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OPENSEQ.org
cIp_6_40_cIV_2_40
Genes: A B A+B
Length: 213 227 395
Sequences: 401 4148 126
Seq/Len: 1.88 18.27 0.32
MirrorTree (Pazo et al. 2001) 0.73
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 0.00 0.00
20 0.01 0.00 0.01
100 0.01 0.01 0.05
∞ 0.01 0.02 0.29
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
201_I 97_I 1.78 0.62 0.00
64_V 63_T 1.55 0.47 0.00
120_M 162_S 1.41 0.37 0.00
191_L 211_L 1.31 0.31 0.00
180_I 219_F 1.27 0.29 0.00
137_V 143_V 1.26 0.28 0.00
189_A 198_E 1.25 0.28 0.00
201_I 218_I 1.24 0.27 0.00
68_D 61_M 1.22 0.26 0.00
99_P 205_S 1.21 0.25 0.00
148_V 68_L 1.20 0.25 0.00
143_E 23_F 1.16 0.23 0.00
47_P 144_L 1.15 0.23 0.00
112_A 168_L 1.15 0.23 0.00
110_F 36_F 1.12 0.21 0.00
68_D 37_L 1.11 0.21 0.00
152_S 56_S 1.10 0.21 0.00
190_L 20_L 1.10 0.20 0.00
109_V 91_N 1.10 0.20 0.00
180_I 20_L 1.10 0.20 0.00
180_I 49_K 1.09 0.20 0.00
143_E 154_I 1.08 0.20 0.00
201_I 212_E 1.07 0.19 0.00
194_I 46_L 1.05 0.18 0.00
167_V 101_G 1.04 0.18 0.00
201_I 42_L 1.04 0.18 0.00
191_L 194_G 1.04 0.18 0.00
176_V 219_F 1.02 0.17 0.00
67_L 28_L 1.00 0.16 0.00
180_I 186_A 0.99 0.16 0.00
194_I 101_G 0.99 0.16 0.00
108_V 169_G 0.98 0.15 0.00
201_I 19_E 0.98 0.15 0.00
191_L 67_I 0.97 0.15 0.00
64_V 36_F 0.97 0.15 0.00
145_R 142_V 0.97 0.15 0.00
171_D 198_E 0.97 0.15 0.00
110_F 80_S 0.96 0.15 0.00
42_T 36_F 0.96 0.15 0.00
120_M 100_I 0.96 0.15 0.00
140_Q 38_V 0.95 0.15 0.00
101_Y 57_D 0.95 0.14 0.00
82_M 157_Q 0.95 0.14 0.00
91_V 197_S 0.95 0.14 0.00
70_L 69_P 0.94 0.14 0.00
45_A 72_I 0.94 0.14 0.00
77_S 80_S 0.94 0.14 0.00
142_P 213_L 0.93 0.14 0.00
195_L 52_N 0.93 0.14 0.00
74_A 77_A 0.93 0.14 0.00
146_Y 184_F 0.93 0.14 0.00
143_E 43_F 0.92 0.14 0.00
43_Q 182_T 0.92 0.14 0.00
121_I 42_L 0.92 0.14 0.00
120_M 208_P 0.92 0.14 0.00
180_I 95_L 0.92 0.14 0.00
125_T 198_E 0.91 0.13 0.00
180_I 47_T 0.91 0.13 0.00
112_A 81_L 0.91 0.13 0.00
152_S 193_Y 0.91 0.13 0.00
49_A 215_P 0.90 0.13 0.00
98_A 147_E 0.90 0.13 0.00
193_G 104_W 0.90 0.13 0.00
122_V 155_T 0.90 0.13 0.00
140_Q 74_V 0.90 0.13 0.00
46_L 188_R 0.90 0.13 0.00
100_R 50_L 0.89 0.13 0.00
205_R 58_A 0.89 0.13 0.00
45_A 144_L 0.89 0.12 0.00
112_A 89_E 0.89 0.12 0.00
154_A 135_L 0.89 0.12 0.00
201_I 148_A 0.88 0.12 0.00
201_I 177_G 0.88 0.12 0.00
180_I 91_N 0.88 0.12 0.00
69_D 43_F 0.88 0.12 0.00
193_G 154_I 0.87 0.12 0.00
99_P 68_L 0.87 0.12 0.00
134_L 80_S 0.87 0.12 0.00
149_S 111_T 0.87 0.12 0.00
189_A 58_A 0.87 0.12 0.00
194_I 216_L 0.87 0.12 0.00
74_A 150_I 0.86 0.12 0.00
95_H 35_C 0.86 0.12 0.00
46_L 216_L 0.86 0.12 0.00
91_V 97_I 0.86 0.12 0.00
106_F 22_T 0.86 0.12 0.00
176_V 71_I 0.86 0.12 0.00
204_E 45_A 0.86 0.12 0.00
77_S 170_L 0.86 0.12 0.00
164_Y 183_T 0.86 0.12 0.00
194_I 34_I 0.85 0.12 0.00
176_V 223_P 0.85 0.12 0.00
139_D 214_I 0.85 0.12 0.00
61_E 50_L 0.85 0.11 0.00
47_P 185_T 0.83 0.11 0.00
127_T 184_F 0.83 0.11 0.00
198_Q 52_N 0.83 0.11 0.00
180_I 188_R 0.83 0.11 0.00
117_S 31_I 0.83 0.11 0.00
146_Y 25_D 0.83 0.11 0.00
200_K 69_P 0.82 0.11 0.00
139_D 28_L 0.82 0.11 0.00
119_V 128_L 0.82 0.11 0.00
62_Y 35_C 0.81 0.10 0.00
82_M 167_T 0.81 0.10 0.00
52_V 189_P 0.81 0.10 0.00
107_G 222_G 0.81 0.10 0.00
81_P 87_T 0.81 0.10 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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