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OPENSEQ.org
cIII_isp_6_cytc1_6_pd
Genes: A B A+B
Length: 190 263 430
Sequences: 1587 962 708
Seq/Len: 8.35 3.66 1.65
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 0.01 0.13
2 0.01 0.01 1.46
5 0.01 0.01 1.47
10 0.01 0.01 1.47
20 0.01 0.01 1.47
100 0.01 0.01 1.48
∞ 0.04 0.01 1.56
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 1.72 0.95 0.71
55_Q 86_R 1.33 0.78 0.39
189_L 120_G 1.23 0.70 0.30
20_Y 248_T 1.18 0.66 0.26
52_A 108_T 1.18 0.65 0.26
180_E 137_Y 1.14 0.62 0.23
19_L 248_T 1.14 0.61 0.23
94_L 16_A 1.11 0.58 0.21
35_A 60_A 1.09 0.56 0.19
24_A 244_L 1.06 0.53 0.17
33_A 235_V 1.04 0.52 0.16
187_I 225_M 1.04 0.51 0.16
54_I 54_Y 1.03 0.49 0.15
153_P 140_G 1.02 0.48 0.15
29_V 82_E 1.01 0.48 0.15
27_G 248_T 1.00 0.47 0.14
181_F 238_L 0.99 0.46 0.13
26_A 244_L 0.99 0.46 0.13
33_A 227_R 0.99 0.46 0.13
21_Y 240_V 0.97 0.43 0.12
42_M 67_V 0.96 0.42 0.12
189_L 182_N 0.95 0.41 0.11
125_W 220_A 0.94 0.41 0.11
15_R 247_L 0.93 0.40 0.11
72_L 47_L 0.93 0.40 0.11
74_K 242_A 0.93 0.39 0.10
23_T 248_T 0.92 0.39 0.10
94_L 156_A 0.92 0.38 0.10
167_R 229_Q 0.92 0.38 0.10
141_G 49_R 0.92 0.38 0.10
168_G 227_R 0.90 0.36 0.09
168_G 49_R 0.89 0.36 0.09
74_K 250_K 0.89 0.36 0.09
168_G 209_A 0.89 0.36 0.09
45_S 173_L 0.89 0.35 0.09
48_V 173_L 0.88 0.35 0.09
28_T 24_A 0.88 0.35 0.09
142_D 64_L 0.88 0.34 0.08
58_V 180_A 0.86 0.33 0.08
59_S 48_Q 0.86 0.32 0.08
8_A 230_V 0.85 0.32 0.08
39_V 243_A 0.85 0.32 0.07
72_L 232_F 0.85 0.32 0.07
44_P 48_Q 0.84 0.31 0.07
29_V 254_Q 0.84 0.31 0.07
114_D 240_V 0.84 0.30 0.07
70_K 98_E 0.83 0.30 0.07
94_L 17_Q 0.83 0.30 0.07
30_A 240_V 0.82 0.29 0.07
185_T 188_A 0.81 0.28 0.06
145_G 212_V 0.81 0.28 0.06
185_T 236_I 0.81 0.28 0.06
49_Q 118_G 0.81 0.28 0.06
65_T 245_L 0.80 0.28 0.06
129_I 67_V 0.80 0.27 0.06
72_L 220_A 0.80 0.27 0.06
126_L 216_L 0.80 0.27 0.06
62_E 151_P 0.80 0.27 0.06
66_Q 129_A 0.80 0.27 0.06
76_V 213_A 0.79 0.27 0.06
78_I 239_I 0.79 0.27 0.06
76_V 156_A 0.79 0.27 0.06
29_V 235_V 0.79 0.27 0.06
126_L 228_K 0.79 0.27 0.06
57_D 74_D 0.79 0.26 0.06
49_Q 74_D 0.79 0.26 0.06
13_A 135_G 0.79 0.26 0.06
175_H 135_G 0.78 0.26 0.06
79_R 104_P 0.78 0.26 0.06
17_D 218_W 0.78 0.26 0.06
24_A 251_K 0.78 0.26 0.06
56_V 227_R 0.78 0.26 0.06
129_I 241_L 0.78 0.26 0.06
42_M 60_A 0.78 0.26 0.06
181_F 221_E 0.78 0.26 0.06
68_T 154_I 0.78 0.26 0.05
94_L 18_E 0.78 0.25 0.05
162_S 223_K 0.78 0.25 0.05
138_V 131_A 0.78 0.25 0.05
36_W 220_A 0.77 0.25 0.05
172_Q 216_L 0.77 0.25 0.05
143_G 39_F 0.77 0.25 0.05
57_D 201_T 0.77 0.24 0.05
9_G 196_T 0.77 0.24 0.05
130_G 221_E 0.76 0.24 0.05
96_Q 28_I 0.76 0.24 0.05
85_E 43_D 0.76 0.24 0.05
145_G 67_V 0.76 0.24 0.05
20_Y 252_L 0.76 0.24 0.05
86_I 54_Y 0.76 0.24 0.05
85_E 70_R 0.76 0.24 0.05
45_S 147_G 0.76 0.24 0.05
168_G 181_G 0.76 0.24 0.05
30_A 229_Q 0.76 0.24 0.05
27_G 75_E 0.76 0.24 0.05
18_F 108_T 0.76 0.24 0.05
52_A 206_D 0.75 0.23 0.05
172_Q 46_Q 0.75 0.23 0.05
82_T 103_R 0.75 0.23 0.05
187_I 108_T 0.75 0.23 0.05
57_D 72_L 0.75 0.23 0.05
42_M 208_M 0.75 0.23 0.05
27_G 194_Q 0.74 0.23 0.05
46_A 70_R 0.74 0.23 0.04
162_S 182_N 0.74 0.23 0.04
141_G 135_G 0.74 0.23 0.04
175_H 241_L 0.74 0.22 0.04
118_T 129_A 0.74 0.22 0.04
18_F 132_G 0.73 0.22 0.04
94_L 15_A 0.72 0.21 0.04
42_M 81_P 0.72 0.21 0.04
188_K 163_G 0.72 0.21 0.04
180_E 85_V 0.72 0.21 0.04
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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