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OPENSEQ.org
7-24sc-c
Genes: A B A+B
Length: 240 224 455
Sequences: 596 694 93
Seq/Len: 2.48 3.1 0.2
MirrorTree (Pazo et al. 2001) 0.37
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 0.03 0.03 0.00
2 0.03 0.03 0.00
5 0.03 0.03 0.00
10 0.03 0.03 0.00
20 0.03 0.03 0.01
100 0.04 0.11 0.06
∞ 0.05 0.14 0.20
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
228_E 18_R 1.50 0.32 0.00
131_D 129_I 1.34 0.24 0.00
124_D 111_L 1.32 0.23 0.00
82_G 47_Q 1.23 0.20 0.00
130_M 69_Y 1.21 0.19 0.00
206_K 82_R 1.20 0.19 0.00
132_E 62_R 1.20 0.18 0.00
91_L 69_Y 1.17 0.18 0.00
50_E 26_K 1.16 0.17 0.00
167_L 121_L 1.15 0.17 0.00
151_L 54_K 1.15 0.17 0.00
52_R 145_V 1.12 0.16 0.00
63_A 65_A 1.12 0.16 0.00
135_E 147_D 1.12 0.16 0.00
74_E 66_K 1.11 0.16 0.00
131_D 133_K 1.11 0.16 0.00
24_V 72_N 1.11 0.15 0.00
108_Q 105_M 1.08 0.15 0.00
52_R 93_D 1.08 0.15 0.00
91_L 147_D 1.08 0.14 0.00
15_N 82_R 1.07 0.14 0.00
95_E 130_E 1.07 0.14 0.00
171_A 148_T 1.07 0.14 0.00
171_A 161_E 1.06 0.14 0.00
26_L 218_R 1.03 0.13 0.00
49_N 123_Q 1.02 0.13 0.00
104_M 66_K 1.02 0.13 0.00
41_R 50_K 1.02 0.13 0.00
33_L 181_N 1.01 0.13 0.00
169_M 69_Y 1.00 0.12 0.00
31_N 88_V 1.00 0.12 0.00
3_S 165_E 0.99 0.12 0.00
134_R 147_D 0.99 0.12 0.00
238_M 62_R 0.99 0.12 0.00
164_D 35_L 0.99 0.12 0.00
138_E 130_E 0.99 0.12 0.00
160_E 160_D 0.99 0.12 0.00
159_D 35_L 0.98 0.12 0.00
47_Q 64_Y 0.98 0.12 0.00
183_V 165_E 0.97 0.12 0.00
93_S 124_L 0.97 0.12 0.00
47_Q 129_I 0.96 0.11 0.00
137_V 147_D 0.96 0.11 0.00
159_D 82_R 0.95 0.11 0.00
79_K 121_L 0.94 0.11 0.00
131_D 54_K 0.93 0.11 0.00
69_K 195_E 0.93 0.11 0.00
89_Q 124_L 0.93 0.11 0.00
154_G 18_R 0.92 0.10 0.00
128_E 39_T 0.92 0.10 0.00
62_M 63_L 0.91 0.10 0.00
67_L 122_P 0.91 0.10 0.00
90_Q 32_E 0.91 0.10 0.00
126_V 84_Q 0.91 0.10 0.00
145_D 66_K 0.91 0.10 0.00
117_I 121_L 0.90 0.10 0.00
15_N 18_R 0.90 0.10 0.00
136_Q 124_L 0.90 0.10 0.00
145_D 184_Q 0.90 0.10 0.00
161_D 167_V 0.90 0.10 0.00
123_I 130_E 0.89 0.10 0.00
132_E 47_Q 0.88 0.10 0.00
95_E 159_M 0.88 0.10 0.00
235_Q 38_L 0.88 0.10 0.00
170_L 97_R 0.88 0.10 0.00
44_I 60_T 0.87 0.09 0.00
127_D 121_L 0.87 0.09 0.00
209_Q 189_E 0.87 0.09 0.00
151_L 85_L 0.87 0.09 0.00
131_D 104_Q 0.86 0.09 0.00
159_D 167_V 0.86 0.09 0.00
22_A 130_E 0.86 0.09 0.00
111_A 46_Q 0.86 0.09 0.00
58_G 121_L 0.86 0.09 0.00
54_F 32_E 0.86 0.09 0.00
119_S 77_R 0.85 0.09 0.00
81_E 223_Q 0.85 0.09 0.00
71_K 31_I 0.85 0.09 0.00
60_K 56_N 0.85 0.09 0.00
7_G 16_Q 0.85 0.09 0.00
35_K 167_V 0.85 0.09 0.00
233_E 220_R 0.85 0.09 0.00
162_E 82_R 0.85 0.09 0.00
141_D 103_N 0.84 0.09 0.00
110_G 38_L 0.84 0.09 0.00
138_E 72_N 0.84 0.09 0.00
87_M 88_V 0.84 0.09 0.00
26_L 130_E 0.83 0.09 0.00
140_G 124_L 0.83 0.09 0.00
51_A 65_A 0.83 0.09 0.00
161_D 47_Q 0.83 0.09 0.00
52_R 73_K 0.83 0.09 0.00
111_A 50_K 0.83 0.09 0.00
70_K 65_A 0.83 0.09 0.00
129_T 69_Y 0.83 0.09 0.00
26_L 177_E 0.83 0.09 0.00
62_M 217_E 0.82 0.08 0.00
143_I 173_Q 0.82 0.08 0.00
110_G 43_N 0.82 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
9419 0.02 7-24sc-d Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9418 0.74 7-24sc-cjckhmmr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9417 0.2 7-24sc-c Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9415 0.02 7-24sc Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
8464 0.11 jckhmmr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed
8463 0.01 Snf7 Vps24 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed
8462 0.01 Snf7 Vps24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
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