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OPENSEQ.org
cIII_cytc1_ISP
Genes: A B A+B
Length: 263 190 431
Sequences: 973 1692 708
Seq/Len: 3.7 8.91 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 0.01 0.00 0.12
2 0.01 0.00 1.46
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
∞ 0.01 0.05 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
244_L 23_T 1.74 0.95 0.74
86_R 55_Q 1.36 0.80 0.43
248_T 19_L 1.17 0.64 0.26
248_T 20_Y 1.13 0.60 0.23
235_V 33_A 1.09 0.56 0.20
137_Y 180_E 1.08 0.56 0.20
131_A 138_V 1.03 0.49 0.16
60_A 35_A 1.02 0.49 0.16
240_V 21_Y 1.02 0.49 0.16
120_G 189_L 1.02 0.49 0.16
82_E 29_V 1.02 0.49 0.16
244_L 24_A 1.02 0.49 0.16
108_T 52_A 1.00 0.47 0.15
220_A 125_W 1.00 0.46 0.14
54_Y 54_I 0.99 0.46 0.14
140_G 153_P 0.99 0.46 0.14
248_T 27_G 0.98 0.45 0.14
156_A 94_L 0.96 0.42 0.12
227_R 33_A 0.95 0.42 0.12
244_L 26_A 0.95 0.42 0.12
67_V 42_M 0.95 0.41 0.12
247_L 15_R 0.94 0.41 0.12
232_F 72_L 0.94 0.40 0.12
24_A 28_T 0.93 0.39 0.11
248_T 23_T 0.92 0.38 0.10
135_G 25_G 0.91 0.37 0.10
47_L 72_L 0.90 0.36 0.10
254_Q 29_V 0.90 0.36 0.10
238_L 181_F 0.90 0.36 0.10
218_W 141_G 0.89 0.35 0.09
173_L 48_V 0.89 0.35 0.09
173_L 45_S 0.88 0.35 0.09
48_Q 44_P 0.88 0.34 0.09
48_Q 59_S 0.88 0.34 0.09
242_A 74_K 0.86 0.33 0.08
109_D 82_T 0.86 0.33 0.08
250_K 74_K 0.86 0.33 0.08
218_W 17_D 0.85 0.32 0.08
209_A 168_G 0.84 0.31 0.07
108_T 18_F 0.83 0.30 0.07
225_M 187_I 0.83 0.29 0.07
22_S 148_G 0.82 0.29 0.07
19_A 58_V 0.82 0.29 0.07
247_L 131_V 0.82 0.29 0.07
85_V 180_E 0.82 0.29 0.07
240_V 144_A 0.81 0.28 0.07
154_I 68_T 0.81 0.28 0.07
129_A 66_Q 0.81 0.28 0.07
118_G 49_Q 0.81 0.28 0.07
75_E 27_G 0.81 0.28 0.07
186_M 145_G 0.80 0.28 0.06
221_E 130_G 0.80 0.27 0.06
235_V 29_V 0.80 0.27 0.06
94_I 187_I 0.80 0.27 0.06
147_G 45_S 0.79 0.27 0.06
245_L 65_T 0.79 0.27 0.06
229_Q 167_R 0.79 0.26 0.06
74_D 49_Q 0.78 0.26 0.06
95_T 186_T 0.78 0.26 0.06
49_R 168_G 0.78 0.26 0.06
163_G 188_K 0.78 0.26 0.06
221_E 181_F 0.78 0.26 0.06
227_R 168_G 0.78 0.25 0.06
64_L 140_I 0.78 0.25 0.06
243_A 39_V 0.78 0.25 0.06
186_M 56_V 0.77 0.25 0.06
16_A 94_L 0.77 0.25 0.05
54_Y 86_I 0.77 0.25 0.05
237_F 30_A 0.77 0.24 0.05
252_L 13_A 0.77 0.24 0.05
163_G 79_R 0.77 0.24 0.05
52_Q 187_I 0.76 0.24 0.05
220_A 36_W 0.76 0.24 0.05
72_L 57_D 0.75 0.23 0.05
60_A 42_M 0.75 0.23 0.05
240_V 30_A 0.75 0.23 0.05
70_R 46_A 0.75 0.23 0.05
206_D 52_A 0.75 0.23 0.05
94_I 138_V 0.74 0.23 0.05
251_K 24_A 0.74 0.22 0.05
208_M 42_M 0.74 0.22 0.05
66_Y 25_G 0.74 0.22 0.05
220_A 72_L 0.74 0.22 0.05
180_A 58_V 0.73 0.22 0.05
74_D 57_D 0.73 0.22 0.05
227_R 56_V 0.73 0.22 0.04
77_G 22_A 0.73 0.22 0.04
54_Y 130_G 0.72 0.21 0.04
230_V 8_A 0.72 0.21 0.04
236_I 78_I 0.72 0.21 0.04
104_P 79_R 0.72 0.21 0.04
29_E 27_G 0.72 0.21 0.04
103_R 82_T 0.72 0.21 0.04
70_R 85_E 0.72 0.21 0.04
241_L 129_I 0.72 0.21 0.04
241_L 175_H 0.72 0.21 0.04
92_F 14_T 0.72 0.21 0.04
59_S 158_H 0.72 0.21 0.04
181_G 168_G 0.71 0.21 0.04
215_F 117_R 0.71 0.20 0.04
228_K 117_R 0.71 0.20 0.04
64_L 48_V 0.71 0.20 0.04
95_T 78_I 0.71 0.20 0.04
28_I 96_Q 0.71 0.20 0.04
111_F 17_D 0.71 0.20 0.04
216_L 126_L 0.70 0.20 0.04
130_R 174_L 0.70 0.20 0.04
131_A 77_F 0.70 0.20 0.04
59_S 95_G 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)
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