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OPENSEQ.org
cIp_6_20_cIV_2_20
Genes: A B A+B
Length: 213 227 395
Sequences: 401 5002 188
Seq/Len: 1.88 22.04 0.48
MirrorTree (Pazo et al. 2001) 0.59
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 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.02
100 0.01 0.02 0.07
∞ 0.01 0.04 0.43
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
191_L 101_G 1.58 0.61 0.00
94_M 156_S 1.35 0.43 0.00
120_M 162_S 1.30 0.40 0.00
194_I 144_L 1.23 0.35 0.00
191_L 211_L 1.19 0.32 0.00
180_I 100_I 1.13 0.28 0.00
74_A 218_I 1.12 0.28 0.00
201_I 212_E 1.12 0.28 0.00
152_S 56_S 1.11 0.27 0.00
194_I 216_L 1.11 0.27 0.00
191_L 215_P 1.09 0.26 0.00
201_I 97_I 1.09 0.26 0.00
109_V 76_I 1.07 0.24 0.00
178_I 71_I 1.03 0.23 0.00
194_I 178_R 1.01 0.21 0.00
195_L 52_N 1.01 0.21 0.00
178_I 223_P 1.00 0.21 0.00
201_I 148_A 0.98 0.20 0.00
193_G 68_L 0.96 0.19 0.00
201_I 71_I 0.95 0.18 0.00
131_A 143_V 0.94 0.18 0.00
176_V 166_P 0.93 0.18 0.00
74_A 150_I 0.93 0.17 0.00
106_F 73_L 0.92 0.17 0.00
91_V 97_I 0.92 0.17 0.00
167_V 107_T 0.92 0.17 0.00
203_R 63_T 0.91 0.17 0.00
75_R 198_E 0.91 0.17 0.00
75_R 199_I 0.91 0.17 0.00
180_I 199_I 0.91 0.17 0.00
120_M 94_S 0.91 0.17 0.00
202_K 150_I 0.91 0.17 0.00
108_V 169_G 0.90 0.17 0.00
180_I 49_K 0.90 0.16 0.00
190_L 20_L 0.89 0.16 0.00
46_L 188_R 0.89 0.16 0.00
193_G 26_H 0.89 0.16 0.00
193_G 212_E 0.88 0.15 0.00
72_N 23_F 0.88 0.15 0.00
108_V 165_V 0.87 0.15 0.00
74_A 189_P 0.87 0.15 0.00
104_D 61_M 0.87 0.15 0.00
148_V 68_L 0.87 0.15 0.00
146_Y 25_D 0.87 0.15 0.00
200_K 68_L 0.86 0.15 0.00
191_L 95_L 0.86 0.15 0.00
122_V 155_T 0.85 0.15 0.00
193_G 47_T 0.85 0.14 0.00
71_V 28_L 0.85 0.14 0.00
113_S 38_V 0.85 0.14 0.00
164_Y 194_G 0.85 0.14 0.00
61_E 70_A 0.85 0.14 0.00
199_R 80_S 0.84 0.14 0.00
69_D 36_F 0.84 0.14 0.00
203_R 174_A 0.83 0.14 0.00
191_L 157_Q 0.83 0.14 0.00
139_D 174_A 0.83 0.14 0.00
131_A 95_L 0.82 0.14 0.00
70_L 34_I 0.82 0.13 0.00
99_P 46_L 0.82 0.13 0.00
63_V 70_A 0.82 0.13 0.00
69_D 48_T 0.81 0.13 0.00
205_R 58_A 0.81 0.13 0.00
123_A 86_M 0.81 0.13 0.00
189_A 198_E 0.80 0.13 0.00
165_S 57_D 0.80 0.13 0.00
131_A 146_I 0.80 0.13 0.00
180_I 168_L 0.80 0.12 0.00
180_I 182_T 0.79 0.12 0.00
120_M 140_N 0.79 0.12 0.00
178_I 215_P 0.79 0.12 0.00
148_V 123_L 0.79 0.12 0.00
97_A 61_M 0.79 0.12 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
4321 0.48 cIp_6_20_cIV_2_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4320 0.32 cIp_6_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4319 0.52 cIp_6_2_cIV_2_4 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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