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OPENSEQ.org
cIp_4_4_cIV_C_4
Genes: A B A+B
Length: 412 274 665
Sequences: 3488 2893 415
Seq/Len: 8.47 10.56 0.62
MirrorTree (Pazo et al. 2001) 0.24
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 0.04 0.00 0.05
20 0.05 0.00 0.10
100 0.06 0.00 0.17
∞ 0.13 0.01 0.60
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 1.34 0.50 0.00
53_V 92_I 1.13 0.34 0.00
265_I 226_I 1.13 0.33 0.00
297_K 223_I 1.12 0.33 0.00
102_I 143_L 1.09 0.31 0.00
262_D 226_I 1.05 0.28 0.00
286_E 135_T 1.03 0.27 0.00
367_K 181_I 1.00 0.25 0.00
326_S 71_V 1.00 0.25 0.00
298_L 52_F 0.98 0.23 0.00
242_G 207_A 0.97 0.23 0.00
99_C 159_A 0.97 0.23 0.00
296_Q 242_Q 0.96 0.23 0.00
312_L 177_I 0.96 0.23 0.00
174_F 159_A 0.94 0.21 0.00
107_G 189_L 0.93 0.21 0.00
295_V 71_V 0.93 0.21 0.00
129_N 105_W 0.93 0.21 0.00
29_I 165_L 0.92 0.20 0.00
172_A 109_F 0.92 0.20 0.00
399_I 52_F 0.91 0.20 0.00
279_C 57_V 0.90 0.19 0.00
398_A 242_Q 0.89 0.19 0.00
139_M 244_Q 0.88 0.18 0.00
335_T 63_M 0.87 0.18 0.00
138_A 128_W 0.87 0.18 0.00
219_L 105_W 0.87 0.18 0.00
208_L 183_G 0.86 0.17 0.00
138_A 243_K 0.85 0.17 0.00
144_L 122_P 0.85 0.17 0.00
112_R 219_A 0.85 0.17 0.00
188_L 19_F 0.84 0.17 0.00
393_L 205_V 0.84 0.17 0.00
298_L 29_L 0.84 0.17 0.00
110_I 154_V 0.83 0.16 0.00
243_S 60_L 0.83 0.16 0.00
29_I 191_A 0.83 0.16 0.00
109_V 267_V 0.83 0.16 0.00
133_G 201_L 0.83 0.16 0.00
312_L 96_M 0.82 0.16 0.00
29_I 47_E 0.82 0.15 0.00
378_F 148_I 0.82 0.15 0.00
53_V 126_G 0.82 0.15 0.00
108_T 191_A 0.81 0.15 0.00
139_M 211_Y 0.81 0.15 0.00
383_S 58_G 0.81 0.15 0.00
342_A 32_A 0.81 0.15 0.00
264_Q 19_F 0.81 0.15 0.00
53_V 114_L 0.81 0.15 0.00
365_T 196_H 0.81 0.15 0.00
189_D 21_G 0.81 0.15 0.00
109_V 26_F 0.80 0.15 0.00
225_V 156_V 0.80 0.15 0.00
45_V 28_M 0.80 0.15 0.00
29_I 232_L 0.80 0.15 0.00
262_D 236_L 0.80 0.15 0.00
110_I 122_P 0.80 0.15 0.00
189_D 28_M 0.80 0.15 0.00
97_A 204_T 0.80 0.14 0.00
228_A 127_V 0.80 0.14 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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