99_A 0.74 0.52 0.23
171_L 89_M 0.74 0.52 0.23
13_P 94_L 0.74 0.52 0.23
129_V 35_T 0.74 0.52 0.23
227_F 94_L 0.74 0.52 0.23
239_A 48_R 0.74 0.52 0.23
157_N 12_L 0.73 0.51 0.22
46_G 75_L 0.73 0.51 0.22
175_L 89_M 0.73 0.51 0.22
10_M 87_M 0.73 0.50 0.22
10_M 76_P 0.73 0.50 0.22
261_S 81_T 0.72 0.50 0.21
179_S 58_V 0.72 0.49 0.21
238_A 99_A 0.72 0.48 0.21
46_G 20_I 0.71 0.48 0.20
22_L 81_T 0.71 0.48 0.20
127_L 70_A 0.71 0.48 0.20
172_Y 53_M 0.71 0.47 0.20
88_T 12_L 0.71 0.47 0.20
248_V 97_I 0.71 0.47 0.20
10_M 37_Y 0.71 0.47 0.20
31_L 29_G 0.71 0.47 0.20
80_R 47_A 0.70 0.47 0.20
8_Y 14_A 0.70 0.47 0.20
44_M 13_L 0.70 0.47 0.20
33_M 61_T 0.70 0.46 0.19
216_T 96_I 0.70 0.46 0.19
10_M 72_L 0.70 0.46 0.19
209_I 22_F 0.70 0.46 0.19
171_L 93_L 0.69 0.45 0.18
21_A 108_Q 0.69 0.44 0.18
228_T 70_A 0.69 0.44 0.18
179_S 76_P 0.69 0.44 0.18
20_G 46_P 0.69 0.44 0.18
191_G 64_L 0.68 0.43 0.18
56_Q 53_M 0.68 0.43 0.17
110_P 92_L 0.68 0.42 0.17
170_G 52_S 0.67 0.42 0.17
33_M 112_D 0.67 0.42 0.17
253_Y 20_I 0.67 0.42 0.17
23_S 34_S 0.67 0.42 0.17
35_F 31_M 0.67 0.42 0.17
28_T 72_L 0.67 0.42 0.17
147_A 17_L 0.67 0.41 0.17
157_N 86_L 0.67 0.41 0.17
120_G 94_L 0.67 0.41 0.17
77_K 21_T 0.67 0.41 0.16
185_P 56_F 0.67 0.41 0.16
12_K 104_Y 0.67 0.41 0.16
81_Y 53_M 0.67 0.41 0.16
106_L 42_D 0.66 0.41 0.16
78_G 47_A 0.66 0.41 0.16
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
4500 6.13 cIV_C_40_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
4499 1.84 cIV_C_60_cI_A_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4497 0.01 cIV_C_40_cI_A_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) Killed - Shared
4494 1.84 cIV_C_40_cI_A_40_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
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