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OPENSEQ.org
cIp_2_40_isp_2_human
Genes: A B A+B
Length: 249 275 418
Sequences: 1028 547 69
Seq/Len: 4.13 1.99 0.17
MirrorTree (Pazo et al. 2001) 0.72
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 0.00
100 0.00 0.00 0.01
∞ 0.00 0.00 0.13
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
204_I 65_L 1.65 0.36 0.00
88_R 266_F 1.41 0.25 0.00
108_P 109_E 1.39 0.24 0.00
200_D 273_I 1.38 0.23 0.00
158_I 268_S 1.35 0.22 0.00
222_R 115_S 1.34 0.22 0.00
66_I 80_S 1.32 0.21 0.00
91_G 134_V 1.27 0.19 0.00
158_I 162_E 1.26 0.19 0.00
55_F 79_Y 1.26 0.19 0.00
147_S 93_R 1.25 0.18 0.00
93_L 217_V 1.25 0.18 0.00
57_P 114_F 1.25 0.18 0.00
163_T 273_I 1.24 0.18 0.00
204_I 138_V 1.23 0.18 0.00
129_K 146_D 1.23 0.18 0.00
150_E 137_F 1.21 0.17 0.00
150_E 91_E 1.20 0.17 0.00
93_L 170_W 1.20 0.17 0.00
200_D 84_I 1.19 0.16 0.00
212_K 66_V 1.18 0.16 0.00
106_Q 65_L 1.16 0.15 0.00
120_T 245_D 1.15 0.15 0.00
121_M 248_G 1.14 0.15 0.00
121_M 174_P 1.12 0.14 0.00
151_A 129_A 1.12 0.14 0.00
67_V 152_K 1.12 0.14 0.00
160_V 177_V 1.11 0.14 0.00
62_R 233_G 1.10 0.14 0.00
230_G 231_D 1.10 0.14 0.00
89_Q 217_V 1.10 0.14 0.00
202_E 106_E 1.10 0.14 0.00
106_Q 205_R 1.09 0.14 0.00
75_K 109_E 1.09 0.14 0.00
89_Q 80_S 1.09 0.14 0.00
237_P 217_V 1.09 0.14 0.00
155_K 172_G 1.07 0.13 0.00
183_A 272_V 1.06 0.13 0.00
57_P 269_D 1.06 0.13 0.00
199_K 268_S 1.06 0.13 0.00
120_T 72_N 1.05 0.12 0.00
82_V 67_A 1.05 0.12 0.00
152_I 139_S 1.04 0.12 0.00
106_Q 251_R 1.04 0.12 0.00
188_I 107_S 1.04 0.12 0.00
158_I 203_L 1.04 0.12 0.00
157_G 87_P 1.04 0.12 0.00
207_E 269_D 1.03 0.12 0.00
124_R 197_R 1.03 0.12 0.00
149_L 104_S 1.03 0.12 0.00
90_N 166_M 1.03 0.12 0.00
89_Q 131_K 1.03 0.12 0.00
106_Q 263_T 1.02 0.12 0.00
59_N 67_A 1.02 0.12 0.00
68_K 268_S 1.02 0.12 0.00
114_E 196_L 1.02 0.12 0.00
199_K 97_V 1.02 0.12 0.00
169_F 189_A 1.01 0.12 0.00
186_V 125_G 1.01 0.12 0.00
192_Y 137_F 1.00 0.11 0.00
228_A 221_L 1.00 0.11 0.00
121_M 256_P 1.00 0.11 0.00
174_V 202_D 1.00 0.11 0.00
131_H 219_T 1.00 0.11 0.00
61_K 197_R 1.00 0.11 0.00
177_L 166_M 0.99 0.11 0.00
120_T 106_E 0.99 0.11 0.00
143_R 269_D 0.99 0.11 0.00
106_Q 104_S 0.99 0.11 0.00
160_V 110_A 0.99 0.11 0.00
197_T 242_S 0.99 0.11 0.00
197_T 253_G 0.99 0.11 0.00
197_T 254_P 0.99 0.11 0.00
197_T 255_A 0.99 0.11 0.00
231_L 212_V 0.99 0.11 0.00
96_S 135_T 0.98 0.11 0.00
231_L 267_T 0.98 0.11 0.00
132_I 125_G 0.98 0.11 0.00
94_P 164_K 0.98 0.11 0.00
165_P 99_D 0.97 0.11 0.00
108_P 113_G 0.97 0.11 0.00
66_I 89_F 0.97 0.11 0.00
193_Y 125_G 0.97 0.11 0.00
206_D 190_A 0.97 0.11 0.00
55_F 273_I 0.97 0.11 0.00
136_T 197_R 0.97 0.10 0.00
64_E 128_Y 0.96 0.10 0.00
75_K 162_E 0.96 0.10 0.00
143_R 153_I 0.96 0.10 0.00
52_P 176_F 0.96 0.10 0.00
173_E 115_S 0.96 0.10 0.00
192_Y 166_M 0.96 0.10 0.00
50_D 109_E 0.96 0.10 0.00
192_Y 133_A 0.96 0.10 0.00
125_K 70_G 0.96 0.10 0.00
212_K 177_V 0.95 0.10 0.00
131_H 123_T 0.95 0.10 0.00
169_F 108_S 0.95 0.10 0.00
82_V 158_S 0.94 0.10 0.00
100_K 213_I 0.94 0.10 0.00
198_A 272_V 0.94 0.10 0.00
64_E 125_G 0.94 0.10 0.00
202_E 77_V 0.94 0.10 0.00
82_V 79_Y 0.94 0.10 0.00
182_N 154_E 0.93 0.10 0.00
162_E 122_T 0.93 0.10 0.00
165_P 101_T 0.93 0.10 0.00
94_P 94_R 0.93 0.10 0.00
182_N 208_K 0.92 0.10 0.00
117_T 124_V 0.92 0.10 0.00
77_A 229_A 0.92 0.10 0.00
162_E 219_T 0.92 0.10 0.00
136_T 123_T 0.92 0.10 0.00
201_I 263_T 0.92 0.10 0.00
105_L 172_G 0.92 0.10 0.00
179_A 172_G 0.92 0.10 0.00
129_K 143_A 0.92 0.10 0.00
221_G 123_T 0.91 0.09 0.00
167_K 270_D 0.91 0.09 0.00
186_V 130_A 0.91 0.09 0.00
57_P 197_R 0.91 0.09 0.00
155_K 100_S 0.91 0.09 0.00
50_D 93_R 0.91 0.09 0.00
67_V 130_A 0.91 0.09 0.00
94_P 200_Q 0.90 0.09 0.00
101_V 228_N 0.90 0.09 0.00
94_P 201_H 0.90 0.09 0.00
146_D 189_A 0.90 0.09 0.00
165_P 125_G 0.90 0.09 0.00
223_F 195_Q 0.90 0.09 0.00
97_A 227_A 0.90 0.09 0.00
141_M 227_A 0.90 0.09 0.00
241_P 109_E 0.89 0.09 0.00
52_P 165_N 0.89 0.09 0.00
240_G 156_K 0.89 0.09 0.00
127_V 256_P 0.89 0.09 0.00
121_M 141_M 0.89 0.09 0.00
123_N 122_T 0.89 0.09 0.00
217_G 268_S 0.89 0.09 0.00
215_K 145_A 0.89 0.09 0.00
82_V 273_I 0.88 0.09 0.00
103_E 193_L 0.88 0.09 0.00
64_E 121_V 0.88 0.09 0.00
143_R 122_T 0.88 0.09 0.00
143_R 166_M 0.88 0.09 0.00
168_L 114_F 0.88 0.09 0.00
210_A 248_G 0.88 0.09 0.00
188_I 138_V 0.88 0.09 0.00
187_Q 233_G 0.88 0.09 0.00
82_V 109_E 0.88 0.09 0.00
214_P 160_I 0.88 0.09 0.00
121_M 123_T 0.87 0.09 0.00
109_P 68_S 0.87 0.09 0.00
137_T 217_V 0.87 0.09 0.00
235_T 270_D 0.87 0.09 0.00
203_E 91_E 0.87 0.09 0.00
193_Y 115_S 0.87 0.09 0.00
150_E 72_N 0.87 0.09 0.00
99_N 127_A 0.87 0.09 0.00
155_K 268_S 0.86 0.09 0.00
99_N 256_P 0.86 0.09 0.00
91_G 248_G 0.86 0.09 0.00
201_I 107_S 0.86 0.08 0.00
66_I 221_L 0.86 0.08 0.00
96_S 76_S 0.86 0.08 0.00
72_E 105_R 0.86 0.08 0.00
51_T 67_A 0.86 0.08 0.00
149_L 133_A 0.85 0.08 0.00
187_Q 67_A 0.85 0.08 0.00
136_T 125_G 0.85 0.08 0.00
63_I 213_I 0.85 0.08 0.00
196_L 264_Y 0.85 0.08 0.00
152_I 226_I 0.85 0.08 0.00
207_E 128_Y 0.85 0.08 0.00
226_E 120_G 0.85 0.08 0.00
199_K 134_V 0.84 0.08 0.00
60_Y 124_V 0.84 0.08 0.00
165_P 76_S 0.84 0.08 0.00
159_K 110_A 0.84 0.08 0.00
123_N 257_L 0.84 0.08 0.00
64_E 72_N 0.84 0.08 0.00
157_G 177_V 0.84 0.08 0.00
65_A 246_A 0.84 0.08 0.00
66_I 251_R 0.84 0.08 0.00
143_R 124_V 0.84 0.08 0.00
205_I 133_A 0.83 0.08 0.00
164_T 67_A 0.83 0.08 0.00
108_P 105_R 0.83 0.08 0.00
50_D 145_A 0.83 0.08 0.00
242_G 166_M 0.83 0.08 0.00
151_A 130_A 0.83 0.08 0.00
229_G 130_A 0.83 0.08 0.00
212_K 269_D 0.83 0.08 0.00
147_S 219_T 0.83 0.08 0.00
165_P 148_L 0.83 0.08 0.00
199_K 272_V 0.83 0.08 0.00
120_T 200_Q 0.83 0.08 0.00
113_Y 104_S 0.83 0.08 0.00
214_P 110_A 0.83 0.08 0.00
158_I 106_E 0.83 0.08 0.00
202_E 205_R 0.83 0.08 0.00
131_H 248_G 0.83 0.08 0.00
72_E 177_V 0.82 0.08 0.00
153_Q 125_G 0.82 0.08 0.00
231_L 226_I 0.82 0.08 0.00
195_D 272_V 0.82 0.08 0.00
66_I 163_G 0.82 0.08 0.00
85_L 270_D 0.82 0.08 0.00
57_P 65_L 0.82 0.08 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
5869 0.03 cIp_2_4_isp_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5868 0.17 cIp_2_40_isp_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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