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OPENSEQ.org
D F coil jackammer
Genes: A B A+B
Length: 246 58 283
Sequences: 302 63 63
Seq/Len: 1.23 1.09 0.22
MirrorTree (Pazo et al. 2001) 0.83
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 0.21
5 0.00 0.00 0.21
10 0.00 0.00 0.21
20 0.00 0.00 0.21
100 0.00 0.00 0.21
∞ 0.01 0.00 0.21
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
197_V 39_D 1.52 0.35 0.00
146_K 17_K 1.47 0.32 0.00
224_M 5_D 1.44 0.31 0.00
154_E 39_D 1.44 0.31 0.00
204_G 36_Q 1.38 0.28 0.00
125_L 25_K 1.37 0.27 0.00
221_K 5_D 1.37 0.27 0.00
197_V 17_K 1.36 0.27 0.00
188_D 4_V 1.35 0.27 0.00
69_E 40_Q 1.34 0.26 0.00
188_D 40_Q 1.33 0.25 0.00
139_P 17_K 1.25 0.22 0.00
183_R 34_V 1.24 0.21 0.00
167_A 29_V 1.21 0.20 0.00
164_M 40_Q 1.19 0.20 0.00
93_V 25_K 1.18 0.19 0.00
231_G 11_Q 1.18 0.19 0.00
221_K 3_D 1.15 0.18 0.00
86_R 25_K 1.15 0.18 0.00
39_G 50_A 1.14 0.17 0.00
197_V 4_V 1.14 0.17 0.00
184_L 34_V 1.11 0.17 0.00
66_N 11_Q 1.11 0.16 0.00
130_M 37_V 1.09 0.16 0.00
130_M 34_V 1.09 0.16 0.00
228_R 45_A 1.09 0.16 0.00
213_D 43_T 1.08 0.16 0.00
237_D 22_A 1.08 0.15 0.00
171_W 53_P 1.08 0.15 0.00
86_R 34_V 1.07 0.15 0.00
184_L 40_Q 1.04 0.14 0.00
238_F 36_Q 1.04 0.14 0.00
104_V 28_A 1.02 0.14 0.00
172_V 19_R 1.01 0.14 0.00
71_K 44_P 1.01 0.13 0.00
153_V 36_Q 1.00 0.13 0.00
227_F 36_Q 0.99 0.13 0.00
229_P 36_Q 0.99 0.13 0.00
221_K 22_A 0.99 0.13 0.00
185_S 5_D 0.99 0.13 0.00
104_V 25_K 0.98 0.13 0.00
100_K 25_K 0.97 0.12 0.00
223_K 28_A 0.96 0.12 0.00
174_I 42_A 0.96 0.12 0.00
145_V 45_A 0.95 0.12 0.00
106_A 25_K 0.94 0.12 0.00
43_I 44_P 0.94 0.12 0.00
123_R 40_Q 0.94 0.12 0.00
28_L 14_L 0.94 0.12 0.00
150_V 3_D 0.94 0.11 0.00
66_N 4_V 0.93 0.11 0.00
223_K 55_D 0.93 0.11 0.00
94_D 40_Q 0.92 0.11 0.00
55_K 14_L 0.92 0.11 0.00
164_M 29_V 0.91 0.11 0.00
84_I 35_R 0.91 0.11 0.00
222_T 34_V 0.91 0.11 0.00
183_R 10_K 0.91 0.11 0.00
145_V 6_I 0.91 0.11 0.00
197_V 5_D 0.90 0.11 0.00
31_L 18_Q 0.90 0.10 0.00
164_M 45_A 0.89 0.10 0.00
104_V 4_V 0.89 0.10 0.00
207_K 40_Q 0.89 0.10 0.00
45_A 40_Q 0.89 0.10 0.00
86_R 15_E 0.88 0.10 0.00
141_T 17_K 0.88 0.10 0.00
183_R 41_P 0.88 0.10 0.00
126_E 18_Q 0.88 0.10 0.00
93_V 42_A 0.88 0.10 0.00
225_N 36_Q 0.88 0.10 0.00
163_V 30_L 0.87 0.10 0.00
177_P 30_L 0.87 0.10 0.00
154_E 36_Q 0.87 0.10 0.00
225_N 48_R 0.87 0.10 0.00
167_A 55_D 0.87 0.10 0.00
128_I 10_K 0.87 0.10 0.00
43_I 19_R 0.86 0.10 0.00
127_S 19_R 0.86 0.10 0.00
183_R 37_V 0.86 0.10 0.00
52_I 52_S 0.85 0.10 0.00
170_D 48_R 0.85 0.09 0.00
65_A 43_T 0.85 0.09 0.00
52_I 2_P 0.85 0.09 0.00
63_R 43_T 0.84 0.09 0.00
44_S 35_R 0.84 0.09 0.00
37_W 44_P 0.83 0.09 0.00
141_T 25_K 0.83 0.09 0.00
65_A 21_E 0.83 0.09 0.00
59_I 47_K 0.83 0.09 0.00
223_K 56_F 0.83 0.09 0.00
147_I 4_V 0.83 0.09 0.00
237_D 55_D 0.82 0.09 0.00
110_L 25_K 0.82 0.09 0.00
183_R 40_Q 0.82 0.09 0.00
227_F 18_Q 0.82 0.09 0.00
229_P 18_Q 0.82 0.09 0.00
234_E 25_K 0.82 0.09 0.00
164_M 6_I 0.81 0.09 0.00
56_V 55_D 0.81 0.09 0.00
184_L 37_V 0.81 0.09 0.00
237_D 39_D 0.81 0.09 0.00
123_R 4_V 0.81 0.09 0.00
36_S 17_K 0.81 0.09 0.00
184_L 41_P 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
7950 0.22 D F coil jackammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7936 0.17 D F coil jackammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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