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OPENSEQ.org
cIV_B_80_cI_A_40_1_human
Genes: A B A+B
Length: 227 115 339
Sequences: 1814 240 83
Seq/Len: 7.99 2.09 0.24
MirrorTree (Pazo et al. 2001) 0.33
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 0.00
5 0.00 0.00 0.24
10 0.00 0.00 0.24
20 0.00 0.00 0.24
100 0.00 0.00 0.24
∞ 0.00 0.00 0.24
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
157_Q 21_T 1.81 0.56 0.00
87_T 21_T 1.75 0.52 0.00
214_I 21_T 1.53 0.38 0.00
100_I 21_T 1.38 0.29 0.00
157_Q 35_T 1.32 0.26 0.00
87_T 15_L 1.29 0.25 0.00
91_N 16_L 1.29 0.25 0.00
91_N 28_N 1.25 0.23 0.00
155_T 97_I 1.22 0.22 0.00
87_T 35_T 1.22 0.21 0.00
157_Q 15_L 1.21 0.21 0.00
27_A 45_S 1.21 0.21 0.00
45_T 112_D 1.20 0.21 0.00
119_N 112_D 1.20 0.21 0.00
153_M 112_D 1.20 0.21 0.00
52_N 112_D 1.20 0.21 0.00
61_M 16_L 1.20 0.21 0.00
214_I 15_L 1.19 0.20 0.00
154_I 9_I 1.18 0.20 0.00
185_T 91_S 1.17 0.20 0.00
45_T 46_P 1.16 0.19 0.00
119_N 46_P 1.16 0.19 0.00
153_M 46_P 1.16 0.19 0.00
100_I 12_L 1.16 0.19 0.00
52_N 46_P 1.15 0.19 0.00
192_Y 18_M 1.14 0.19 0.00
42_L 112_D 1.14 0.18 0.00
31_I 21_T 1.13 0.18 0.00
21_I 21_T 1.13 0.18 0.00
63_T 82_T 1.11 0.17 0.00
9_L 35_T 1.11 0.17 0.00
75_L 96_I 1.11 0.17 0.00
148_T 35_T 1.11 0.17 0.00
87_T 16_L 1.09 0.17 0.00
42_L 46_P 1.09 0.17 0.00
184_F 112_D 1.09 0.17 0.00
191_V 9_I 1.08 0.16 0.00
157_Q 12_L 1.07 0.16 0.00
191_V 82_T 1.05 0.15 0.00
52_N 49_V 1.05 0.15 0.00
41_A 46_P 1.05 0.15 0.00
45_T 49_V 1.05 0.15 0.00
119_N 49_V 1.05 0.15 0.00
153_M 49_V 1.05 0.15 0.00
157_Q 16_L 1.04 0.15 0.00
182_T 28_N 1.04 0.15 0.00
21_I 35_T 1.04 0.15 0.00
127_F 16_L 1.04 0.15 0.00
61_M 21_T 1.04 0.15 0.00
184_F 46_P 1.03 0.15 0.00
115_G 97_I 1.03 0.15 0.00
214_I 16_L 1.02 0.14 0.00
9_L 15_L 1.02 0.14 0.00
43_F 28_N 1.02 0.14 0.00
170_L 107_L 1.02 0.14 0.00
114_G 112_D 1.00 0.14 0.00
127_F 21_T 1.00 0.14 0.00
42_L 49_V 1.00 0.14 0.00
152_M 28_N 1.00 0.14 0.00
43_F 31_M 0.99 0.14 0.00
61_M 91_S 0.99 0.14 0.00
87_T 101_S 0.99 0.14 0.00
214_I 12_L 0.99 0.14 0.00
75_L 18_M 0.99 0.14 0.00
114_G 46_P 0.99 0.13 0.00
27_A 4_A 0.99 0.13 0.00
43_F 107_L 0.97 0.13 0.00
9_L 101_S 0.97 0.13 0.00
202_A 96_I 0.97 0.13 0.00
115_G 6_I 0.97 0.13 0.00
87_T 12_L 0.97 0.13 0.00
172_T 100_L 0.97 0.13 0.00
146_I 18_M 0.97 0.13 0.00
13_T 91_S 0.96 0.13 0.00
155_T 88_V 0.96 0.13 0.00
152_M 35_T 0.95 0.12 0.00
222_G 112_D 0.95 0.12 0.00
146_I 96_I 0.95 0.12 0.00
41_A 112_D 0.95 0.12 0.00
36_F 46_P 0.95 0.12 0.00
186_A 6_I 0.94 0.12 0.00
191_V 44_M 0.94 0.12 0.00
71_I 16_L 0.94 0.12 0.00
184_F 49_V 0.94 0.12 0.00
129_E 4_A 0.93 0.12 0.00
214_I 35_T 0.93 0.12 0.00
191_V 96_I 0.93 0.12 0.00
90_V 21_T 0.93 0.12 0.00
182_T 101_S 0.93 0.12 0.00
191_V 91_S 0.93 0.12 0.00
9_L 28_N 0.92 0.12 0.00
132_D 82_T 0.92 0.11 0.00
21_I 16_L 0.92 0.11 0.00
94_S 6_I 0.92 0.11 0.00
100_I 35_T 0.92 0.11 0.00
142_V 6_I 0.91 0.11 0.00
222_G 46_P 0.91 0.11 0.00
222_G 49_V 0.91 0.11 0.00
125_P 112_D 0.91 0.11 0.00
165_V 99_A 0.91 0.11 0.00
123_L 97_I 0.91 0.11 0.00
146_I 112_D 0.91 0.11 0.00
214_I 8_M 0.90 0.11 0.00
31_I 11_T 0.90 0.11 0.00
75_L 79_X 0.89 0.11 0.00
155_T 100_L 0.89 0.11 0.00
165_V 103_A 0.89 0.11 0.00
43_F 90_S 0.89 0.11 0.00
107_T 85_P 0.89 0.11 0.00
148_T 21_T 0.88 0.11 0.00
150_I 34_S 0.88 0.11 0.00
220_E 30_Y 0.88 0.10 0.00
187_T 3_F 0.88 0.10 0.00
114_G 18_M 0.88 0.10 0.00
185_T 96_I 0.88 0.10 0.00
157_Q 101_S 0.88 0.10 0.00
167_T 19_I 0.88 0.10 0.00
172_T 97_I 0.88 0.10 0.00
127_F 4_A 0.87 0.10 0.00
165_V 58_V 0.87 0.10 0.00
114_G 82_T 0.87 0.10 0.00
36_F 90_S 0.87 0.10 0.00
55_I 112_D 0.87 0.10 0.00
214_I 3_F 0.87 0.10 0.00
32_F 13_L 0.86 0.10 0.00
146_I 46_P 0.86 0.10 0.00
90_V 19_I 0.86 0.10 0.00
91_N 4_A 0.86 0.10 0.00
152_M 15_L 0.86 0.10 0.00
157_Q 8_M 0.85 0.10 0.00
94_S 81_T 0.85 0.10 0.00
114_G 49_V 0.85 0.10 0.00
125_P 46_P 0.85 0.10 0.00
63_T 9_I 0.85 0.10 0.00
36_F 112_D 0.85 0.10 0.00
87_T 8_M 0.85 0.10 0.00
187_T 16_L 0.84 0.10 0.00
61_M 18_M 0.84 0.10 0.00
182_T 20_I 0.84 0.10 0.00
61_M 96_I 0.84 0.10 0.00
152_M 14_A 0.84 0.10 0.00
71_I 19_I 0.84 0.10 0.00
61_M 34_S 0.84 0.10 0.00
21_I 12_L 0.83 0.10 0.00
97_I 34_S 0.83 0.10 0.00
99_S 19_I 0.83 0.10 0.00
152_M 107_L 0.83 0.09 0.00
97_I 107_L 0.83 0.09 0.00
45_T 18_M 0.83 0.09 0.00
119_N 18_M 0.83 0.09 0.00
153_M 18_M 0.83 0.09 0.00
41_A 82_T 0.83 0.09 0.00
164_A 79_X 0.83 0.09 0.00
223_P 15_L 0.82 0.09 0.00
184_F 82_T 0.82 0.09 0.00
191_V 112_D 0.82 0.09 0.00
36_F 88_V 0.82 0.09 0.00
55_I 46_P 0.82 0.09 0.00
52_N 18_M 0.82 0.09 0.00
142_V 97_I 0.81 0.09 0.00
216_L 34_S 0.81 0.09 0.00
185_T 34_S 0.81 0.09 0.00
211_L 58_V 0.81 0.09 0.00
54_N 86_L 0.81 0.09 0.00
41_A 49_V 0.81 0.09 0.00
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
4484 2.13 cIV_B_80_cI_A_40_4_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 4) msa: Jackhmmer (2015_06) 0.92 Done - Shared
4481 1.3 cIV_B_80_cI_A_40_2_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4479 0.24 cIV_B_80_cI_A_40_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4478 2.15 cIV_B_80_cI_A_40_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4477 2.1 cIV_B_60_cI_A_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.93 Done - Shared
4476 0.01 cIV_B_40_cI_A_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) Killed - Shared
4475 2.13 cIV_B_40_cI_A_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
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