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OPENSEQ.org
cI_E2_cIII_cyt1_2_Pdenitr
Genes: A B A+B
Length: 239 263 485
Sequences: 761 973 201
Seq/Len: 3.18 3.7 0.41
MirrorTree (Pazo et al. 2001) 0.63
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.01 0.01 0.03
∞ 0.04 0.01 0.40
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
36_Q 80_L 1.23 0.32 0.00
187_E 235_V 1.23 0.31 0.00
149_I 47_L 1.23 0.31 0.00
25_A 59_S 1.21 0.30 0.00
186_A 241_L 1.21 0.30 0.00
93_I 86_R 1.20 0.29 0.00
14_E 48_Q 1.17 0.28 0.00
165_L 236_I 1.16 0.27 0.00
47_Q 215_F 1.15 0.27 0.00
93_I 88_Y 1.10 0.24 0.00
14_E 64_L 1.07 0.23 0.00
237_N 150_G 1.07 0.23 0.00
103_I 250_K 1.07 0.22 0.00
126_A 91_N 1.06 0.22 0.00
108_D 105_R 1.06 0.22 0.00
158_T 195_V 1.05 0.21 0.00
125_S 25_A 1.05 0.21 0.00
141_C 211_D 1.05 0.21 0.00
93_I 34_S 1.04 0.21 0.00
142_T 90_A 1.04 0.21 0.00
125_S 51_L 1.02 0.20 0.00
19_N 55_T 1.01 0.19 0.00
158_T 204_T 1.01 0.19 0.00
103_I 234_S 1.00 0.19 0.00
85_Q 52_Q 1.00 0.19 0.00
82_F 66_Y 0.99 0.19 0.00
20_L 254_Q 0.99 0.19 0.00
44_W 77_G 0.97 0.18 0.00
72_A 60_A 0.97 0.18 0.00
20_L 236_I 0.97 0.18 0.00
114_K 42_F 0.97 0.17 0.00
207_S 256_I 0.96 0.17 0.00
8_I 48_Q 0.96 0.17 0.00
45_R 122_D 0.96 0.17 0.00
85_Q 56_E 0.96 0.17 0.00
125_S 19_A 0.95 0.17 0.00
107_E 54_Y 0.95 0.17 0.00
116_K 213_A 0.94 0.17 0.00
53_L 241_L 0.94 0.17 0.00
161_K 137_Y 0.94 0.17 0.00
21_E 154_I 0.94 0.16 0.00
196_A 16_A 0.93 0.16 0.00
40_I 56_E 0.93 0.16 0.00
168_R 64_L 0.92 0.16 0.00
45_R 128_K 0.92 0.16 0.00
66_G 46_Q 0.92 0.16 0.00
163_A 166_K 0.92 0.16 0.00
59_E 107_P 0.92 0.15 0.00
89_S 225_M 0.92 0.15 0.00
190_G 240_V 0.91 0.15 0.00
54_S 180_A 0.91 0.15 0.00
126_A 60_A 0.91 0.15 0.00
187_E 236_I 0.91 0.15 0.00
55_R 68_P 0.90 0.15 0.00
174_V 80_L 0.89 0.15 0.00
53_L 242_A 0.89 0.14 0.00
7_P 166_K 0.89 0.14 0.00
190_G 207_Q 0.89 0.14 0.00
147_A 191_S 0.88 0.14 0.00
60_Y 64_L 0.88 0.14 0.00
28_T 65_R 0.88 0.14 0.00
124_L 78_P 0.88 0.14 0.00
61_C 180_A 0.88 0.14 0.00
52_W 109_D 0.87 0.14 0.00
48_E 122_D 0.87 0.14 0.00
39_I 60_A 0.87 0.14 0.00
111_R 169_A 0.87 0.14 0.00
195_L 215_F 0.87 0.14 0.00
124_L 64_L 0.87 0.14 0.00
85_Q 74_D 0.86 0.14 0.00
48_E 51_L 0.86 0.13 0.00
54_S 156_A 0.86 0.13 0.00
61_C 175_H 0.86 0.13 0.00
33_G 47_L 0.85 0.13 0.00
142_T 257_K 0.85 0.13 0.00
35_Q 82_E 0.85 0.13 0.00
190_G 18_E 0.85 0.13 0.00
97_G 69_L 0.85 0.13 0.00
132_W 232_F 0.85 0.13 0.00
82_F 36_E 0.84 0.13 0.00
183_R 220_A 0.84 0.13 0.00
17_P 221_E 0.84 0.13 0.00
82_F 56_E 0.84 0.13 0.00
26_Q 241_L 0.84 0.13 0.00
166_I 64_L 0.84 0.13 0.00
82_F 127_A 0.84 0.13 0.00
160_E 220_A 0.84 0.13 0.00
212_L 45_H 0.84 0.13 0.00
175_P 209_A 0.83 0.13 0.00
59_E 78_P 0.83 0.13 0.00
17_P 240_V 0.83 0.12 0.00
158_T 154_I 0.82 0.12 0.00
62_A 207_Q 0.82 0.12 0.00
7_P 60_A 0.82 0.12 0.00
93_I 102_D 0.82 0.12 0.00
106_A 241_L 0.82 0.12 0.00
118_A 247_L 0.82 0.12 0.00
42_V 79_Q 0.82 0.12 0.00
82_F 156_A 0.82 0.12 0.00
132_W 124_S 0.82 0.12 0.00
159_V 180_A 0.82 0.12 0.00
187_E 92_F 0.82 0.12 0.00
122_H 28_I 0.81 0.12 0.00
197_D 101_E 0.81 0.12 0.00
86_P 158_L 0.81 0.12 0.00
11_D 69_L 0.81 0.12 0.00
110_I 65_R 0.81 0.12 0.00
170_A 69_L 0.81 0.12 0.00
203_A 63_G 0.81 0.12 0.00
44_W 78_P 0.81 0.12 0.00
61_C 88_Y 0.81 0.12 0.00
149_I 45_H 0.81 0.12 0.00
47_Q 49_R 0.80 0.12 0.00
93_I 221_E 0.80 0.12 0.00
69_Y 81_P 0.80 0.12 0.00
193_T 214_A 0.80 0.12 0.00
164_A 151_P 0.80 0.12 0.00
28_T 252_L 0.80 0.12 0.00
76_A 158_L 0.80 0.11 0.00
109_L 210_T 0.80 0.11 0.00
237_N 129_A 0.79 0.11 0.00
85_Q 237_F 0.79 0.11 0.00
114_K 224_M 0.79 0.11 0.00
58_I 130_R 0.79 0.11 0.00
36_Q 21_D 0.79 0.11 0.00
24_R 154_I 0.79 0.11 0.00
14_E 149_G 0.79 0.11 0.00
37_S 76_G 0.79 0.11 0.00
140_A 59_S 0.79 0.11 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
3016 0.42 cI_E_6_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2798 0.41 cI_E2_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2797 0.42 cI_E4_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2796 0.39 cI_E_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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