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OPENSEQ.org
cIII_isp_20_cytc1_20_pd
Genes: A B A+B
Length: 190 263 436
Sequences: 1043 651 410
Seq/Len: 5.49 2.48 0.94
MirrorTree (Pazo et al. 2001) 0.85
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 0.01 0.02 0.08
2 0.01 0.02 0.82
5 0.01 0.02 0.82
10 0.01 0.02 0.82
20 0.01 0.02 0.83
100 0.01 0.02 0.84
∞ 0.02 0.02 0.91
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
138_V 94_I 1.43 0.70 0.01
19_L 248_T 1.41 0.69 0.01
45_S 147_G 1.40 0.68 0.00
23_T 248_T 1.40 0.67 0.00
20_Y 248_T 1.34 0.63 0.00
55_Q 86_R 1.31 0.60 0.00
52_A 108_T 1.23 0.53 0.00
176_I 219_T 1.22 0.52 0.00
124_E 196_T 1.20 0.50 0.00
95_G 59_S 1.18 0.48 0.00
67_L 232_F 1.17 0.48 0.00
85_E 161_Y 1.16 0.47 0.00
47_D 147_G 1.16 0.46 0.00
96_Q 28_I 1.15 0.46 0.00
54_I 54_Y 1.15 0.46 0.00
28_T 24_A 1.12 0.43 0.00
94_L 156_A 1.11 0.42 0.00
117_R 109_D 1.09 0.41 0.00
81_R 135_G 1.08 0.39 0.00
72_L 232_F 1.07 0.38 0.00
40_N 105_R 1.06 0.38 0.00
178_V 8_G 1.04 0.36 0.00
80_R 14_G 1.03 0.35 0.00
148_G 22_S 1.02 0.34 0.00
45_S 208_M 1.00 0.33 0.00
69_V 230_V 1.00 0.33 0.00
74_K 131_A 0.99 0.32 0.00
125_W 220_A 0.99 0.32 0.00
158_H 187_A 0.98 0.31 0.00
44_P 48_Q 0.97 0.31 0.00
23_T 244_L 0.97 0.31 0.00
35_A 60_A 0.97 0.30 0.00
32_G 237_F 0.95 0.29 0.00
185_T 219_T 0.95 0.29 0.00
27_G 248_T 0.94 0.28 0.00
29_V 82_E 0.92 0.26 0.00
33_A 235_V 0.92 0.26 0.00
78_I 7_P 0.90 0.26 0.00
85_E 187_A 0.90 0.25 0.00
131_V 257_K 0.90 0.25 0.00
187_I 73_A 0.89 0.24 0.00
92_V 87_A 0.88 0.24 0.00
185_T 196_T 0.88 0.24 0.00
142_D 75_E 0.87 0.23 0.00
185_T 236_I 0.87 0.23 0.00
76_V 156_A 0.87 0.23 0.00
94_L 16_A 0.87 0.23 0.00
19_L 249_N 0.87 0.23 0.00
51_L 108_T 0.87 0.23 0.00
180_E 64_L 0.86 0.23 0.00
68_T 105_R 0.86 0.22 0.00
162_S 75_E 0.86 0.22 0.00
84_D 216_L 0.85 0.22 0.00
29_V 52_Q 0.85 0.22 0.00
13_A 252_L 0.85 0.22 0.00
55_Q 234_S 0.84 0.21 0.00
25_G 145_F 0.84 0.21 0.00
148_G 71_T 0.84 0.21 0.00
168_G 181_G 0.84 0.21 0.00
112_A 67_V 0.84 0.21 0.00
129_I 134_H 0.82 0.20 0.00
117_R 153_Y 0.82 0.20 0.00
94_L 17_Q 0.82 0.20 0.00
84_D 195_V 0.82 0.20 0.00
78_I 107_P 0.82 0.20 0.00
58_V 126_M 0.82 0.20 0.00
183_D 234_S 0.82 0.20 0.00
78_I 159_T 0.82 0.20 0.00
61_V 73_A 0.82 0.20 0.00
12_G 187_A 0.82 0.20 0.00
150_W 135_G 0.81 0.20 0.00
54_I 29_E 0.81 0.20 0.00
103_Q 142_S 0.81 0.20 0.00
129_I 241_L 0.81 0.20 0.00
130_G 221_E 0.81 0.20 0.00
101_S 207_Q 0.81 0.19 0.00
44_P 237_F 0.80 0.19 0.00
95_G 8_G 0.80 0.19 0.00
93_D 213_A 0.80 0.19 0.00
188_K 64_L 0.80 0.19 0.00
67_L 235_V 0.80 0.19 0.00
182_L 250_K 0.80 0.19 0.00
97_L 195_V 0.80 0.19 0.00
48_V 179_F 0.79 0.19 0.00
30_A 143_Q 0.79 0.18 0.00
165_I 43_D 0.79 0.18 0.00
184_D 144_L 0.79 0.18 0.00
22_A 253_W 0.79 0.18 0.00
103_Q 81_P 0.79 0.18 0.00
47_D 208_M 0.79 0.18 0.00
31_A 169_A 0.79 0.18 0.00
187_I 240_V 0.79 0.18 0.00
29_V 254_Q 0.79 0.18 0.00
142_D 23_H 0.78 0.18 0.00
176_I 173_L 0.78 0.18 0.00
53_S 106_V 0.78 0.18 0.00
55_Q 206_D 0.78 0.18 0.00
180_E 144_L 0.78 0.18 0.00
35_A 155_H 0.78 0.18 0.00
175_H 132_G 0.78 0.18 0.00
75_P 199_D 0.78 0.18 0.00
91_E 219_T 0.78 0.18 0.00
60_G 182_N 0.78 0.18 0.00
187_I 164_E 0.78 0.18 0.00
127_V 124_S 0.77 0.17 0.00
122_A 224_M 0.77 0.17 0.00
52_A 97_P 0.77 0.17 0.00
45_S 88_Y 0.77 0.17 0.00
16_R 244_L 0.77 0.17 0.00
24_A 251_K 0.76 0.17 0.00
58_V 155_H 0.76 0.17 0.00
58_V 156_A 0.76 0.17 0.00
19_L 166_K 0.76 0.17 0.00
27_G 29_E 0.76 0.17 0.00
38_L 249_N 0.76 0.17 0.00
67_L 73_A 0.76 0.17 0.00
95_G 10_T 0.76 0.17 0.00
178_V 71_T 0.76 0.17 0.00
41_Q 223_K 0.76 0.17 0.00
130_G 54_Y 0.76 0.17 0.00
159_Y 70_R 0.76 0.17 0.00
33_A 164_E 0.75 0.17 0.00
75_P 201_T 0.75 0.17 0.00
91_E 54_Y 0.75 0.16 0.00
122_A 221_E 0.75 0.16 0.00
167_R 106_V 0.75 0.16 0.00
130_G 131_A 0.75 0.16 0.00
166_R 70_R 0.75 0.16 0.00
98_I 235_V 0.75 0.16 0.00
178_V 252_L 0.75 0.16 0.00
77_F 85_V 0.75 0.16 0.00
109_D 57_V 0.75 0.16 0.00
22_A 244_L 0.74 0.16 0.00
127_V 21_D 0.74 0.16 0.00
181_F 63_G 0.74 0.16 0.00
150_W 181_G 0.74 0.16 0.00
149_G 222_P 0.74 0.16 0.00
123_G 46_Q 0.74 0.16 0.00
85_E 152_E 0.74 0.16 0.00
48_V 208_M 0.73 0.16 0.00
26_A 86_R 0.73 0.16 0.00
92_V 242_A 0.73 0.15 0.00
28_T 32_S 0.73 0.15 0.00
187_I 60_A 0.73 0.15 0.00
176_I 177_A 0.73 0.15 0.00
48_V 235_V 0.73 0.15 0.00
74_K 250_K 0.73 0.15 0.00
18_F 246_Y 0.73 0.15 0.00
38_L 108_T 0.73 0.15 0.00
58_V 247_L 0.73 0.15 0.00
117_R 186_M 0.72 0.15 0.00
27_G 194_Q 0.72 0.15 0.00
131_V 201_T 0.72 0.15 0.00
126_L 141_L 0.72 0.15 0.00
131_V 221_E 0.72 0.15 0.00
20_Y 251_K 0.72 0.15 0.00
114_D 135_G 0.72 0.15 0.00
115_E 20_G 0.72 0.15 0.00
32_G 71_T 0.72 0.15 0.00
122_A 196_T 0.72 0.15 0.00
81_R 35_F 0.72 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
5177 1.63 cIII_isp_4_cytc1_10_pd Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.52 Done - Shared
5176 1.66 cIII_isp_2_cytc1_6_pd Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.63 Done - Shared
5175 1.65 cIII_isp_6_cytc1_6_pd Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.71 Done - Shared
5174 1.66 cIII_isp_4_cytc1_6_pd Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.74 Done - Shared
5173 1.64 cIII_isp_4_cytc1_4_pd Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.73 Done - Shared
5169 0.94 cIII_isp_20_cytc1_20_pd Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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