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OPENSEQ.org
cIII_isp_4_cytc1_4_pd
Genes: A B A+B
Length: 190 263 431
Sequences: 1692 973 708
Seq/Len: 8.91 3.7 1.64
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 1.47
5 0.01 0.01 1.48
10 0.01 0.01 1.48
20 0.01 0.01 1.48
100 0.01 0.01 1.49
∞ 0.05 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 1.74 0.95 0.73
55_Q 86_R 1.37 0.81 0.43
19_L 248_T 1.17 0.64 0.25
20_Y 248_T 1.14 0.61 0.23
29_V 82_E 1.08 0.55 0.19
180_E 137_Y 1.06 0.53 0.18
24_A 244_L 1.04 0.51 0.17
138_V 131_A 1.03 0.50 0.16
35_A 60_A 1.01 0.48 0.15
21_Y 240_V 1.01 0.47 0.15
52_A 108_T 1.00 0.46 0.14
33_A 235_V 0.99 0.46 0.14
27_G 248_T 0.99 0.46 0.14
153_P 140_G 0.99 0.45 0.14
54_I 54_Y 0.98 0.44 0.13
42_M 67_V 0.97 0.43 0.13
189_L 120_G 0.95 0.41 0.12
33_A 227_R 0.94 0.40 0.11
15_R 247_L 0.94 0.40 0.11
181_F 238_L 0.94 0.40 0.11
125_W 220_A 0.93 0.39 0.11
28_T 24_A 0.93 0.39 0.11
72_L 232_F 0.93 0.39 0.11
94_L 156_A 0.93 0.39 0.11
59_S 48_Q 0.92 0.38 0.10
74_K 250_K 0.92 0.38 0.10
23_T 248_T 0.91 0.38 0.10
26_A 244_L 0.91 0.38 0.10
48_V 173_L 0.90 0.36 0.10
141_G 218_W 0.90 0.36 0.10
82_T 109_D 0.90 0.36 0.10
45_S 173_L 0.90 0.36 0.09
44_P 48_Q 0.89 0.36 0.09
25_G 135_G 0.89 0.35 0.09
187_I 94_I 0.88 0.34 0.09
72_L 47_L 0.87 0.34 0.09
74_K 242_A 0.87 0.33 0.08
86_I 54_Y 0.85 0.32 0.08
17_D 218_W 0.85 0.32 0.08
168_G 227_R 0.85 0.31 0.08
29_V 254_Q 0.84 0.31 0.07
18_F 108_T 0.84 0.31 0.07
168_G 209_A 0.83 0.30 0.07
187_I 225_M 0.83 0.30 0.07
168_G 49_R 0.83 0.30 0.07
58_V 180_A 0.83 0.30 0.07
94_L 16_A 0.83 0.30 0.07
68_T 154_I 0.82 0.29 0.07
66_Q 129_A 0.81 0.28 0.07
180_E 85_V 0.81 0.28 0.06
49_Q 118_G 0.81 0.28 0.06
172_Q 216_L 0.81 0.28 0.06
39_V 243_A 0.80 0.27 0.06
167_R 229_Q 0.80 0.27 0.06
131_V 247_L 0.80 0.27 0.06
52_A 206_D 0.80 0.27 0.06
45_S 147_G 0.79 0.27 0.06
181_F 221_E 0.79 0.27 0.06
130_G 221_E 0.79 0.27 0.06
145_G 186_M 0.79 0.26 0.06
187_I 52_Q 0.79 0.26 0.06
27_G 75_E 0.79 0.26 0.06
144_A 240_V 0.78 0.26 0.06
79_R 163_G 0.78 0.26 0.06
188_K 163_G 0.78 0.26 0.06
148_G 22_S 0.78 0.26 0.06
78_I 239_I 0.78 0.26 0.06
49_Q 74_D 0.77 0.25 0.06
186_T 95_T 0.77 0.25 0.05
72_L 220_A 0.77 0.24 0.05
79_R 104_P 0.77 0.24 0.05
30_A 237_F 0.76 0.24 0.05
138_V 94_I 0.76 0.24 0.05
42_M 60_A 0.76 0.24 0.05
82_T 103_R 0.76 0.24 0.05
85_E 70_R 0.75 0.23 0.05
36_W 220_A 0.75 0.23 0.05
13_A 252_L 0.74 0.23 0.05
25_G 66_Y 0.74 0.23 0.05
56_V 227_R 0.74 0.23 0.05
62_E 151_P 0.74 0.23 0.05
65_T 245_L 0.74 0.23 0.05
22_A 77_G 0.74 0.23 0.05
30_A 240_V 0.74 0.22 0.05
126_L 216_L 0.73 0.22 0.04
57_D 74_D 0.73 0.22 0.04
29_V 235_V 0.73 0.22 0.04
39_V 41_K 0.73 0.22 0.04
46_A 70_R 0.73 0.22 0.04
42_M 208_M 0.73 0.22 0.04
130_G 54_Y 0.73 0.22 0.04
48_V 64_L 0.73 0.21 0.04
57_D 72_L 0.73 0.21 0.04
175_H 241_L 0.72 0.21 0.04
24_A 251_K 0.72 0.21 0.04
8_A 230_V 0.72 0.21 0.04
76_V 156_A 0.72 0.21 0.04
78_I 95_T 0.72 0.21 0.04
110_A 249_N 0.71 0.21 0.04
56_V 186_M 0.71 0.20 0.04
27_G 29_E 0.71 0.20 0.04
95_G 59_S 0.71 0.20 0.04
129_I 241_L 0.71 0.20 0.04
140_I 64_L 0.71 0.20 0.04
78_I 236_I 0.70 0.20 0.04
77_F 131_A 0.70 0.20 0.04
42_M 194_Q 0.70 0.20 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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