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OPENSEQ.org
c1-c2
Genes: A B A+B
Length: 289 113 387
Sequences: 1783 382 371
Seq/Len: 6.17 3.38 0.96
MirrorTree (Pazo et al. 2001) 0.83
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 0.90
2 0.01 0.00 0.92
5 0.01 0.00 0.92
10 0.02 0.00 0.92
20 0.02 0.00 0.92
100 0.04 0.00 0.92
∞ 0.10 0.00 0.93
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
37_E 47_K 1.85 0.92 0.46
65_V 72_I 1.69 0.86 0.34
157_F 79_E 1.68 0.86 0.33
157_F 7_R 1.52 0.77 0.22
20_N 88_L 1.40 0.68 0.16
67_F 37_F 1.33 0.63 0.13
257_G 72_I 1.30 0.60 0.12
97_W 25_Y 1.24 0.55 0.10
226_V 62_L 1.22 0.53 0.09
65_V 18_T 1.20 0.51 0.09
41_L 103_L 1.20 0.51 0.08
55_V 32_L 1.20 0.51 0.08
67_F 96_I 1.17 0.48 0.08
110_I 69_K 1.12 0.43 0.06
254_S 72_I 1.11 0.42 0.06
213_N 7_R 1.11 0.42 0.06
36_S 58_M 1.09 0.41 0.06
131_Q 23_K 1.09 0.41 0.06
140_L 26_R 1.08 0.40 0.06
133_I 44_I 1.08 0.40 0.06
36_S 35_E 1.08 0.40 0.06
66_I 30_K 1.07 0.39 0.05
34_H 47_K 1.06 0.38 0.05
110_I 21_E 1.06 0.38 0.05
180_G 37_F 1.05 0.38 0.05
161_F 75_L 1.04 0.36 0.05
198_M 11_M 1.03 0.36 0.05
203_L 84_R 1.03 0.36 0.05
193_V 25_Y 1.01 0.34 0.04
70_D 44_I 1.01 0.34 0.04
107_T 102_R 1.01 0.34 0.04
83_G 8_M 1.00 0.33 0.04
90_Q 82_F 1.00 0.33 0.04
269_Y 25_Y 1.00 0.33 0.04
219_M 53_T 1.00 0.33 0.04
256_N 26_R 0.99 0.32 0.04
37_E 53_T 0.99 0.32 0.04
133_I 9_I 0.98 0.32 0.04
178_D 8_M 0.98 0.32 0.04
269_Y 26_R 0.98 0.32 0.04
157_F 88_L 0.97 0.31 0.04
55_V 65_H 0.96 0.30 0.04
219_M 73_T 0.96 0.30 0.04
136_L 16_T 0.96 0.30 0.03
108_T 18_T 0.96 0.30 0.03
36_S 47_K 0.95 0.29 0.03
81_F 85_M 0.95 0.29 0.03
178_D 88_L 0.95 0.29 0.03
79_M 11_M 0.94 0.28 0.03
253_F 8_M 0.94 0.28 0.03
105_V 80_K 0.93 0.28 0.03
193_V 77_V 0.93 0.28 0.03
117_Q 15_P 0.93 0.28 0.03
213_N 79_E 0.93 0.28 0.03
66_I 37_F 0.92 0.27 0.03
117_Q 12_F 0.92 0.27 0.03
187_M 22_R 0.92 0.27 0.03
161_F 39_M 0.92 0.27 0.03
10_N 8_M 0.92 0.27 0.03
150_G 30_K 0.92 0.27 0.03
4_W 85_M 0.92 0.27 0.03
96_S 92_R 0.91 0.26 0.03
183_L 58_M 0.91 0.26 0.03
240_K 44_I 0.91 0.26 0.03
277_L 26_R 0.91 0.26 0.03
107_T 11_M 0.91 0.26 0.03
264_N 49_L 0.90 0.26 0.03
27_A 80_K 0.90 0.26 0.03
262_L 23_K 0.90 0.26 0.03
154_R 44_I 0.90 0.26 0.03
137_Y 33_L 0.89 0.25 0.03
188_F 22_R 0.89 0.25 0.03
258_K 20_E 0.89 0.25 0.03
152_A 72_I 0.89 0.24 0.03
24_F 46_S 0.88 0.24 0.02
176_G 72_I 0.88 0.24 0.02
19_N 38_I 0.87 0.23 0.02
54_L 106_L 0.87 0.23 0.02
7_V 20_E 0.86 0.23 0.02
7_V 83_A 0.86 0.23 0.02
232_E 72_I 0.85 0.23 0.02
46_T 75_L 0.85 0.22 0.02
117_Q 70_G 0.85 0.22 0.02
45_T 77_V 0.85 0.22 0.02
164_D 56_N 0.84 0.22 0.02
38_I 17_D 0.84 0.22 0.02
69_D 40_H 0.83 0.21 0.02
23_I 59_I 0.83 0.21 0.02
37_E 49_L 0.83 0.21 0.02
225_L 51_N 0.83 0.21 0.02
258_K 88_L 0.83 0.21 0.02
65_V 98_N 0.83 0.21 0.02
244_E 77_V 0.83 0.21 0.02
178_D 11_M 0.82 0.20 0.02
197_C 25_Y 0.82 0.20 0.02
36_S 61_R 0.82 0.20 0.02
83_G 42_F 0.82 0.20 0.02
245_L 76_T 0.82 0.20 0.02
209_F 82_F 0.82 0.20 0.02
242_K 99_S 0.81 0.20 0.02
195_S 16_T 0.81 0.20 0.02
267_S 73_T 0.81 0.20 0.02
182_T 87_Y 0.81 0.20 0.02
49_V 53_T 0.81 0.20 0.02
184_L 57_A 0.81 0.20 0.02
256_N 59_I 0.81 0.20 0.02
280_E 23_K 0.80 0.19 0.02
193_V 65_H 0.80 0.19 0.02
160_L 82_F 0.80 0.19 0.02
72_R 83_A 0.80 0.19 0.02
235_N 75_L 0.80 0.19 0.02
154_R 8_M 0.80 0.19 0.02
158_N 64_E 0.79 0.19 0.02
83_G 86_I 0.79 0.19 0.02
249_F 92_R 0.79 0.19 0.02
26_D 26_R 0.79 0.19 0.02
189_A 47_K 0.79 0.19 0.02
243_R 105_F 0.79 0.18 0.02
91_L 40_H 0.79 0.18 0.02
161_F 22_R 0.79 0.18 0.02
245_L 23_K 0.78 0.18 0.02
186_S 38_I 0.78 0.18 0.02
194_V 21_E 0.78 0.18 0.02
222_F 104_V 0.78 0.18 0.01
98_S 83_A 0.78 0.18 0.01
67_F 21_E 0.78 0.18 0.01
185_L 50_L 0.77 0.18 0.01
260_M 25_Y 0.77 0.18 0.01
209_F 51_N 0.77 0.17 0.01
126_Y 72_I 0.77 0.17 0.01
130_S 91_E 0.77 0.17 0.01
216_S 97_A 0.77 0.17 0.01
196_G 36_G 0.77 0.17 0.01
256_N 86_I 0.77 0.17 0.01
19_N 30_K 0.77 0.17 0.01
84_R 49_L 0.77 0.17 0.01
248_L 77_V 0.77 0.17 0.01
213_N 89_H 0.76 0.17 0.01
86_D 47_K 0.76 0.17 0.01
176_G 7_R 0.76 0.17 0.01
150_G 63_R 0.76 0.17 0.01
203_L 11_M 0.76 0.17 0.01
240_K 91_E 0.76 0.17 0.01
170_E 27_K 0.76 0.17 0.01
6_T 103_L 0.76 0.17 0.01
45_T 94_N 0.76 0.17 0.01
98_S 77_V 0.76 0.17 0.01
62_N 48_L 0.76 0.17 0.01
95_M 82_F 0.76 0.17 0.01
60_D 31_F 0.76 0.17 0.01
22_L 72_I 0.75 0.17 0.01
126_Y 84_R 0.75 0.17 0.01
221_P 37_F 0.75 0.17 0.01
246_F 87_Y 0.75 0.17 0.01
66_I 9_I 0.75 0.17 0.01
40_I 11_M 0.75 0.17 0.01
270_T 79_E 0.75 0.16 0.01
262_L 55_N 0.75 0.16 0.01
274_V 8_M 0.75 0.16 0.01
92_G 8_M 0.74 0.16 0.01
128_E 83_A 0.74 0.16 0.01
19_N 34_S 0.74 0.16 0.01
119_C 77_V 0.74 0.16 0.01
150_G 51_N 0.74 0.16 0.01
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
9323 2.05 JModell-1 Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 0.99 Done
4585 0.96 c1-c2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.46 Done - Shared
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