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OPENSEQ.org
cIII_isp_4_cytc1_10_pd
Genes: A B A+B
Length: 190 263 431
Sequences: 1692 954 704
Seq/Len: 8.91 3.63 1.63
MirrorTree (Pazo et al. 2001) 0.86
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 0.12
2 0.00 0.01 1.45
5 0.01 0.01 1.46
10 0.01 0.01 1.46
20 0.01 0.01 1.46
100 0.01 0.01 1.47
∞ 0.05 0.01 1.55
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
23_T 244_L 1.62 0.92 0.52
55_Q 86_R 1.33 0.78 0.28
20_Y 248_T 1.18 0.65 0.18
19_L 248_T 1.17 0.64 0.18
180_E 137_Y 1.08 0.55 0.13
35_A 60_A 1.07 0.54 0.13
33_A 235_V 1.07 0.54 0.12
24_A 244_L 1.06 0.53 0.12
187_I 89_A 1.05 0.52 0.12
94_L 156_A 1.04 0.51 0.12
180_E 85_V 1.03 0.50 0.11
52_A 108_T 1.03 0.50 0.11
153_P 140_G 1.01 0.48 0.10
54_I 54_Y 1.01 0.47 0.10
21_Y 240_V 1.00 0.47 0.10
33_A 227_R 0.99 0.45 0.09
74_K 242_A 0.99 0.45 0.09
138_V 131_A 0.98 0.44 0.09
23_T 248_T 0.97 0.43 0.09
181_F 238_L 0.96 0.43 0.09
42_M 67_V 0.96 0.42 0.08
29_V 82_E 0.96 0.42 0.08
27_G 248_T 0.95 0.41 0.08
15_R 247_L 0.95 0.41 0.08
125_W 220_A 0.94 0.40 0.08
72_L 232_F 0.94 0.40 0.08
66_Q 129_A 0.94 0.40 0.08
141_G 218_W 0.91 0.37 0.07
168_G 49_R 0.90 0.36 0.07
49_Q 74_D 0.89 0.35 0.06
74_K 250_K 0.89 0.35 0.06
80_R 107_P 0.88 0.35 0.06
58_V 93_D 0.88 0.34 0.06
45_S 173_L 0.88 0.34 0.06
62_E 151_P 0.88 0.34 0.06
187_I 225_M 0.88 0.34 0.06
187_I 52_Q 0.85 0.32 0.05
138_V 94_I 0.85 0.32 0.05
168_G 227_R 0.85 0.32 0.05
28_T 24_A 0.85 0.31 0.05
129_I 241_L 0.84 0.31 0.05
48_V 173_L 0.84 0.31 0.05
59_S 48_Q 0.84 0.31 0.05
94_L 16_A 0.84 0.30 0.05
189_L 120_G 0.84 0.30 0.05
168_G 209_A 0.83 0.30 0.05
17_D 218_W 0.83 0.30 0.05
110_A 249_N 0.82 0.29 0.05
44_P 48_Q 0.82 0.29 0.05
56_V 227_R 0.81 0.28 0.04
26_A 244_L 0.81 0.28 0.04
144_A 240_V 0.80 0.27 0.04
140_I 64_L 0.80 0.27 0.04
85_E 70_R 0.79 0.26 0.04
85_E 43_D 0.79 0.26 0.04
45_S 147_G 0.78 0.26 0.04
72_L 47_L 0.78 0.26 0.04
96_Q 28_I 0.78 0.26 0.04
95_G 59_S 0.78 0.26 0.04
149_G 222_P 0.78 0.25 0.04
168_G 109_D 0.78 0.25 0.04
78_I 239_I 0.77 0.25 0.04
39_V 104_P 0.77 0.25 0.04
27_G 75_E 0.77 0.25 0.04
76_V 213_A 0.77 0.25 0.04
69_V 230_V 0.77 0.24 0.04
30_A 237_F 0.77 0.24 0.04
38_L 130_R 0.76 0.24 0.04
148_G 22_S 0.76 0.24 0.04
29_V 254_Q 0.76 0.24 0.04
57_D 72_L 0.76 0.23 0.04
82_T 105_R 0.75 0.23 0.03
65_T 245_L 0.75 0.23 0.03
114_D 96_D 0.75 0.23 0.03
42_M 60_A 0.75 0.23 0.03
68_T 154_I 0.75 0.23 0.03
85_E 103_R 0.75 0.23 0.03
85_E 161_Y 0.75 0.23 0.03
126_L 216_L 0.75 0.23 0.03
39_V 187_A 0.74 0.23 0.03
150_W 93_D 0.74 0.23 0.03
46_A 70_R 0.74 0.22 0.03
183_D 90_A 0.74 0.22 0.03
43_N 100_E 0.74 0.22 0.03
76_V 156_A 0.74 0.22 0.03
29_V 220_A 0.74 0.22 0.03
69_V 235_V 0.73 0.22 0.03
42_M 208_M 0.73 0.22 0.03
29_V 235_V 0.73 0.22 0.03
172_Q 216_L 0.73 0.21 0.03
185_T 236_I 0.73 0.21 0.03
52_A 206_D 0.73 0.21 0.03
143_G 44_Q 0.73 0.21 0.03
57_D 201_T 0.73 0.21 0.03
13_A 252_L 0.72 0.21 0.03
181_F 221_E 0.72 0.21 0.03
30_A 240_V 0.72 0.21 0.03
39_V 41_K 0.72 0.21 0.03
60_G 111_F 0.72 0.21 0.03
67_L 232_F 0.72 0.21 0.03
29_V 246_Y 0.72 0.21 0.03
60_G 165_E 0.72 0.21 0.03
58_V 125_L 0.72 0.21 0.03
188_K 163_G 0.72 0.21 0.03
86_I 54_Y 0.72 0.21 0.03
38_L 95_T 0.72 0.21 0.03
148_G 71_T 0.72 0.21 0.03
174_L 130_R 0.71 0.21 0.03
168_G 231_G 0.71 0.20 0.03
84_D 116_G 0.71 0.20 0.03
72_L 220_A 0.71 0.20 0.03
126_L 109_D 0.71 0.20 0.03
22_A 239_I 0.71 0.20 0.03
151_F 218_W 0.71 0.20 0.03
79_R 163_G 0.71 0.20 0.03
103_Q 81_P 0.71 0.20 0.03
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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