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OPENSEQ.org
retry
Genes: A B A+B
Length: 174 248 399
Sequences: 176 2535 96
Seq/Len: 1.01 10.22 0.24
MirrorTree (Pazo et al. 2001) 0.13
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.12 0.00
2 0.01 0.12 0.00
5 0.01 0.12 0.00
10 0.01 0.13 0.00
20 0.01 0.13 0.00
100 0.01 0.16 0.00
∞ 0.01 0.27 0.23
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
145_R 171_Y 1.42 0.31 0.00
90_A 168_K 1.37 0.29 0.00
145_R 40_L 1.33 0.27 0.00
52_T 115_A 1.28 0.25 0.00
169_G 40_L 1.28 0.25 0.00
62_R 231_Q 1.25 0.23 0.00
40_L 105_Q 1.25 0.23 0.00
70_S 171_Y 1.24 0.23 0.00
55_K 230_L 1.23 0.22 0.00
109_V 225_I 1.22 0.22 0.00
95_E 79_I 1.19 0.20 0.00
94_R 165_N 1.18 0.20 0.00
86_E 156_M 1.17 0.20 0.00
109_V 166_A 1.16 0.19 0.00
105_N 53_I 1.14 0.18 0.00
83_R 176_S 1.14 0.18 0.00
43_Q 202_T 1.13 0.18 0.00
95_E 36_A 1.11 0.17 0.00
17_I 96_G 1.10 0.17 0.00
90_A 171_Y 1.08 0.16 0.00
158_P 175_A 1.08 0.16 0.00
63_A 109_T 1.07 0.16 0.00
86_E 98_Q 1.07 0.16 0.00
39_D 186_A 1.06 0.16 0.00
149_Q 171_Y 1.05 0.15 0.00
82_I 113_E 1.05 0.15 0.00
37_L 175_A 1.04 0.15 0.00
112_D 115_A 1.03 0.14 0.00
75_R 171_Y 1.03 0.14 0.00
62_R 34_A 1.02 0.14 0.00
12_D 39_V 1.02 0.14 0.00
90_A 110_I 1.01 0.14 0.00
32_S 228_S 1.01 0.14 0.00
75_R 18_E 1.00 0.14 0.00
172_Q 173_E 1.00 0.14 0.00
43_Q 171_Y 1.00 0.14 0.00
19_G 51_Q 1.00 0.14 0.00
62_R 130_Y 1.00 0.14 0.00
62_R 97_R 0.99 0.14 0.00
37_L 36_A 0.99 0.14 0.00
155_A 118_Y 0.99 0.13 0.00
112_D 98_Q 0.99 0.13 0.00
90_A 114_Q 0.99 0.13 0.00
119_Q 85_R 0.99 0.13 0.00
153_Q 229_A 0.98 0.13 0.00
154_G 19_L 0.97 0.13 0.00
95_E 228_S 0.96 0.12 0.00
164_G 166_A 0.95 0.12 0.00
87_D 232_A 0.95 0.12 0.00
45_A 13_M 0.94 0.12 0.00
21_D 51_Q 0.94 0.12 0.00
101_T 225_I 0.93 0.12 0.00
169_G 18_E 0.93 0.12 0.00
158_P 122_L 0.93 0.12 0.00
111_S 183_I 0.93 0.12 0.00
52_T 79_I 0.93 0.12 0.00
40_L 168_K 0.92 0.12 0.00
154_G 138_L 0.92 0.12 0.00
43_Q 96_G 0.91 0.11 0.00
75_R 14_R 0.91 0.11 0.00
52_T 222_F 0.90 0.11 0.00
15_E 230_L 0.90 0.11 0.00
23_R 39_V 0.89 0.11 0.00
14_V 124_V 0.89 0.11 0.00
138_F 79_I 0.89 0.11 0.00
94_R 113_E 0.89 0.11 0.00
21_D 72_D 0.89 0.11 0.00
153_Q 215_A 0.89 0.11 0.00
55_K 17_S 0.89 0.11 0.00
31_D 183_I 0.89 0.11 0.00
75_R 49_S 0.88 0.11 0.00
112_D 33_L 0.88 0.11 0.00
94_R 176_S 0.88 0.10 0.00
62_R 37_G 0.88 0.10 0.00
77_I 2_S 0.88 0.10 0.00
40_L 175_A 0.88 0.10 0.00
70_S 153_F 0.88 0.10 0.00
52_T 185_V 0.87 0.10 0.00
153_Q 70_E 0.87 0.10 0.00
145_R 92_R 0.87 0.10 0.00
38_T 7_I 0.87 0.10 0.00
65_P 29_S 0.87 0.10 0.00
145_R 18_E 0.87 0.10 0.00
170_T 112_T 0.87 0.10 0.00
14_V 40_L 0.86 0.10 0.00
80_T 15_E 0.86 0.10 0.00
80_T 34_A 0.86 0.10 0.00
131_H 100_A 0.86 0.10 0.00
10_D 182_R 0.86 0.10 0.00
153_Q 136_P 0.86 0.10 0.00
55_K 135_R 0.86 0.10 0.00
68_E 98_Q 0.86 0.10 0.00
113_A 216_N 0.86 0.10 0.00
119_Q 87_Y 0.85 0.10 0.00
88_G 34_A 0.85 0.10 0.00
106_E 36_A 0.85 0.10 0.00
76_D 61_G 0.85 0.10 0.00
52_T 138_L 0.85 0.10 0.00
31_D 225_I 0.84 0.10 0.00
79_A 109_T 0.84 0.10 0.00
169_G 92_R 0.84 0.10 0.00
107_D 176_S 0.84 0.10 0.00
39_D 171_Y 0.83 0.09 0.00
62_R 176_S 0.83 0.09 0.00
112_D 112_T 0.83 0.09 0.00
111_S 151_P 0.83 0.09 0.00
90_A 40_L 0.83 0.09 0.00
75_R 187_A 0.83 0.09 0.00
156_L 34_A 0.82 0.09 0.00
68_E 135_R 0.82 0.09 0.00
41_V 142_T 0.82 0.09 0.00
68_E 5_Y 0.82 0.09 0.00
68_E 76_R 0.82 0.09 0.00
155_A 95_T 0.82 0.09 0.00
19_G 122_L 0.81 0.09 0.00
154_G 123_C 0.81 0.09 0.00
75_R 15_E 0.81 0.09 0.00
79_A 37_G 0.81 0.09 0.00
135_T 190_A 0.81 0.09 0.00
136_A 88_A 0.81 0.09 0.00
155_A 5_Y 0.81 0.09 0.00
106_E 133_T 0.80 0.09 0.00
109_V 153_F 0.80 0.09 0.00
170_T 232_A 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
4358 0.24 retry Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done
4357 0.81 retry Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done
4354 0 activmatch Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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