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cIII_isp_2_cytc1_6_pd

Genes: A B A+B
Length: 190 263 430
Sequences: 1785 962 715
Seq/Len: 9.39 3.66 1.66
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 1.48
5 0.01 0.01 1.49
10 0.01 0.01 1.49
20 0.01 0.01 1.49
100 0.02 0.01 1.50
0.05 0.01 1.58
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 1.67 0.94 0.63
55_Q 86_R 1.24 0.71 0.27
112_A 241_L 1.18 0.66 0.23
20_Y 248_T 1.14 0.62 0.20
19_L 248_T 1.12 0.60 0.19
33_A 235_V 1.09 0.56 0.17
180_E 137_Y 1.08 0.56 0.16
189_L 120_G 1.06 0.53 0.15
24_A 244_L 1.06 0.53 0.15
52_A 108_T 1.03 0.51 0.14
35_A 60_A 1.02 0.49 0.13
54_I 54_Y 0.99 0.46 0.12
181_F 238_L 0.97 0.43 0.11
26_A 244_L 0.96 0.43 0.11
42_M 67_V 0.96 0.42 0.10
29_V 82_E 0.96 0.42 0.10
27_G 248_T 0.95 0.41 0.10
15_R 247_L 0.94 0.41 0.10
153_P 140_G 0.92 0.39 0.09
21_Y 240_V 0.92 0.39 0.09
167_R 229_Q 0.91 0.38 0.09
74_K 250_K 0.90 0.37 0.08
187_I 225_M 0.90 0.37 0.08
74_K 242_A 0.90 0.36 0.08
33_A 227_R 0.89 0.36 0.08
138_V 131_A 0.89 0.35 0.08
72_L 47_L 0.88 0.35 0.08
141_G 218_W 0.88 0.35 0.08
44_P 48_Q 0.88 0.35 0.07
49_Q 118_G 0.87 0.34 0.07
126_L 216_L 0.87 0.34 0.07
189_L 182_N 0.87 0.34 0.07
23_T 248_T 0.87 0.33 0.07
48_V 173_L 0.86 0.33 0.07
45_S 173_L 0.86 0.33 0.07
168_G 227_R 0.86 0.33 0.07
187_I 93_D 0.85 0.32 0.07
94_L 16_A 0.85 0.32 0.07
125_W 220_A 0.84 0.31 0.06
28_T 24_A 0.83 0.30 0.06
130_G 221_E 0.82 0.29 0.06
113_T 241_L 0.81 0.28 0.06
168_G 209_A 0.81 0.28 0.05
49_Q 74_D 0.80 0.28 0.05
72_L 232_F 0.80 0.28 0.05
59_S 48_Q 0.80 0.28 0.05
70_K 98_E 0.80 0.27 0.05
168_G 49_R 0.80 0.27 0.05
30_A 240_V 0.79 0.27 0.05
187_I 108_T 0.79 0.27 0.05
68_T 154_I 0.79 0.27 0.05
56_V 227_R 0.79 0.26 0.05
74_K 166_K 0.78 0.25 0.05
67_L 232_F 0.77 0.25 0.05
29_V 235_V 0.77 0.25 0.05
57_D 74_D 0.77 0.25 0.05
168_G 181_G 0.77 0.25 0.05
175_H 135_G 0.77 0.24 0.04
36_W 220_A 0.76 0.24 0.04
13_A 135_G 0.76 0.24 0.04
39_V 243_A 0.75 0.24 0.04
24_A 251_K 0.75 0.24 0.04
42_M 208_M 0.75 0.23 0.04
66_Q 129_A 0.75 0.23 0.04
62_E 151_P 0.74 0.23 0.04
85_E 43_D 0.74 0.23 0.04
57_D 201_T 0.74 0.23 0.04
178_V 118_G 0.74 0.23 0.04
131_V 221_E 0.74 0.23 0.04
185_T 190_L 0.74 0.23 0.04
72_L 220_A 0.73 0.22 0.04
87_Q 240_V 0.73 0.22 0.04
27_G 29_E 0.73 0.22 0.04
95_G 59_S 0.72 0.21 0.04
27_G 75_E 0.72 0.21 0.04
85_E 53_V 0.72 0.21 0.04
94_L 18_E 0.72 0.21 0.04
57_D 72_L 0.72 0.21 0.04
33_A 164_E 0.72 0.21 0.04
29_V 246_Y 0.72 0.21 0.04
70_K 112_P 0.72 0.21 0.04
42_M 60_A 0.72 0.21 0.04
138_V 94_I 0.72 0.21 0.04
162_S 223_K 0.72 0.21 0.04
141_G 217_M 0.72 0.21 0.04
76_V 156_A 0.71 0.21 0.04
46_A 70_R 0.71 0.21 0.04
45_S 147_G 0.71 0.21 0.04
140_I 64_L 0.71 0.21 0.04
126_L 228_K 0.71 0.21 0.04
94_L 17_Q 0.71 0.21 0.04
94_L 156_A 0.71 0.21 0.04
131_V 183_W 0.71 0.20 0.04
18_F 108_T 0.71 0.20 0.03
29_V 254_Q 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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