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OPENSEQ.org
cIp_1_4_cyt1_2_human
Genes: A B A+B
Length: 455 325 693
Sequences: 3873 747 171
Seq/Len: 8.51 2.3 0.25
MirrorTree (Pazo et al. 2001) 0.01
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 0.02 0.01
2 0.00 0.02 0.01
5 0.00 0.02 0.01
10 0.00 0.02 0.01
20 0.00 0.02 0.01
100 0.01 0.02 0.04
∞ 0.06 0.02 0.22
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
164_I 220_E 1.65 0.46 0.00
284_S 278_S 1.57 0.41 0.00
224_V 307_K 1.33 0.28 0.00
125_D 109_S 1.33 0.28 0.00
68_L 127_M 1.33 0.28 0.00
284_S 240_Q 1.31 0.26 0.00
176_N 290_L 1.27 0.25 0.00
158_S 84_A 1.22 0.22 0.00
203_L 190_N 1.21 0.22 0.00
173_I 294_M 1.21 0.22 0.00
155_N 109_S 1.20 0.21 0.00
319_P 96_W 1.18 0.21 0.00
356_K 282_H 1.14 0.19 0.00
58_E 308_R 1.12 0.18 0.00
207_I 129_F 1.12 0.18 0.00
173_I 208_E 1.11 0.18 0.00
356_K 134_H 1.10 0.17 0.00
164_I 187_A 1.07 0.17 0.00
426_V 139_C 1.06 0.16 0.00
224_V 122_A 1.06 0.16 0.00
130_L 175_F 1.05 0.16 0.00
48_L 213_S 1.05 0.16 0.00
231_T 296_M 1.04 0.15 0.00
290_L 186_R 1.04 0.15 0.00
250_G 283_D 1.04 0.15 0.00
282_E 310_K 1.04 0.15 0.00
69_G 182_S 1.03 0.15 0.00
48_L 240_Q 1.03 0.15 0.00
234_A 103_S 1.00 0.14 0.00
254_A 251_D 1.00 0.14 0.00
254_A 260_P 0.99 0.14 0.00
122_L 131_A 0.98 0.14 0.00
130_L 122_A 0.98 0.14 0.00
345_V 120_V 0.98 0.13 0.00
306_L 313_V 0.98 0.13 0.00
323_C 271_C 0.98 0.13 0.00
183_D 312_S 0.98 0.13 0.00
255_G 82_V 0.97 0.13 0.00
103_Y 191_G 0.97 0.13 0.00
69_G 148_L 0.97 0.13 0.00
405_E 88_E 0.96 0.13 0.00
103_Y 299_L 0.96 0.13 0.00
45_K 226_S 0.96 0.13 0.00
284_S 282_H 0.96 0.13 0.00
387_M 223_T 0.95 0.13 0.00
335_Q 245_A 0.95 0.13 0.00
49_S 168_P 0.95 0.13 0.00
334_V 169_G 0.95 0.13 0.00
204_I 142_E 0.95 0.12 0.00
65_D 105_L 0.94 0.12 0.00
155_N 110_I 0.94 0.12 0.00
171_G 268_K 0.94 0.12 0.00
71_I 168_P 0.94 0.12 0.00
122_L 174_Y 0.94 0.12 0.00
398_A 126_S 0.93 0.12 0.00
170_A 145_A 0.93 0.12 0.00
158_S 110_I 0.93 0.12 0.00
134_L 238_P 0.93 0.12 0.00
255_G 72_A 0.92 0.12 0.00
178_C 281_E 0.92 0.12 0.00
211_Q 103_S 0.92 0.12 0.00
435_P 115_Q 0.91 0.12 0.00
158_S 130_V 0.91 0.11 0.00
99_G 159_N 0.91 0.11 0.00
68_L 254_E 0.90 0.11 0.00
106_V 221_P 0.90 0.11 0.00
298_V 271_C 0.90 0.11 0.00
40_H 138_V 0.90 0.11 0.00
284_S 205_H 0.90 0.11 0.00
106_V 154_V 0.90 0.11 0.00
125_D 272_T 0.89 0.11 0.00
102_K 123_S 0.89 0.11 0.00
282_E 154_V 0.89 0.11 0.00
256_F 299_L 0.89 0.11 0.00
290_L 200_I 0.88 0.11 0.00
120_E 145_A 0.88 0.11 0.00
133_C 123_S 0.88 0.11 0.00
226_V 243_A 0.88 0.11 0.00
55_K 144_E 0.87 0.10 0.00
186_V 169_G 0.87 0.10 0.00
122_L 107_H 0.87 0.10 0.00
141_G 177_K 0.87 0.10 0.00
356_K 248_I 0.86 0.10 0.00
410_I 281_E 0.86 0.10 0.00
132_G 210_Y 0.86 0.10 0.00
179_G 242_I 0.86 0.10 0.00
155_N 272_T 0.85 0.10 0.00
332_A 180_P 0.85 0.10 0.00
52_D 109_S 0.85 0.10 0.00
145_A 253_L 0.85 0.10 0.00
275_H 150_A 0.85 0.10 0.00
137_G 142_E 0.85 0.10 0.00
69_G 160_E 0.84 0.10 0.00
229_C 295_M 0.84 0.10 0.00
145_A 288_M 0.84 0.10 0.00
275_H 245_A 0.83 0.10 0.00
238_T 316_S 0.83 0.10 0.00
243_P 107_H 0.83 0.10 0.00
439_E 268_K 0.83 0.10 0.00
318_I 271_C 0.83 0.10 0.00
213_K 129_F 0.83 0.10 0.00
234_A 295_M 0.83 0.10 0.00
317_L 243_A 0.83 0.10 0.00
207_I 180_P 0.83 0.10 0.00
36_L 165_F 0.82 0.09 0.00
204_I 146_K 0.82 0.09 0.00
435_P 172_F 0.82 0.09 0.00
361_L 168_P 0.82 0.09 0.00
130_L 306_I 0.82 0.09 0.00
383_M 302_L 0.82 0.09 0.00
285_V 279_E 0.82 0.09 0.00
325_T 109_S 0.81 0.09 0.00
437_L 266_I 0.81 0.09 0.00
343_A 122_A 0.81 0.09 0.00
337_Q 172_F 0.81 0.09 0.00
130_L 180_P 0.81 0.09 0.00
404_W 177_K 0.81 0.09 0.00
45_K 174_Y 0.81 0.09 0.00
327_L 169_G 0.81 0.09 0.00
436_E 175_F 0.81 0.09 0.00
164_I 206_G 0.81 0.09 0.00
60_L 287_R 0.81 0.09 0.00
46_G 118_K 0.81 0.09 0.00
175_K 232_Y 0.81 0.09 0.00
317_L 105_L 0.80 0.09 0.00
318_I 179_Y 0.80 0.09 0.00
289_E 144_E 0.80 0.09 0.00
167_A 240_Q 0.80 0.09 0.00
282_E 188_A 0.80 0.09 0.00
335_Q 94_Y 0.80 0.09 0.00
128_K 179_Y 0.80 0.09 0.00
97_S 150_A 0.80 0.09 0.00
149_I 292_M 0.80 0.09 0.00
128_K 109_S 0.79 0.09 0.00
354_I 172_F 0.79 0.09 0.00
288_K 301_P 0.79 0.09 0.00
169_E 119_Q 0.79 0.09 0.00
134_L 311_W 0.79 0.09 0.00
321_S 141_T 0.79 0.09 0.00
290_L 204_R 0.79 0.09 0.00
44_L 154_V 0.78 0.09 0.00
137_G 151_E 0.78 0.09 0.00
134_L 160_E 0.78 0.09 0.00
49_S 208_E 0.78 0.09 0.00
204_I 213_S 0.78 0.09 0.00
254_A 190_N 0.78 0.09 0.00
147_I 312_S 0.78 0.08 0.00
69_G 94_Y 0.78 0.08 0.00
188_V 130_V 0.78 0.08 0.00
45_K 310_K 0.78 0.08 0.00
307_A 175_F 0.78 0.08 0.00
356_K 127_M 0.77 0.08 0.00
345_V 238_P 0.77 0.08 0.00
128_K 138_V 0.77 0.08 0.00
250_G 118_K 0.77 0.08 0.00
125_D 271_C 0.77 0.08 0.00
137_G 140_Y 0.77 0.08 0.00
48_L 134_H 0.77 0.08 0.00
58_E 172_F 0.77 0.08 0.00
144_A 69_A 0.77 0.08 0.00
182_Y 314_L 0.77 0.08 0.00
65_D 223_T 0.77 0.08 0.00
290_L 197_L 0.77 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
5861 0.25 cIp_1_4_cyt1_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5857 0.24 cIp_1_4_cyt1_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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