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OPENSEQ.org
cIp_2_40_cIV_2_40
Genes: A B A+B
Length: 249 227 428
Sequences: 654 4148 203
Seq/Len: 2.63 18.27 0.47
MirrorTree (Pazo et al. 2001) 0.66
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.01 0.02
∞ 0.00 0.02 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
76_A 211_L 1.65 0.65 0.00
106_Q 40_Y 1.55 0.58 0.00
76_A 74_V 1.27 0.37 0.00
197_T 147_E 1.18 0.31 0.00
145_S 97_I 1.14 0.29 0.00
198_A 23_F 1.14 0.28 0.00
197_T 219_F 1.11 0.27 0.00
193_Y 43_F 1.08 0.25 0.00
106_Q 46_L 1.06 0.24 0.00
94_P 223_P 1.05 0.23 0.00
91_G 160_L 1.04 0.23 0.00
108_P 23_F 1.02 0.22 0.00
56_T 192_Y 1.01 0.21 0.00
170_T 12_A 1.00 0.21 0.00
56_T 187_T 1.00 0.21 0.00
186_V 13_T 1.00 0.21 0.00
99_N 147_E 0.99 0.20 0.00
150_E 29_M 0.97 0.19 0.00
203_E 92_D 0.97 0.19 0.00
206_D 185_T 0.96 0.19 0.00
61_K 95_L 0.95 0.18 0.00
61_K 14_S 0.95 0.18 0.00
64_E 219_F 0.95 0.18 0.00
107_V 59_Q 0.95 0.18 0.00
89_Q 169_G 0.95 0.18 0.00
104_V 99_S 0.95 0.18 0.00
202_E 67_I 0.95 0.18 0.00
204_I 33_L 0.94 0.18 0.00
221_G 61_M 0.94 0.18 0.00
212_K 91_N 0.94 0.18 0.00
103_E 67_I 0.94 0.18 0.00
216_P 125_P 0.94 0.18 0.00
93_L 220_E 0.93 0.18 0.00
154_K 127_F 0.93 0.18 0.00
93_L 46_L 0.93 0.17 0.00
231_L 192_Y 0.93 0.17 0.00
94_P 131_G 0.92 0.17 0.00
82_V 175_I 0.92 0.17 0.00
148_I 213_L 0.92 0.17 0.00
150_E 188_R 0.92 0.17 0.00
197_T 123_L 0.92 0.17 0.00
132_I 97_I 0.92 0.17 0.00
145_S 64_V 0.91 0.17 0.00
147_S 147_E 0.91 0.17 0.00
233_S 39_L 0.91 0.17 0.00
167_K 160_L 0.91 0.17 0.00
104_V 12_A 0.91 0.17 0.00
104_V 219_F 0.90 0.16 0.00
165_P 215_P 0.90 0.16 0.00
120_T 180_N 0.89 0.16 0.00
46_E 188_R 0.89 0.16 0.00
181_V 134_R 0.89 0.16 0.00
91_G 176_P 0.89 0.16 0.00
156_L 198_E 0.89 0.16 0.00
242_G 58_A 0.88 0.15 0.00
93_L 218_I 0.88 0.15 0.00
204_I 23_F 0.87 0.15 0.00
122_Y 12_A 0.87 0.15 0.00
101_V 15_P 0.87 0.15 0.00
147_S 25_D 0.87 0.15 0.00
68_K 118_F 0.86 0.15 0.00
210_A 216_L 0.86 0.15 0.00
214_P 221_M 0.86 0.15 0.00
57_P 33_L 0.86 0.15 0.00
208_L 148_A 0.86 0.15 0.00
208_L 35_C 0.86 0.15 0.00
208_L 14_S 0.86 0.15 0.00
48_N 101_G 0.86 0.14 0.00
148_I 103_Q 0.86 0.14 0.00
132_I 156_S 0.85 0.14 0.00
186_V 85_Y 0.85 0.14 0.00
146_D 103_Q 0.85 0.14 0.00
106_Q 142_V 0.84 0.14 0.00
114_E 5_A 0.84 0.14 0.00
47_N 215_P 0.84 0.14 0.00
165_P 185_T 0.84 0.14 0.00
65_A 61_M 0.84 0.14 0.00
95_I 219_F 0.83 0.14 0.00
220_S 192_Y 0.83 0.14 0.00
199_K 221_M 0.83 0.14 0.00
96_S 76_I 0.83 0.13 0.00
82_V 89_E 0.83 0.13 0.00
107_V 14_S 0.82 0.13 0.00
188_I 175_I 0.82 0.13 0.00
165_P 46_L 0.82 0.13 0.00
162_E 86_M 0.81 0.13 0.00
170_T 186_A 0.81 0.13 0.00
68_K 113_Y 0.81 0.13 0.00
193_Y 63_T 0.81 0.13 0.00
61_K 144_L 0.81 0.13 0.00
79_V 39_L 0.81 0.13 0.00
110_M 154_I 0.81 0.13 0.00
153_Q 37_L 0.81 0.13 0.00
67_V 165_V 0.81 0.13 0.00
57_P 162_S 0.81 0.13 0.00
169_F 127_F 0.81 0.13 0.00
235_T 40_Y 0.81 0.13 0.00
216_P 37_L 0.81 0.13 0.00
106_Q 58_A 0.80 0.13 0.00
111_R 168_L 0.80 0.13 0.00
64_E 94_S 0.80 0.12 0.00
91_G 162_S 0.80 0.12 0.00
185_M 198_E 0.79 0.12 0.00
47_N 44_L 0.79 0.12 0.00
127_V 155_T 0.79 0.12 0.00
56_T 225_F 0.79 0.12 0.00
54_D 213_L 0.79 0.12 0.00
76_A 30_I 0.79 0.12 0.00
177_L 111_T 0.79 0.12 0.00
218_P 61_M 0.79 0.12 0.00
57_P 101_G 0.78 0.12 0.00
134_V 171_K 0.78 0.12 0.00
189_N 82_R 0.78 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
4181 0.35 cIp_2_4_cIV_2_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4180 0.47 cIp_2_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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