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OPENSEQ.org
cI_I_40_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 163 263 408
Sequences: 644 570 148
Seq/Len: 3.95 2.17 0.36
MirrorTree (Pazo et al. 2001) 0.42
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.00
100 0.00 0.02 0.02
∞ 0.01 0.02 0.35
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
152_I 130_R 1.75 0.64 0.00
73_V 42_F 1.64 0.56 0.00
101_T 257_K 1.57 0.51 0.00
90_S 142_S 1.51 0.47 0.00
16_D 249_N 1.41 0.40 0.00
87_E 208_M 1.34 0.36 0.00
21_F 69_L 1.33 0.35 0.00
90_S 147_G 1.32 0.35 0.00
35_L 178_A 1.29 0.32 0.00
108_F 17_Q 1.29 0.32 0.00
13_L 164_E 1.26 0.31 0.00
13_L 237_F 1.25 0.30 0.00
90_S 208_M 1.25 0.30 0.00
84_E 142_S 1.22 0.28 0.00
90_S 146_N 1.21 0.28 0.00
77_Q 228_K 1.21 0.28 0.00
159_D 47_L 1.21 0.28 0.00
28_F 64_L 1.20 0.27 0.00
73_V 170_G 1.18 0.26 0.00
143_A 91_N 1.17 0.25 0.00
127_A 230_V 1.17 0.25 0.00
58_P 87_A 1.15 0.24 0.00
11_Y 249_N 1.12 0.23 0.00
7_R 185_Q 1.10 0.22 0.00
84_E 203_A 1.05 0.20 0.00
26_R 166_K 1.04 0.19 0.00
84_E 147_G 1.04 0.19 0.00
23_L 46_Q 1.04 0.19 0.00
21_F 191_S 1.03 0.19 0.00
147_R 110_H 1.03 0.19 0.00
42_G 101_E 1.03 0.19 0.00
131_R 244_L 1.03 0.19 0.00
44_L 241_L 1.02 0.18 0.00
90_S 36_E 1.00 0.18 0.00
108_F 38_P 1.00 0.17 0.00
10_K 130_R 0.99 0.17 0.00
90_S 143_Q 0.99 0.17 0.00
77_Q 132_G 0.99 0.17 0.00
24_G 143_Q 0.98 0.17 0.00
84_E 146_N 0.98 0.17 0.00
127_A 141_L 0.98 0.17 0.00
41_K 179_F 0.97 0.16 0.00
101_T 154_I 0.96 0.16 0.00
84_E 208_M 0.96 0.16 0.00
130_T 56_E 0.96 0.16 0.00
39_H 85_V 0.96 0.16 0.00
90_S 203_A 0.96 0.16 0.00
7_R 69_L 0.95 0.15 0.00
82_D 138_G 0.94 0.15 0.00
101_T 203_A 0.94 0.15 0.00
19_K 164_E 0.94 0.15 0.00
35_L 132_G 0.94 0.15 0.00
30_S 82_E 0.93 0.15 0.00
87_E 142_S 0.93 0.15 0.00
12_F 36_E 0.93 0.15 0.00
33_P 223_K 0.93 0.15 0.00
156_L 191_S 0.93 0.15 0.00
44_L 85_V 0.92 0.15 0.00
25_M 154_I 0.92 0.14 0.00
16_D 182_N 0.92 0.14 0.00
101_T 143_Q 0.92 0.14 0.00
135_F 217_M 0.92 0.14 0.00
126_Y 148_I 0.92 0.14 0.00
131_R 39_F 0.91 0.14 0.00
90_S 233_V 0.91 0.14 0.00
44_L 11_A 0.90 0.14 0.00
73_V 247_L 0.90 0.14 0.00
116_D 131_A 0.90 0.14 0.00
143_A 95_T 0.90 0.14 0.00
19_K 100_E 0.89 0.14 0.00
42_G 168_E 0.89 0.14 0.00
21_F 96_D 0.89 0.14 0.00
153_A 47_L 0.89 0.14 0.00
155_N 130_R 0.89 0.14 0.00
140_K 88_Y 0.89 0.14 0.00
15_W 107_P 0.88 0.13 0.00
24_G 232_F 0.88 0.13 0.00
24_G 74_D 0.88 0.13 0.00
140_K 223_K 0.88 0.13 0.00
127_A 201_T 0.87 0.13 0.00
10_K 11_A 0.87 0.13 0.00
151_E 228_K 0.87 0.13 0.00
6_A 184_I 0.87 0.13 0.00
20_G 25_A 0.87 0.13 0.00
5_F 45_H 0.87 0.13 0.00
44_L 247_L 0.87 0.13 0.00
9_T 164_E 0.87 0.13 0.00
155_N 166_K 0.86 0.13 0.00
44_L 154_I 0.86 0.13 0.00
154_R 236_I 0.86 0.12 0.00
82_D 140_G 0.86 0.12 0.00
33_P 27_H 0.85 0.12 0.00
32_K 40_G 0.85 0.12 0.00
108_F 237_F 0.85 0.12 0.00
24_G 126_M 0.85 0.12 0.00
28_F 254_Q 0.85 0.12 0.00
10_K 59_S 0.85 0.12 0.00
143_A 250_K 0.84 0.12 0.00
108_F 173_L 0.84 0.12 0.00
10_K 56_E 0.84 0.12 0.00
24_G 77_G 0.84 0.12 0.00
94_T 142_S 0.84 0.12 0.00
135_F 228_K 0.84 0.12 0.00
77_Q 32_S 0.83 0.12 0.00
156_L 98_E 0.83 0.12 0.00
90_S 156_A 0.83 0.12 0.00
18_I 108_T 0.83 0.12 0.00
139_Q 152_E 0.83 0.12 0.00
24_G 78_P 0.83 0.12 0.00
45_S 200_G 0.82 0.11 0.00
147_R 64_L 0.82 0.11 0.00
23_L 238_L 0.82 0.11 0.00
156_L 202_P 0.82 0.11 0.00
98_I 165_E 0.82 0.11 0.00
85_R 237_F 0.82 0.11 0.00
17_F 224_M 0.82 0.11 0.00
30_S 86_R 0.82 0.11 0.00
28_F 163_G 0.82 0.11 0.00
155_N 77_G 0.82 0.11 0.00
12_F 191_S 0.82 0.11 0.00
23_L 214_A 0.82 0.11 0.00
39_H 59_S 0.82 0.11 0.00
140_K 93_D 0.81 0.11 0.00
24_G 142_S 0.81 0.11 0.00
154_R 154_I 0.81 0.11 0.00
42_G 187_A 0.81 0.11 0.00
156_L 192_D 0.81 0.11 0.00
35_L 151_P 0.81 0.11 0.00
5_F 232_F 0.80 0.11 0.00
152_I 85_V 0.80 0.11 0.00
26_R 90_A 0.80 0.11 0.00
159_D 214_A 0.80 0.11 0.00
101_T 134_H 0.80 0.11 0.00
151_E 181_G 0.80 0.11 0.00
20_G 143_Q 0.80 0.11 0.00
35_L 91_N 0.79 0.11 0.00
42_G 5_T 0.79 0.11 0.00
35_L 26_A 0.79 0.10 0.00
31_P 253_W 0.79 0.10 0.00
25_M 173_L 0.79 0.10 0.00
157_Q 52_Q 0.79 0.10 0.00
84_E 36_E 0.79 0.10 0.00
73_V 48_Q 0.79 0.10 0.00
58_P 152_E 0.79 0.10 0.00
25_M 141_L 0.79 0.10 0.00
126_Y 52_Q 0.79 0.10 0.00
85_R 46_Q 0.79 0.10 0.00
137_D 38_P 0.79 0.10 0.00
73_V 229_Q 0.78 0.10 0.00
85_R 47_L 0.78 0.10 0.00
140_K 193_D 0.78 0.10 0.00
41_K 199_D 0.78 0.10 0.00
137_D 213_A 0.77 0.10 0.00
143_A 137_Y 0.77 0.10 0.00
95_R 47_L 0.77 0.10 0.00
18_I 12_P 0.77 0.10 0.00
73_V 92_F 0.77 0.10 0.00
147_R 105_R 0.77 0.10 0.00
127_A 85_V 0.77 0.10 0.00
137_D 194_Q 0.77 0.10 0.00
13_L 99_T 0.77 0.10 0.00
82_D 234_S 0.77 0.10 0.00
124_F 242_A 0.77 0.10 0.00
12_F 33_F 0.76 0.10 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
3057 0.35 cI_I_60_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3056 1.02 cI_I_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3055 0.36 cI_I_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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