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OPENSEQ.org
cIp_4_20_cIV_C_20
Genes: A B A+B
Length: 412 274 666
Sequences: 2346 2632 352
Seq/Len: 5.69 9.61 0.53
MirrorTree (Pazo et al. 2001) 0.55
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 0.00 0.01
2 0.00 0.00 0.02
5 0.01 0.00 0.03
10 0.02 0.00 0.05
20 0.02 0.00 0.09
100 0.03 0.00 0.15
∞ 0.10 0.00 0.51
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
361_V 267_V 1.62 0.67 0.00
102_I 143_L 1.52 0.59 0.00
53_V 92_I 1.39 0.49 0.00
388_S 180_V 1.29 0.42 0.00
286_E 135_T 1.28 0.41 0.00
384_I 271_I 1.26 0.39 0.00
225_V 156_V 1.25 0.38 0.00
393_L 205_V 1.24 0.38 0.00
402_T 29_L 1.22 0.37 0.00
53_V 147_L 1.14 0.31 0.00
211_E 26_F 1.13 0.30 0.00
219_L 105_W 1.12 0.29 0.00
349_V 183_G 1.10 0.28 0.00
292_Q 19_F 1.10 0.28 0.00
342_A 141_L 1.10 0.28 0.00
323_D 148_I 1.08 0.27 0.00
240_V 105_W 1.07 0.26 0.00
242_G 207_A 1.07 0.26 0.00
147_P 52_F 1.05 0.25 0.00
393_L 139_W 1.04 0.25 0.00
134_V 166_E 1.04 0.24 0.00
286_E 223_I 1.03 0.24 0.00
306_V 26_F 1.02 0.24 0.00
204_D 168_D 1.02 0.24 0.00
98_W 109_F 1.01 0.23 0.00
53_V 168_D 1.00 0.22 0.00
129_N 105_W 1.00 0.22 0.00
239_M 9_Y 1.00 0.22 0.00
238_V 166_E 1.00 0.22 0.00
208_L 183_G 0.99 0.22 0.00
279_C 57_V 0.99 0.22 0.00
335_T 156_V 0.98 0.21 0.00
245_L 144_I 0.98 0.21 0.00
99_C 159_A 0.98 0.21 0.00
29_I 63_M 0.96 0.20 0.00
136_T 21_G 0.96 0.20 0.00
295_V 144_I 0.96 0.20 0.00
270_N 232_L 0.95 0.20 0.00
107_G 189_L 0.95 0.20 0.00
318_A 211_Y 0.95 0.20 0.00
133_G 183_G 0.95 0.20 0.00
102_I 235_L 0.95 0.20 0.00
262_D 236_L 0.95 0.20 0.00
392_M 246_V 0.95 0.20 0.00
129_N 109_F 0.94 0.20 0.00
251_R 88_Q 0.94 0.19 0.00
401_A 179_A 0.94 0.19 0.00
192_E 125_D 0.94 0.19 0.00
403_L 239_Q 0.94 0.19 0.00
374_R 113_A 0.93 0.19 0.00
303_A 74_G 0.93 0.19 0.00
132_M 148_I 0.93 0.19 0.00
382_Q 56_L 0.93 0.19 0.00
298_L 22_A 0.93 0.19 0.00
121_Y 180_V 0.92 0.18 0.00
309_R 24_G 0.92 0.18 0.00
308_A 223_I 0.92 0.18 0.00
29_I 20_F 0.92 0.18 0.00
53_V 191_A 0.91 0.18 0.00
264_Q 155_A 0.91 0.18 0.00
183_L 9_Y 0.91 0.18 0.00
262_D 166_E 0.91 0.18 0.00
286_E 144_I 0.91 0.18 0.00
327_L 88_Q 0.90 0.17 0.00
383_S 58_G 0.90 0.17 0.00
193_E 147_L 0.90 0.17 0.00
204_D 141_L 0.90 0.17 0.00
27_F 92_I 0.89 0.17 0.00
262_D 185_C 0.89 0.17 0.00
286_E 170_K 0.89 0.17 0.00
135_T 132_G 0.89 0.17 0.00
109_V 235_L 0.89 0.17 0.00
29_I 165_L 0.89 0.17 0.00
79_N 222_I 0.89 0.17 0.00
295_V 114_L 0.89 0.17 0.00
55_R 175_G 0.88 0.17 0.00
262_D 206_Y 0.88 0.17 0.00
222_I 32_A 0.88 0.17 0.00
345_V 271_I 0.88 0.17 0.00
208_L 47_E 0.88 0.17 0.00
165_C 113_A 0.88 0.16 0.00
150_G 173_I 0.87 0.16 0.00
316_R 135_T 0.87 0.16 0.00
99_C 269_I 0.86 0.16 0.00
54_E 181_I 0.86 0.16 0.00
204_D 124_K 0.86 0.16 0.00
295_V 202_A 0.86 0.16 0.00
387_M 148_I 0.86 0.16 0.00
335_T 219_A 0.86 0.15 0.00
206_D 72_N 0.85 0.15 0.00
265_I 192_Y 0.85 0.15 0.00
116_L 208_G 0.85 0.15 0.00
81_P 194_Y 0.85 0.15 0.00
303_A 185_C 0.85 0.15 0.00
120_L 8_D 0.85 0.15 0.00
309_R 134_V 0.85 0.15 0.00
136_T 183_G 0.85 0.15 0.00
335_T 63_M 0.85 0.15 0.00
298_L 29_L 0.85 0.15 0.00
313_T 233_I 0.84 0.15 0.00
45_V 28_M 0.84 0.15 0.00
401_A 142_P 0.84 0.15 0.00
393_L 174_N 0.84 0.15 0.00
265_I 61_Y 0.84 0.15 0.00
48_L 268_V 0.84 0.15 0.00
55_R 104_A 0.84 0.15 0.00
297_K 223_I 0.84 0.15 0.00
262_D 181_I 0.84 0.15 0.00
201_L 211_Y 0.84 0.15 0.00
53_V 201_L 0.84 0.15 0.00
194_W 109_F 0.83 0.15 0.00
135_T 89_Y 0.83 0.15 0.00
159_I 8_D 0.83 0.15 0.00
112_R 219_A 0.83 0.15 0.00
160_F 7_H 0.83 0.15 0.00
29_I 181_I 0.83 0.15 0.00
402_T 96_M 0.83 0.15 0.00
172_A 72_N 0.83 0.14 0.00
53_V 128_W 0.83 0.14 0.00
174_F 84_R 0.83 0.14 0.00
403_L 75_E 0.83 0.14 0.00
306_V 104_A 0.83 0.14 0.00
101_A 28_M 0.82 0.14 0.00
108_T 19_F 0.82 0.14 0.00
204_D 154_V 0.82 0.14 0.00
264_Q 19_F 0.82 0.14 0.00
107_G 26_F 0.82 0.14 0.00
388_S 141_L 0.82 0.14 0.00
243_S 60_L 0.81 0.14 0.00
152_E 143_L 0.81 0.14 0.00
25_R 266_F 0.81 0.14 0.00
186_D 211_Y 0.81 0.14 0.00
185_P 173_I 0.81 0.14 0.00
367_K 138_P 0.81 0.14 0.00
245_L 40_T 0.81 0.14 0.00
245_L 11_I 0.81 0.14 0.00
52_I 189_L 0.81 0.14 0.00
246_A 235_L 0.81 0.14 0.00
286_E 64_F 0.80 0.14 0.00
242_G 162_A 0.80 0.13 0.00
104_R 135_T 0.80 0.13 0.00
132_M 158_W 0.80 0.13 0.00
106_T 54_I 0.80 0.13 0.00
224_I 233_I 0.80 0.13 0.00
262_D 124_K 0.80 0.13 0.00
139_M 244_Q 0.80 0.13 0.00
29_I 230_V 0.80 0.13 0.00
303_A 211_Y 0.80 0.13 0.00
298_L 52_F 0.80 0.13 0.00
390_G 165_L 0.80 0.13 0.00
219_L 8_D 0.80 0.13 0.00
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
4000 0.41 cIp_4_20_cIV_C_60 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3999 0.53 cIp_4_20_cIV_C_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3998 0.52 cIp_4_10_cIV_C_40 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3997 0.48 cIp_4_20_cIV_C_40 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3996 0.47 cIp_4_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3995 0.62 cIp_4_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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