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OPENSEQ.org
cIV_B_60_cI_K_10_human
Genes: A B A+B
Length: 227 98 324
Sequences: 2677 3525 1911
Seq/Len: 11.79 35.97 5.9
MirrorTree (Pazo et al. 2001) 0.67
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 0.16
2 0.00 0.00 0.30
5 0.00 0.00 2.64
10 0.00 0.00 4.96
20 0.00 0.00 5.11
100 0.00 0.01 5.25
∞ 0.00 0.02 5.88
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
175_I 40_L 1.42 0.98 0.76
23_F 27_M 1.24 0.95 0.61
146_I 29_S 1.21 0.94 0.59
73_L 77_L 1.21 0.94 0.58
63_T 77_L 1.17 0.93 0.55
156_S 90_V 1.13 0.92 0.51
76_I 15_S 1.13 0.91 0.51
58_A 68_A 1.12 0.91 0.49
57_D 11_A 1.10 0.90 0.47
131_G 71_A 1.08 0.89 0.45
9_L 14_I 1.07 0.88 0.45
76_I 96_L 1.03 0.85 0.40
180_N 78_L 1.01 0.84 0.38
83_I 22_Y 1.00 0.83 0.37
12_A 90_V 0.99 0.83 0.36
10_Q 83_N 0.97 0.81 0.34
175_I 68_A 0.97 0.80 0.34
160_L 64_L 0.96 0.80 0.33
182_T 61_I 0.95 0.79 0.32
33_L 87_L 0.94 0.78 0.31
38_V 67_A 0.93 0.76 0.29
21_I 39_S 0.92 0.75 0.29
83_I 15_S 0.92 0.75 0.29
143_V 15_S 0.91 0.74 0.28
9_L 91_H 0.90 0.73 0.28
160_L 19_M 0.90 0.72 0.27
192_Y 20_L 0.89 0.71 0.26
165_V 94_N 0.89 0.71 0.26
140_N 5_Y 0.88 0.70 0.25
143_V 17_L 0.88 0.70 0.25
71_I 77_L 0.86 0.68 0.24
221_M 79_V 0.86 0.68 0.23
81_L 60_P 0.86 0.68 0.23
41_A 72_A 0.85 0.66 0.22
143_V 9_M 0.84 0.66 0.22
219_F 87_L 0.84 0.66 0.22
183_T 18_G 0.84 0.65 0.22
90_V 40_L 0.84 0.65 0.22
175_I 53_S 0.84 0.65 0.22
136_L 42_I 0.82 0.63 0.21
192_Y 22_Y 0.82 0.63 0.21
67_I 53_S 0.82 0.63 0.20
57_D 62_A 0.82 0.62 0.20
153_M 77_L 0.82 0.62 0.20
13_T 29_S 0.82 0.62 0.20
5_A 66_F 0.81 0.61 0.20
212_E 69_C 0.81 0.61 0.20
126_L 36_M 0.81 0.61 0.19
219_F 61_I 0.81 0.61 0.19
42_L 24_S 0.80 0.59 0.19
43_F 64_L 0.80 0.59 0.18
8_G 29_S 0.80 0.59 0.18
54_N 36_M 0.79 0.58 0.18
42_L 82_S 0.79 0.58 0.18
23_F 2_P 0.78 0.57 0.18
99_S 59_V 0.78 0.57 0.17
146_I 57_N 0.78 0.56 0.17
158_D 34_E 0.78 0.56 0.17
221_M 45_T 0.77 0.56 0.17
110_Y 31_L 0.77 0.55 0.16
6_Q 68_A 0.77 0.55 0.16
46_L 8_I 0.77 0.55 0.16
156_S 23_R 0.76 0.53 0.16
33_L 44_G 0.75 0.53 0.15
133_L 77_L 0.75 0.52 0.15
71_I 26_L 0.75 0.52 0.15
153_M 7_N 0.74 0.52 0.15
213_L 40_L 0.74 0.51 0.15
153_M 61_I 0.74 0.51 0.15
5_A 98_C 0.74 0.51 0.15
87_T 96_L 0.74 0.51 0.15
85_Y 95_L 0.74 0.51 0.15
8_G 18_G 0.74 0.51 0.14
189_P 94_N 0.74 0.51 0.14
28_L 67_A 0.74 0.51 0.14
67_I 52_H 0.74 0.50 0.14
170_L 20_L 0.74 0.50 0.14
174_A 45_T 0.73 0.50 0.14
82_R 82_S 0.73 0.50 0.14
163_W 27_M 0.73 0.50 0.14
163_W 30_L 0.73 0.49 0.14
148_T 72_A 0.72 0.49 0.14
45_T 15_S 0.72 0.49 0.14
131_G 62_A 0.72 0.49 0.14
76_I 22_Y 0.72 0.49 0.14
220_E 73_V 0.72 0.49 0.14
193_Y 13_T 0.72 0.49 0.14
117_I 86_G 0.72 0.48 0.13
28_L 66_F 0.72 0.48 0.13
211_L 67_A 0.72 0.47 0.13
142_V 53_S 0.72 0.47 0.13
213_L 44_G 0.72 0.47 0.13
226_T 41_F 0.71 0.47 0.13
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
4514 5.9 cIV_B_60_cI_K_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.76 Done - Shared
4513 2.12 cIV_B_60_cI_K_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4510 2.09 cIV_B_40_cI_K_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
4509 0.18 cIV_B_40_cI_K_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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