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OPENSEQ.org
cIp_4_20_cIV_C_60
Genes: A B A+B
Length: 412 274 664
Sequences: 2346 2418 275
Seq/Len: 5.69 8.82 0.41
MirrorTree (Pazo et al. 2001) 0.30
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 0.08
100 0.03 0.00 0.12
∞ 0.10 0.00 0.40
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 1.94 0.78 0.05
102_I 143_L 1.58 0.56 0.02
286_E 135_T 1.51 0.51 0.02
169_L 207_A 1.32 0.37 0.01
239_M 9_Y 1.31 0.37 0.01
208_L 183_G 1.29 0.36 0.01
225_V 156_V 1.29 0.35 0.01
384_I 271_I 1.29 0.35 0.01
392_M 246_V 1.28 0.35 0.01
402_T 29_L 1.26 0.33 0.01
211_E 26_F 1.25 0.33 0.01
55_R 104_A 1.23 0.32 0.01
107_G 189_L 1.22 0.31 0.01
245_L 144_I 1.20 0.29 0.01
240_V 105_W 1.19 0.29 0.01
323_D 148_I 1.16 0.27 0.01
335_T 63_M 1.14 0.26 0.01
134_V 166_E 1.13 0.26 0.01
393_L 139_W 1.12 0.25 0.01
309_R 134_V 1.11 0.25 0.01
335_T 219_A 1.11 0.25 0.01
342_A 141_L 1.11 0.25 0.01
147_P 52_F 1.11 0.24 0.01
132_M 158_W 1.11 0.24 0.01
219_L 105_W 1.10 0.24 0.01
358_V 211_Y 1.10 0.24 0.01
286_E 144_I 1.10 0.24 0.01
308_A 223_I 1.08 0.23 0.01
194_W 209_A 1.08 0.23 0.01
120_L 141_L 1.07 0.23 0.01
306_V 104_A 1.06 0.22 0.01
99_C 269_I 1.05 0.21 0.00
286_E 223_I 1.05 0.21 0.00
174_F 159_A 1.04 0.21 0.00
97_A 151_L 1.04 0.21 0.00
27_F 92_I 1.03 0.20 0.00
298_L 9_Y 1.03 0.20 0.00
53_V 191_A 1.02 0.20 0.00
136_T 21_G 1.02 0.20 0.00
29_I 165_L 1.02 0.20 0.00
393_L 174_N 1.01 0.20 0.00
279_C 71_V 1.01 0.19 0.00
222_I 32_A 1.01 0.19 0.00
262_D 206_Y 1.00 0.19 0.00
98_W 109_F 1.00 0.19 0.00
133_G 201_L 1.00 0.19 0.00
129_N 105_W 0.99 0.19 0.00
303_A 74_G 0.99 0.19 0.00
242_G 207_A 0.98 0.18 0.00
351_A 90_G 0.98 0.18 0.00
389_R 64_F 0.97 0.18 0.00
224_I 246_V 0.97 0.18 0.00
390_G 155_A 0.97 0.18 0.00
204_D 154_V 0.96 0.17 0.00
400_I 103_V 0.96 0.17 0.00
210_T 11_I 0.96 0.17 0.00
53_V 126_G 0.96 0.17 0.00
318_A 211_Y 0.95 0.17 0.00
295_V 212_M 0.95 0.17 0.00
127_I 237_K 0.95 0.17 0.00
66_G 137_D 0.94 0.17 0.00
326_S 29_L 0.94 0.17 0.00
196_E 167_G 0.94 0.17 0.00
383_S 242_Q 0.94 0.17 0.00
238_V 207_A 0.94 0.17 0.00
28_N 71_V 0.94 0.17 0.00
388_S 180_V 0.94 0.16 0.00
326_S 71_V 0.94 0.16 0.00
164_A 141_L 0.94 0.16 0.00
410_V 269_I 0.94 0.16 0.00
279_C 243_K 0.93 0.16 0.00
144_L 89_Y 0.93 0.16 0.00
270_N 232_L 0.93 0.16 0.00
403_L 219_A 0.92 0.16 0.00
371_A 114_L 0.92 0.16 0.00
121_Y 59_V 0.92 0.16 0.00
295_V 114_L 0.92 0.16 0.00
81_P 30_T 0.92 0.15 0.00
256_E 76_T 0.91 0.15 0.00
261_F 167_G 0.91 0.15 0.00
159_I 8_D 0.91 0.15 0.00
53_V 92_I 0.91 0.15 0.00
169_L 85_I 0.91 0.15 0.00
160_F 10_Q 0.91 0.15 0.00
97_A 183_G 0.91 0.15 0.00
120_L 219_A 0.91 0.15 0.00
386_W 159_A 0.91 0.15 0.00
55_R 175_G 0.90 0.15 0.00
313_T 233_I 0.90 0.15 0.00
374_R 113_A 0.90 0.15 0.00
294_A 189_L 0.90 0.15 0.00
335_T 159_A 0.90 0.15 0.00
29_I 47_E 0.89 0.15 0.00
115_S 156_V 0.89 0.15 0.00
230_A 206_Y 0.89 0.14 0.00
335_T 131_E 0.89 0.14 0.00
410_V 29_L 0.89 0.14 0.00
367_K 138_P 0.89 0.14 0.00
308_A 54_I 0.88 0.14 0.00
219_L 201_L 0.88 0.14 0.00
382_Q 56_L 0.88 0.14 0.00
383_S 168_D 0.88 0.14 0.00
316_R 135_T 0.88 0.14 0.00
133_G 115_Y 0.87 0.14 0.00
136_T 183_G 0.87 0.14 0.00
394_A 158_W 0.87 0.14 0.00
144_L 118_G 0.87 0.14 0.00
398_A 183_G 0.86 0.14 0.00
188_L 70_V 0.86 0.14 0.00
183_L 104_A 0.86 0.14 0.00
45_V 28_M 0.86 0.14 0.00
400_I 72_N 0.86 0.14 0.00
388_S 197_A 0.86 0.14 0.00
112_R 267_V 0.86 0.14 0.00
393_L 6_N 0.86 0.14 0.00
327_L 175_G 0.86 0.14 0.00
383_S 28_M 0.86 0.13 0.00
211_E 172_T 0.86 0.13 0.00
79_N 199_F 0.85 0.13 0.00
345_V 271_I 0.85 0.13 0.00
159_I 9_Y 0.85 0.13 0.00
104_R 191_A 0.85 0.13 0.00
294_A 155_A 0.85 0.13 0.00
208_L 47_E 0.85 0.13 0.00
297_K 223_I 0.85 0.13 0.00
242_G 143_L 0.85 0.13 0.00
136_T 62_V 0.85 0.13 0.00
374_R 196_H 0.85 0.13 0.00
262_D 148_I 0.85 0.13 0.00
137_G 154_V 0.85 0.13 0.00
172_A 72_N 0.84 0.13 0.00
372_K 209_A 0.84 0.13 0.00
252_S 211_Y 0.84 0.13 0.00
279_C 57_V 0.84 0.13 0.00
317_R 19_F 0.84 0.13 0.00
117_I 174_N 0.84 0.13 0.00
342_A 19_F 0.83 0.13 0.00
193_E 25_A 0.83 0.13 0.00
309_R 223_I 0.83 0.13 0.00
295_V 127_V 0.83 0.12 0.00
393_L 205_V 0.83 0.12 0.00
402_T 96_M 0.83 0.12 0.00
79_N 222_I 0.83 0.12 0.00
246_A 181_I 0.83 0.12 0.00
132_M 148_I 0.83 0.12 0.00
285_R 77_G 0.83 0.12 0.00
83_L 10_Q 0.82 0.12 0.00
224_I 233_I 0.82 0.12 0.00
165_C 113_A 0.82 0.12 0.00
226_T 241_T 0.82 0.12 0.00
66_G 17_W 0.82 0.12 0.00
80_L 173_I 0.82 0.12 0.00
159_I 105_W 0.82 0.12 0.00
139_M 211_Y 0.82 0.12 0.00
97_A 269_I 0.82 0.12 0.00
215_F 89_Y 0.82 0.12 0.00
226_T 33_V 0.82 0.12 0.00
144_L 271_I 0.82 0.12 0.00
204_D 207_A 0.82 0.12 0.00
215_F 78_E 0.82 0.12 0.00
219_L 8_D 0.81 0.12 0.00
53_V 24_G 0.81 0.12 0.00
362_A 91_F 0.81 0.12 0.00
189_D 21_G 0.81 0.12 0.00
295_V 71_V 0.81 0.12 0.00
361_V 188_G 0.81 0.12 0.00
267_V 148_I 0.81 0.12 0.00
215_F 96_M 0.81 0.12 0.00
25_R 202_A 0.81 0.12 0.00
48_L 77_G 0.81 0.12 0.00
179_V 77_G 0.81 0.12 0.00
294_A 179_A 0.81 0.12 0.00
335_T 156_V 0.81 0.12 0.00
349_V 236_L 0.81 0.12 0.00
262_D 236_L 0.80 0.12 0.00
335_T 205_V 0.80 0.12 0.00
251_R 88_Q 0.80 0.12 0.00
314_P 228_L 0.80 0.12 0.00
158_M 72_N 0.80 0.12 0.00
309_R 37_K 0.80 0.12 0.00
267_V 267_V 0.80 0.12 0.00
349_V 183_G 0.80 0.12 0.00
115_S 219_A 0.80 0.12 0.00
133_G 183_G 0.80 0.12 0.00
121_Y 180_V 0.80 0.12 0.00
233_W 62_V 0.80 0.12 0.00
66_G 266_F 0.80 0.11 0.00
277_Y 11_I 0.80 0.11 0.00
183_L 9_Y 0.79 0.11 0.00
206_D 207_A 0.79 0.11 0.00
127_I 70_V 0.79 0.11 0.00
28_N 208_G 0.79 0.11 0.00
190_D 109_F 0.79 0.11 0.00
21_E 59_V 0.79 0.11 0.00
219_L 115_Y 0.79 0.11 0.00
112_R 219_A 0.79 0.11 0.00
205_L 127_V 0.79 0.11 0.00
286_E 219_A 0.79 0.11 0.00
397_P 105_W 0.79 0.11 0.00
104_R 135_T 0.79 0.11 0.00
289_K 246_V 0.79 0.11 0.00
246_A 237_K 0.79 0.11 0.00
326_S 169_R 0.79 0.11 0.00
306_V 26_F 0.79 0.11 0.00
402_T 115_Y 0.79 0.11 0.00
240_V 204_T 0.78 0.11 0.00
286_E 138_P 0.78 0.11 0.00
215_F 213_A 0.78 0.11 0.00
306_V 70_V 0.78 0.11 0.00
112_R 167_G 0.78 0.11 0.00
410_V 174_N 0.78 0.11 0.00
209_L 173_I 0.78 0.11 0.00
319_E 223_I 0.78 0.11 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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