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OPENSEQ.org
cIV_B_40_cI_J_20_human
Genes: A B A+B
Length: 227 174 389
Sequences: 4037 1614 1055
Seq/Len: 17.78 9.28 2.71
MirrorTree (Pazo et al. 2001) 0.68
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 0.00
2 0.00 0.00 0.01
5 0.00 0.00 0.06
10 0.00 0.00 2.62
20 0.00 0.00 2.63
100 0.01 0.00 2.63
∞ 0.01 0.00 2.63
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
149_P 138_D 1.41 0.92 0.47
16_I 24_S 1.40 0.92 0.46
57_D 29_G 1.38 0.91 0.45
53_T 157_G 1.35 0.90 0.42
213_L 154_V 1.28 0.86 0.36
68_L 64_M 1.27 0.86 0.35
73_L 8_L 1.25 0.85 0.34
73_L 73_M 1.19 0.80 0.29
52_N 29_G 1.18 0.80 0.28
9_L 33_I 1.18 0.80 0.28
94_S 27_Y 1.18 0.79 0.28
137_D 89_L 1.18 0.79 0.28
64_V 94_V 1.14 0.76 0.25
143_V 18_G 1.14 0.76 0.25
97_I 51_M 1.10 0.73 0.22
95_L 28_G 1.09 0.71 0.21
115_G 145_L 1.08 0.70 0.21
154_I 106_V 1.08 0.70 0.21
3_H 167_V 1.07 0.69 0.20
156_S 95_G 1.06 0.68 0.20
46_L 157_G 1.05 0.68 0.19
129_E 93_L 1.04 0.66 0.18
133_L 52_G 1.04 0.66 0.18
141_R 52_G 1.03 0.65 0.18
154_I 132_S 1.03 0.65 0.18
184_F 55_V 1.03 0.65 0.18
127_F 14_M 1.03 0.65 0.17
186_A 74_A 1.02 0.64 0.17
4_A 146_Y 1.01 0.63 0.17
110_Y 48_G 1.01 0.63 0.17
42_L 165_Y 1.01 0.62 0.16
97_I 16_F 1.00 0.62 0.16
23_F 52_G 1.00 0.61 0.16
68_L 48_G 0.99 0.61 0.16
63_T 52_G 0.98 0.60 0.15
188_R 131_G 0.98 0.59 0.15
64_V 7_L 0.98 0.59 0.15
58_A 157_G 0.97 0.59 0.15
220_E 170_I 0.97 0.58 0.15
132_D 51_M 0.96 0.57 0.14
64_V 24_S 0.96 0.57 0.14
48_T 167_V 0.96 0.57 0.14
74_V 5_L 0.95 0.56 0.14
149_P 74_A 0.95 0.56 0.14
5_A 27_Y 0.94 0.55 0.13
112_D 41_V 0.94 0.55 0.13
111_T 162_V 0.94 0.55 0.13
202_A 9_S 0.94 0.55 0.13
220_E 72_A 0.94 0.55 0.13
175_I 64_M 0.94 0.55 0.13
9_L 52_G 0.94 0.55 0.13
32_F 17_V 0.93 0.53 0.12
155_T 133_G 0.93 0.53 0.12
116_L 137_E 0.93 0.53 0.12
16_I 128_E 0.92 0.53 0.12
170_L 138_D 0.92 0.53 0.12
47_S 10_V 0.92 0.52 0.12
5_A 167_V 0.92 0.52 0.12
61_M 145_L 0.92 0.52 0.12
187_T 76_E 0.92 0.52 0.12
68_L 18_G 0.91 0.50 0.11
74_V 27_Y 0.91 0.50 0.11
52_N 28_G 0.90 0.50 0.11
165_V 44_L 0.90 0.50 0.11
11_D 30_L 0.90 0.50 0.11
155_T 156_T 0.90 0.49 0.11
213_L 138_D 0.90 0.49 0.11
142_V 171_A 0.89 0.49 0.11
133_L 43_I 0.89 0.48 0.11
192_Y 127_Y 0.89 0.48 0.11
116_L 134_L 0.89 0.48 0.10
33_L 3_Y 0.88 0.47 0.10
9_L 162_V 0.88 0.47 0.10
82_R 23_P 0.88 0.47 0.10
191_V 35_S 0.88 0.47 0.10
133_L 161_F 0.88 0.47 0.10
47_S 21_S 0.87 0.46 0.10
224_V 51_M 0.87 0.46 0.10
172_T 165_Y 0.87 0.46 0.10
221_M 159_T 0.86 0.45 0.10
111_T 136_R 0.86 0.45 0.10
193_Y 19_F 0.86 0.45 0.10
144_L 162_V 0.86 0.45 0.09
57_D 20_S 0.86 0.45 0.09
57_D 23_P 0.85 0.44 0.09
52_N 128_E 0.85 0.44 0.09
140_N 73_M 0.85 0.44 0.09
138_V 157_G 0.85 0.44 0.09
31_I 101_G 0.85 0.44 0.09
97_I 144_A 0.85 0.43 0.09
27_A 22_K 0.85 0.43 0.09
175_I 46_F 0.84 0.43 0.09
110_Y 41_V 0.84 0.43 0.09
191_V 6_F 0.84 0.43 0.09
187_T 45_N 0.84 0.42 0.09
54_N 11_G 0.84 0.42 0.09
148_T 170_I 0.83 0.41 0.08
146_I 163_G 0.83 0.41 0.08
56_S 27_Y 0.83 0.41 0.08
40_Y 57_L 0.83 0.41 0.08
92_D 126_I 0.82 0.41 0.08
110_Y 56_F 0.82 0.41 0.08
88_D 27_Y 0.82 0.40 0.08
53_T 145_L 0.82 0.40 0.08
46_L 26_I 0.82 0.40 0.08
99_S 109_Y 0.82 0.40 0.08
43_F 11_G 0.82 0.40 0.08
156_S 22_K 0.82 0.40 0.08
92_D 11_G 0.82 0.40 0.08
23_F 78_Y 0.81 0.39 0.08
45_T 148_Y 0.81 0.39 0.08
191_V 98_M 0.81 0.39 0.08
64_V 85_G 0.81 0.39 0.08
73_L 156_T 0.81 0.39 0.08
165_V 106_V 0.81 0.39 0.08
154_I 35_S 0.81 0.39 0.08
55_I 9_S 0.81 0.39 0.08
186_A 130_E 0.81 0.39 0.08
193_Y 7_L 0.81 0.38 0.08
75_L 52_G 0.81 0.38 0.08
168_L 154_V 0.80 0.38 0.07
142_V 107_K 0.80 0.38 0.07
92_D 165_Y 0.80 0.38 0.07
154_I 7_L 0.80 0.38 0.07
112_D 27_Y 0.80 0.38 0.07
47_S 15_G 0.80 0.38 0.07
113_Y 171_A 0.80 0.38 0.07
64_V 4_A 0.80 0.38 0.07
113_Y 70_T 0.80 0.37 0.07
52_N 144_A 0.80 0.37 0.07
52_N 30_L 0.79 0.37 0.07
30_I 41_V 0.79 0.37 0.07
146_I 94_V 0.79 0.37 0.07
138_V 24_S 0.79 0.36 0.07
112_D 145_L 0.79 0.36 0.07
97_I 3_Y 0.79 0.36 0.07
123_L 108_E 0.79 0.36 0.07
148_T 64_M 0.79 0.36 0.07
183_T 52_G 0.79 0.36 0.07
54_N 156_T 0.79 0.36 0.07
111_T 1_M 0.78 0.36 0.07
165_V 90_V 0.78 0.36 0.07
57_D 30_L 0.78 0.35 0.07
138_V 110_D 0.78 0.35 0.07
215_P 143_G 0.78 0.35 0.07
164_A 106_V 0.78 0.35 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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