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OPENSEQ.org
cIV_C_40_cI_K_40_4_human
Genes: A B A+B
Length: 261 98 359
Sequences: 2457 171 89
Seq/Len: 9.41 1.74 0.25
MirrorTree (Pazo et al. 2001) 0.36
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 0.01
2 0.00 0.00 0.25
5 0.00 0.00 0.25
10 0.00 0.00 0.25
20 0.00 0.00 0.25
100 0.00 0.00 0.25
∞ 0.00 0.00 0.25
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
12_K 38_L 1.50 0.37 0.00
12_K 28_S 1.42 0.32 0.00
153_E 28_S 1.37 0.30 0.00
251_F 71_A 1.37 0.29 0.00
153_E 38_L 1.34 0.28 0.00
153_E 49_L 1.32 0.27 0.00
78_G 49_L 1.30 0.26 0.00
251_F 91_H 1.29 0.26 0.00
143_S 87_L 1.24 0.23 0.00
12_K 90_V 1.23 0.23 0.00
54_M 38_L 1.22 0.22 0.00
212_S 12_F 1.21 0.22 0.00
67_Y 81_I 1.20 0.21 0.00
135_S 48_T 1.18 0.21 0.00
112_L 12_F 1.18 0.21 0.00
12_K 91_H 1.16 0.20 0.00
112_L 84_T 1.16 0.20 0.00
251_F 28_S 1.14 0.19 0.00
54_M 71_A 1.14 0.19 0.00
199_V 49_L 1.13 0.19 0.00
54_M 28_S 1.12 0.18 0.00
230_K 63_M 1.12 0.18 0.00
12_K 49_L 1.11 0.18 0.00
230_K 59_V 1.11 0.18 0.00
153_E 91_H 1.10 0.17 0.00
61_V 6_M 1.09 0.17 0.00
254_V 59_V 1.09 0.17 0.00
27_M 54_L 1.08 0.17 0.00
78_G 28_S 1.08 0.17 0.00
199_V 28_S 1.08 0.17 0.00
54_M 91_H 1.04 0.15 0.00
254_V 87_L 1.04 0.15 0.00
110_P 63_M 1.04 0.15 0.00
12_K 57_N 1.03 0.15 0.00
223_L 84_T 1.03 0.15 0.00
251_F 38_L 1.02 0.15 0.00
223_L 12_F 1.02 0.15 0.00
199_V 38_L 1.01 0.14 0.00
110_P 22_Y 1.01 0.14 0.00
67_Y 43_M 1.01 0.14 0.00
12_K 80_S 1.00 0.14 0.00
127_L 12_F 0.99 0.14 0.00
158_Q 81_I 0.99 0.14 0.00
158_Q 14_I 0.99 0.14 0.00
192_I 81_I 0.98 0.14 0.00
153_E 90_V 0.98 0.13 0.00
78_G 38_L 0.97 0.13 0.00
38_H 87_L 0.96 0.13 0.00
78_G 91_H 0.96 0.13 0.00
12_K 14_I 0.95 0.12 0.00
61_V 14_I 0.94 0.12 0.00
40_M 53_S 0.94 0.12 0.00
199_V 14_I 0.94 0.12 0.00
212_S 84_T 0.94 0.12 0.00
67_Y 21_V 0.93 0.12 0.00
184_S 14_I 0.93 0.12 0.00
159_M 80_S 0.93 0.12 0.00
219_F 19_M 0.93 0.12 0.00
182_F 3_L 0.92 0.12 0.00
61_V 2_P 0.92 0.12 0.00
184_S 13_T 0.92 0.12 0.00
159_M 12_F 0.92 0.12 0.00
5_S 90_V 0.92 0.12 0.00
153_E 57_N 0.91 0.12 0.00
52_L 12_F 0.91 0.12 0.00
12_K 19_M 0.91 0.12 0.00
220_I 79_V 0.90 0.11 0.00
155_N 59_V 0.90 0.11 0.00
127_L 84_T 0.90 0.11 0.00
168_L 5_Y 0.90 0.11 0.00
153_E 71_A 0.89 0.11 0.00
112_L 3_L 0.89 0.11 0.00
52_L 84_T 0.89 0.11 0.00
187_T 55_L 0.88 0.11 0.00
212_S 6_M 0.88 0.11 0.00
45_L 12_F 0.88 0.11 0.00
182_F 6_M 0.88 0.11 0.00
12_K 71_A 0.88 0.11 0.00
160_I 19_M 0.88 0.11 0.00
61_V 84_T 0.88 0.11 0.00
50_N 3_L 0.87 0.11 0.00
159_M 3_L 0.87 0.10 0.00
39_S 12_F 0.87 0.10 0.00
220_I 57_N 0.86 0.10 0.00
199_V 91_H 0.86 0.10 0.00
78_G 90_V 0.86 0.10 0.00
135_S 12_F 0.86 0.10 0.00
219_F 53_S 0.86 0.10 0.00
74_P 87_L 0.86 0.10 0.00
254_V 79_V 0.86 0.10 0.00
12_K 54_L 0.86 0.10 0.00
216_T 58_I 0.85 0.10 0.00
110_P 59_V 0.85 0.10 0.00
110_P 19_M 0.85 0.10 0.00
135_S 14_I 0.85 0.10 0.00
50_N 84_T 0.85 0.10 0.00
158_Q 87_L 0.85 0.10 0.00
54_M 90_V 0.85 0.10 0.00
73_P 13_T 0.84 0.10 0.00
54_M 48_T 0.84 0.10 0.00
50_N 12_F 0.84 0.10 0.00
12_K 48_T 0.84 0.10 0.00
171_L 9_M 0.84 0.10 0.00
225_F 38_L 0.83 0.10 0.00
55_Y 56_A 0.83 0.10 0.00
52_L 48_T 0.83 0.10 0.00
223_L 14_I 0.83 0.10 0.00
38_H 73_V 0.83 0.10 0.00
52_L 80_S 0.83 0.10 0.00
217_I 53_S 0.83 0.10 0.00
168_L 80_S 0.83 0.10 0.00
39_S 84_T 0.83 0.10 0.00
168_L 58_I 0.83 0.10 0.00
45_L 84_T 0.83 0.10 0.00
219_F 48_T 0.82 0.09 0.00
111_Q 3_L 0.82 0.09 0.00
223_L 3_L 0.82 0.09 0.00
61_V 90_V 0.82 0.09 0.00
187_T 19_M 0.82 0.09 0.00
61_V 19_M 0.81 0.09 0.00
49_T 48_T 0.81 0.09 0.00
112_L 5_Y 0.81 0.09 0.00
160_I 14_I 0.81 0.09 0.00
65_S 59_V 0.81 0.09 0.00
54_M 94_N 0.81 0.09 0.00
143_S 80_S 0.81 0.09 0.00
135_S 84_T 0.81 0.09 0.00
74_P 43_M 0.81 0.09 0.00
219_F 58_I 0.81 0.09 0.00
178_A 21_V 0.81 0.09 0.00
27_M 53_S 0.81 0.09 0.00
155_N 22_Y 0.80 0.09 0.00
159_M 84_T 0.80 0.09 0.00
168_L 19_M 0.80 0.09 0.00
187_T 63_M 0.80 0.09 0.00
168_L 28_S 0.80 0.09 0.00
164_L 9_M 0.80 0.09 0.00
111_Q 53_S 0.80 0.09 0.00
115_H 43_M 0.80 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
4504 5.5 cIV_C_40_cI_K_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
4503 1.78 cIV_C_60_cI_K_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4502 1.79 cIV_C_40_cI_K_20_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4501 0.25 cIV_C_40_cI_K_40_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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