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OPENSEQ.org
cIV_B_40_cI_J_6_human
Genes: A B A+B
Length: 227 174 398
Sequences: 4037 5223 2950
Seq/Len: 17.78 30.02 7.41
MirrorTree (Pazo et al. 2001) 0.59
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 0.11
2 0.00 0.00 0.19
5 0.00 0.00 0.65
10 0.00 0.00 5.73
20 0.00 0.00 5.86
100 0.01 0.01 5.93
∞ 0.01 0.02 7.36
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 71_T 1.27 0.97 0.47
172_T 59_Y 1.20 0.96 0.41
72_I 167_V 1.13 0.94 0.34
71_I 123_S 1.09 0.93 0.31
219_F 63_M 1.05 0.91 0.28
146_I 166_I 1.02 0.89 0.26
116_L 46_F 1.02 0.89 0.25
131_G 59_Y 0.90 0.79 0.17
9_L 52_G 0.90 0.79 0.17
27_A 77_E 0.90 0.79 0.17
46_L 153_V 0.88 0.76 0.16
191_V 32_L 0.88 0.76 0.16
23_F 52_G 0.87 0.76 0.15
102_H 54_M 0.86 0.75 0.15
150_I 151_W 0.85 0.73 0.14
68_L 64_M 0.84 0.72 0.14
115_G 81_A 0.84 0.72 0.14
68_L 48_G 0.84 0.72 0.14
11_D 32_L 0.84 0.72 0.14
27_A 156_T 0.84 0.72 0.14
193_Y 105_W 0.84 0.72 0.14
117_I 159_T 0.83 0.71 0.13
154_I 163_G 0.83 0.71 0.13
160_L 154_V 0.82 0.69 0.13
137_D 170_I 0.81 0.68 0.12
112_D 58_I 0.81 0.68 0.12
192_Y 61_G 0.80 0.66 0.12
51_T 60_L 0.80 0.66 0.12
167_T 73_M 0.80 0.66 0.12
148_T 59_Y 0.79 0.66 0.11
82_R 56_F 0.79 0.65 0.11
27_A 141_G 0.78 0.64 0.11
133_L 56_F 0.78 0.64 0.11
114_G 46_F 0.78 0.64 0.11
156_S 142_A 0.78 0.63 0.11
76_I 35_S 0.78 0.63 0.11
5_A 40_C 0.77 0.63 0.10
164_A 63_M 0.76 0.60 0.10
214_I 13_V 0.76 0.60 0.10
191_V 105_W 0.75 0.59 0.10
146_I 60_L 0.75 0.59 0.10
129_E 58_I 0.75 0.59 0.09
9_L 62_G 0.74 0.58 0.09
82_R 61_G 0.74 0.58 0.09
92_D 16_F 0.74 0.58 0.09
130_P 165_Y 0.74 0.58 0.09
58_A 153_V 0.74 0.58 0.09
150_I 133_G 0.73 0.57 0.09
156_S 66_V 0.73 0.57 0.09
224_V 132_S 0.73 0.56 0.09
218_I 45_N 0.73 0.56 0.09
152_M 97_A 0.73 0.56 0.09
53_T 71_T 0.73 0.56 0.09
150_I 100_V 0.72 0.55 0.09
95_L 48_G 0.72 0.55 0.09
6_Q 161_F 0.72 0.55 0.09
4_A 53_L 0.72 0.55 0.09
91_N 57_L 0.72 0.55 0.08
152_M 138_D 0.72 0.55 0.08
155_T 88_V 0.72 0.55 0.08
33_L 29_G 0.71 0.53 0.08
10_Q 29_G 0.71 0.53 0.08
61_M 169_E 0.71 0.53 0.08
13_T 142_A 0.71 0.53 0.08
175_I 59_Y 0.71 0.53 0.08
36_F 58_I 0.70 0.52 0.08
54_N 58_I 0.70 0.51 0.08
67_I 139_P 0.70 0.51 0.08
36_F 38_V 0.70 0.51 0.08
165_V 85_G 0.70 0.51 0.08
185_T 171_A 0.69 0.51 0.07
160_L 20_S 0.69 0.51 0.07
175_I 9_S 0.69 0.50 0.07
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
4649 7.41 cIV_B_40_cI_J_6_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
4648 2.8 cIV_B_40_cI_J_10_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 4) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4647 5.35 cIV_B_40_cI_J_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
4646 2.7 cIV_B_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
4645 0.29 cIV_B_60_cI_J_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4644 2.71 cIV_B_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
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