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OPENSEQ.org
cIp_4_10_cIV_C_40
Genes: A B A+B
Length: 412 274 666
Sequences: 3493 2529 345
Seq/Len: 8.48 9.23 0.52
MirrorTree (Pazo et al. 2001) 0.29
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 0.01
2 0.01 0.00 0.02
5 0.03 0.00 0.03
10 0.03 0.00 0.05
20 0.05 0.00 0.09
100 0.06 0.00 0.14
∞ 0.13 0.00 0.50
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 1.61 0.66 0.00
120_L 159_A 1.29 0.41 0.00
53_V 168_D 1.28 0.41 0.00
102_I 143_L 1.27 0.40 0.00
296_Q 242_Q 1.27 0.39 0.00
208_L 183_G 1.25 0.39 0.00
53_V 92_I 1.22 0.36 0.00
335_T 156_V 1.18 0.33 0.00
302_P 223_I 1.17 0.33 0.00
129_N 105_W 1.17 0.32 0.00
367_K 181_I 1.14 0.31 0.00
286_E 223_I 1.12 0.29 0.00
242_G 207_A 1.09 0.28 0.00
239_M 9_Y 1.08 0.27 0.00
225_V 156_V 1.08 0.27 0.00
383_S 28_M 1.07 0.26 0.00
286_E 135_T 1.06 0.25 0.00
219_L 105_W 1.05 0.25 0.00
388_S 180_V 1.04 0.25 0.00
134_V 166_E 1.04 0.25 0.00
29_I 165_L 1.04 0.24 0.00
133_G 201_L 1.03 0.24 0.00
136_T 183_G 1.02 0.23 0.00
326_S 71_V 1.02 0.23 0.00
147_P 52_F 1.02 0.23 0.00
243_S 60_L 1.02 0.23 0.00
228_A 167_G 1.01 0.23 0.00
327_L 88_Q 1.01 0.23 0.00
144_L 118_G 1.00 0.22 0.00
300_A 35_W 0.99 0.22 0.00
298_L 127_V 0.99 0.22 0.00
226_T 241_T 0.99 0.21 0.00
392_M 246_V 0.98 0.21 0.00
183_L 147_L 0.98 0.21 0.00
98_W 109_F 0.98 0.21 0.00
99_C 159_A 0.98 0.21 0.00
298_L 52_F 0.97 0.21 0.00
240_V 105_W 0.97 0.20 0.00
53_V 126_G 0.96 0.20 0.00
403_L 183_G 0.96 0.20 0.00
197_R 181_I 0.95 0.20 0.00
335_T 63_M 0.95 0.20 0.00
298_L 29_L 0.95 0.20 0.00
107_G 189_L 0.95 0.20 0.00
367_K 138_P 0.94 0.19 0.00
386_W 159_A 0.94 0.19 0.00
222_I 150_L 0.94 0.19 0.00
45_V 28_M 0.94 0.19 0.00
109_V 267_V 0.94 0.19 0.00
245_L 11_I 0.93 0.18 0.00
298_L 156_V 0.93 0.18 0.00
384_I 271_I 0.92 0.18 0.00
120_L 65_G 0.92 0.18 0.00
115_S 191_A 0.92 0.18 0.00
183_L 9_Y 0.92 0.18 0.00
53_V 175_G 0.92 0.18 0.00
374_R 113_A 0.92 0.18 0.00
157_L 77_G 0.92 0.18 0.00
232_D 24_G 0.92 0.18 0.00
53_V 80_T 0.92 0.18 0.00
384_I 252_A 0.91 0.18 0.00
211_E 26_F 0.90 0.17 0.00
297_K 223_I 0.90 0.17 0.00
393_L 139_W 0.89 0.17 0.00
245_L 26_F 0.89 0.17 0.00
403_L 239_Q 0.89 0.17 0.00
196_E 141_L 0.89 0.17 0.00
52_I 189_L 0.89 0.17 0.00
133_G 183_G 0.89 0.17 0.00
159_I 105_W 0.88 0.17 0.00
200_K 141_L 0.88 0.17 0.00
390_G 155_A 0.88 0.16 0.00
393_L 205_V 0.88 0.16 0.00
262_D 148_I 0.88 0.16 0.00
109_V 26_F 0.87 0.16 0.00
233_W 62_V 0.87 0.16 0.00
113_R 101_F 0.86 0.16 0.00
135_T 89_Y 0.86 0.16 0.00
48_L 237_K 0.86 0.16 0.00
169_L 207_A 0.86 0.15 0.00
295_V 212_M 0.86 0.15 0.00
322_R 183_G 0.85 0.15 0.00
120_L 219_A 0.85 0.15 0.00
135_T 118_G 0.85 0.15 0.00
29_I 63_M 0.85 0.15 0.00
139_M 244_Q 0.84 0.15 0.00
323_D 148_I 0.84 0.15 0.00
364_G 238_G 0.84 0.15 0.00
291_M 20_F 0.84 0.15 0.00
262_D 22_A 0.83 0.14 0.00
97_A 204_T 0.83 0.14 0.00
245_L 19_F 0.83 0.14 0.00
124_I 77_G 0.82 0.14 0.00
303_A 74_G 0.82 0.14 0.00
174_F 84_R 0.82 0.14 0.00
136_T 62_V 0.82 0.14 0.00
367_K 52_F 0.82 0.14 0.00
252_S 211_Y 0.82 0.14 0.00
147_P 159_A 0.82 0.14 0.00
286_E 219_A 0.81 0.14 0.00
79_N 199_F 0.81 0.14 0.00
295_V 127_V 0.81 0.14 0.00
28_N 71_V 0.81 0.14 0.00
29_I 47_E 0.81 0.14 0.00
359_Y 91_F 0.81 0.14 0.00
203_D 167_G 0.81 0.14 0.00
265_I 232_L 0.81 0.14 0.00
109_V 191_A 0.81 0.14 0.00
112_R 219_A 0.80 0.13 0.00
127_I 242_Q 0.80 0.13 0.00
115_S 156_V 0.80 0.13 0.00
374_R 238_G 0.80 0.13 0.00
224_I 233_I 0.80 0.13 0.00
188_L 19_F 0.80 0.13 0.00
279_C 57_V 0.80 0.13 0.00
99_C 235_L 0.80 0.13 0.00
205_L 87_L 0.79 0.13 0.00
120_L 141_L 0.79 0.13 0.00
265_I 226_I 0.79 0.13 0.00
114_A 209_A 0.79 0.13 0.00
281_M 151_L 0.78 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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