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OPENSEQ.org
cIV_B_40_cI_K_40_human
Genes: A B A+B
Length: 227 98 323
Sequences: 4037 171 59
Seq/Len: 17.78 1.74 0.18
MirrorTree (Pazo et al. 2001) 0.21
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 0.18
10 0.00 0.00 0.18
20 0.00 0.00 0.18
100 0.01 0.00 0.18
∞ 0.01 0.00 0.18
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
75_L 58_I 1.35 0.23 0.00
3_H 21_V 1.29 0.21 0.00
107_T 91_H 1.28 0.20 0.00
155_T 17_L 1.27 0.20 0.00
164_A 90_V 1.24 0.19 0.00
9_L 40_L 1.21 0.18 0.00
63_T 17_L 1.20 0.17 0.00
157_Q 43_M 1.20 0.17 0.00
27_A 81_I 1.14 0.15 0.00
100_I 43_M 1.14 0.15 0.00
13_T 43_M 1.14 0.15 0.00
192_Y 13_T 1.12 0.15 0.00
27_A 17_L 1.10 0.14 0.00
5_A 21_V 1.09 0.14 0.00
90_V 53_S 1.08 0.14 0.00
64_V 15_S 1.07 0.14 0.00
97_I 59_V 1.07 0.13 0.00
149_P 58_I 1.05 0.13 0.00
167_T 58_I 1.03 0.12 0.00
114_G 58_I 1.03 0.12 0.00
146_I 58_I 1.02 0.12 0.00
217_K 58_I 1.00 0.12 0.00
216_L 6_M 1.00 0.12 0.00
92_D 62_A 1.00 0.12 0.00
87_T 21_V 0.99 0.12 0.00
75_L 6_M 0.99 0.11 0.00
119_N 91_H 0.99 0.11 0.00
153_M 91_H 0.99 0.11 0.00
27_A 80_S 0.98 0.11 0.00
41_A 20_L 0.98 0.11 0.00
87_T 43_M 0.98 0.11 0.00
87_T 62_A 0.97 0.11 0.00
202_A 2_P 0.97 0.11 0.00
115_G 40_L 0.97 0.11 0.00
157_Q 21_V 0.96 0.11 0.00
182_T 13_T 0.96 0.11 0.00
191_V 90_V 0.96 0.11 0.00
127_F 81_I 0.96 0.11 0.00
61_M 81_I 0.96 0.11 0.00
146_I 6_M 0.95 0.10 0.00
99_S 58_I 0.94 0.10 0.00
217_K 53_S 0.94 0.10 0.00
42_L 91_H 0.94 0.10 0.00
75_L 53_S 0.94 0.10 0.00
167_T 54_L 0.93 0.10 0.00
147_E 61_I 0.93 0.10 0.00
3_H 42_I 0.93 0.10 0.00
172_T 93_L 0.92 0.10 0.00
155_T 81_I 0.92 0.10 0.00
95_L 54_L 0.92 0.10 0.00
211_L 90_V 0.92 0.10 0.00
216_L 53_S 0.92 0.10 0.00
183_T 59_V 0.91 0.10 0.00
22_T 53_S 0.91 0.10 0.00
220_E 52_H 0.91 0.10 0.00
47_S 40_L 0.91 0.10 0.00
164_A 46_F 0.91 0.10 0.00
31_I 21_V 0.91 0.10 0.00
183_T 47_M 0.91 0.10 0.00
164_A 54_L 0.91 0.10 0.00
114_G 14_I 0.90 0.10 0.00
218_I 43_M 0.90 0.10 0.00
133_L 53_S 0.90 0.09 0.00
115_G 54_L 0.90 0.09 0.00
202_A 90_V 0.90 0.09 0.00
36_F 81_I 0.89 0.09 0.00
172_T 95_L 0.89 0.09 0.00
36_F 80_S 0.89 0.09 0.00
184_F 91_H 0.89 0.09 0.00
187_T 3_L 0.89 0.09 0.00
167_T 57_N 0.89 0.09 0.00
99_S 53_S 0.89 0.09 0.00
125_P 91_H 0.88 0.09 0.00
107_T 54_L 0.88 0.09 0.00
11_D 53_S 0.88 0.09 0.00
111_T 53_S 0.88 0.09 0.00
122_M 53_S 0.88 0.09 0.00
170_L 44_G 0.88 0.09 0.00
115_G 91_H 0.88 0.09 0.00
215_P 53_S 0.88 0.09 0.00
164_A 21_V 0.87 0.09 0.00
172_T 94_N 0.86 0.09 0.00
43_F 63_M 0.86 0.09 0.00
100_I 21_V 0.86 0.09 0.00
91_N 52_H 0.86 0.09 0.00
45_T 91_H 0.86 0.09 0.00
55_I 91_H 0.86 0.09 0.00
216_L 58_I 0.86 0.09 0.00
114_G 54_L 0.86 0.09 0.00
221_M 59_V 0.86 0.09 0.00
74_V 80_S 0.85 0.09 0.00
9_L 43_M 0.85 0.09 0.00
127_F 87_L 0.85 0.09 0.00
175_I 28_S 0.85 0.09 0.00
175_I 38_L 0.85 0.09 0.00
218_I 57_N 0.85 0.09 0.00
143_V 53_S 0.85 0.09 0.00
223_P 62_A 0.84 0.08 0.00
126_L 58_I 0.84 0.08 0.00
31_I 59_V 0.84 0.08 0.00
132_D 54_L 0.84 0.08 0.00
21_I 51_T 0.84 0.08 0.00
165_V 80_S 0.84 0.08 0.00
191_V 91_H 0.84 0.08 0.00
99_S 6_M 0.84 0.08 0.00
57_D 54_L 0.84 0.08 0.00
147_E 47_M 0.84 0.08 0.00
187_T 40_L 0.83 0.08 0.00
192_Y 17_L 0.83 0.08 0.00
100_I 59_V 0.83 0.08 0.00
183_T 53_S 0.83 0.08 0.00
155_T 80_S 0.83 0.08 0.00
113_Y 35_G 0.83 0.08 0.00
169_G 35_G 0.83 0.08 0.00
132_D 42_I 0.83 0.08 0.00
21_I 62_A 0.83 0.08 0.00
9_L 62_A 0.83 0.08 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
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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