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OPENSEQ.org
cI_J_cIII_cyt1_10_Pdenitr
Genes: A B A+B
Length: 200 263 445
Sequences: 2148 954 290
Seq/Len: 10.74 3.63 0.65
MirrorTree (Pazo et al. 2001) 0.48
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 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.05
∞ 0.03 0.01 0.63
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
176_N 241_L 1.44 0.59 0.00
99_V 157_V 1.43 0.59 0.00
135_L 96_D 1.29 0.47 0.00
53_A 157_V 1.27 0.46 0.00
23_G 250_K 1.26 0.45 0.00
108_F 101_E 1.22 0.42 0.00
135_L 84_Q 1.21 0.41 0.00
169_R 80_L 1.18 0.39 0.00
197_G 136_P 1.17 0.38 0.00
159_I 201_T 1.16 0.37 0.00
132_T 105_R 1.16 0.37 0.00
188_T 27_H 1.16 0.36 0.00
193_D 96_D 1.14 0.35 0.00
17_G 100_E 1.14 0.35 0.00
98_V 232_F 1.09 0.32 0.00
22_I 254_Q 1.07 0.31 0.00
16_A 191_S 1.07 0.30 0.00
150_A 206_D 1.07 0.30 0.00
153_V 44_Q 1.07 0.30 0.00
41_A 46_Q 1.06 0.30 0.00
87_A 154_I 1.05 0.29 0.00
93_A 215_F 1.05 0.29 0.00
144_V 241_L 1.04 0.28 0.00
148_Q 33_F 1.03 0.28 0.00
108_F 88_Y 1.03 0.27 0.00
127_A 125_L 1.03 0.27 0.00
115_D 243_A 1.01 0.26 0.00
162_I 224_M 0.99 0.25 0.00
16_A 236_I 0.98 0.24 0.00
166_M 104_P 0.98 0.24 0.00
48_G 49_R 0.97 0.24 0.00
110_G 90_A 0.97 0.24 0.00
21_V 55_T 0.97 0.24 0.00
139_L 240_V 0.97 0.24 0.00
159_I 87_A 0.96 0.23 0.00
45_V 81_P 0.96 0.23 0.00
52_V 143_Q 0.96 0.23 0.00
36_A 151_P 0.95 0.23 0.00
174_R 96_D 0.95 0.23 0.00
23_G 218_W 0.95 0.23 0.00
136_G 220_A 0.95 0.22 0.00
86_L 255_P 0.95 0.22 0.00
10_A 158_L 0.95 0.22 0.00
189_M 220_A 0.95 0.22 0.00
102_A 232_F 0.94 0.22 0.00
58_V 154_I 0.94 0.22 0.00
86_L 230_V 0.94 0.22 0.00
42_G 76_G 0.94 0.22 0.00
42_G 41_K 0.93 0.21 0.00
126_D 81_P 0.92 0.21 0.00
41_A 135_G 0.92 0.21 0.00
23_G 72_L 0.92 0.21 0.00
20_V 219_T 0.92 0.21 0.00
171_D 229_Q 0.92 0.21 0.00
147_F 136_P 0.91 0.20 0.00
18_F 206_D 0.91 0.20 0.00
198_Q 63_G 0.91 0.20 0.00
192_K 165_E 0.91 0.20 0.00
97_G 72_L 0.91 0.20 0.00
98_V 91_N 0.91 0.20 0.00
103_Q 88_Y 0.90 0.20 0.00
103_Q 212_V 0.90 0.20 0.00
195_K 216_L 0.90 0.20 0.00
151_G 241_L 0.90 0.20 0.00
79_F 214_A 0.90 0.20 0.00
104_L 246_Y 0.90 0.20 0.00
191_L 100_E 0.89 0.20 0.00
77_V 78_P 0.89 0.20 0.00
152_L 161_Y 0.89 0.19 0.00
191_L 237_F 0.89 0.19 0.00
135_L 149_G 0.89 0.19 0.00
149_L 256_I 0.88 0.19 0.00
54_M 42_F 0.88 0.19 0.00
167_R 253_W 0.88 0.19 0.00
21_V 224_M 0.88 0.18 0.00
146_M 164_E 0.87 0.18 0.00
98_V 246_Y 0.87 0.18 0.00
45_V 249_N 0.87 0.18 0.00
103_Q 93_D 0.87 0.18 0.00
58_V 139_T 0.87 0.18 0.00
169_R 232_F 0.87 0.18 0.00
175_Q 109_D 0.87 0.18 0.00
171_D 67_V 0.86 0.18 0.00
133_L 167_E 0.85 0.18 0.00
186_A 214_A 0.85 0.17 0.00
149_L 143_Q 0.85 0.17 0.00
30_V 88_Y 0.85 0.17 0.00
173_K 127_A 0.85 0.17 0.00
123_A 94_I 0.85 0.17 0.00
148_Q 135_G 0.85 0.17 0.00
158_M 244_L 0.85 0.17 0.00
169_R 69_L 0.85 0.17 0.00
11_I 90_A 0.84 0.17 0.00
30_V 178_A 0.84 0.17 0.00
105_G 240_V 0.84 0.17 0.00
14_C 121_P 0.84 0.17 0.00
137_L 254_Q 0.84 0.17 0.00
89_Y 220_A 0.84 0.17 0.00
151_G 219_T 0.83 0.17 0.00
102_A 63_G 0.83 0.17 0.00
150_A 255_P 0.83 0.17 0.00
12_S 111_F 0.83 0.17 0.00
22_I 93_D 0.83 0.17 0.00
107_A 219_T 0.83 0.16 0.00
79_F 213_A 0.83 0.16 0.00
48_G 213_A 0.83 0.16 0.00
82_L 67_V 0.83 0.16 0.00
54_M 215_F 0.82 0.16 0.00
142_R 131_A 0.82 0.16 0.00
84_G 130_R 0.82 0.16 0.00
170_K 108_T 0.82 0.16 0.00
147_F 103_R 0.82 0.16 0.00
14_C 133_F 0.82 0.16 0.00
80_A 214_A 0.82 0.16 0.00
175_Q 199_D 0.82 0.16 0.00
90_L 215_F 0.82 0.16 0.00
159_I 188_A 0.82 0.16 0.00
10_A 67_V 0.81 0.16 0.00
185_P 49_R 0.81 0.16 0.00
41_A 49_R 0.81 0.16 0.00
100_L 173_L 0.81 0.15 0.00
21_V 30_D 0.81 0.15 0.00
150_A 112_P 0.81 0.15 0.00
145_L 243_A 0.80 0.15 0.00
132_T 237_F 0.80 0.15 0.00
40_A 60_A 0.80 0.15 0.00
30_V 136_P 0.80 0.15 0.00
171_D 74_D 0.80 0.15 0.00
36_A 210_T 0.80 0.15 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
2924 0.44 cI_J_10_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.49 Done - Shared
2923 0.33 cI_J_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2922 0.65 cI_J_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2921 0.41 cI_J_40_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
2920 0.44 cI_J_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
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