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OPENSEQ.org
cIp_1_4_isp_2_human
Genes: A B A+B
Length: 455 275 628
Sequences: 3873 547 103
Seq/Len: 8.51 1.99 0.16
MirrorTree (Pazo et al. 2001) 0.21
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 0.01 0.00 0.01
∞ 0.06 0.00 0.14
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
251_T 97_V 1.35 0.21 0.00
304_N 118_V 1.27 0.18 0.00
229_C 176_F 1.22 0.17 0.00
73_T 217_V 1.22 0.17 0.00
298_V 205_R 1.16 0.15 0.00
62_K 273_I 1.15 0.15 0.00
401_D 80_S 1.13 0.14 0.00
137_G 90_S 1.12 0.14 0.00
397_P 82_T 1.11 0.14 0.00
245_I 249_R 1.08 0.13 0.00
423_A 67_A 1.07 0.13 0.00
105_V 249_R 1.07 0.12 0.00
414_T 114_F 1.06 0.12 0.00
438_E 127_A 1.03 0.12 0.00
186_V 265_E 1.01 0.11 0.00
127_H 137_F 1.01 0.11 0.00
66_W 90_S 1.01 0.11 0.00
398_A 167_A 1.00 0.11 0.00
302_W 273_I 0.99 0.11 0.00
42_W 111_R 0.99 0.11 0.00
102_K 188_E 0.98 0.10 0.00
240_A 197_R 0.97 0.10 0.00
188_V 80_S 0.97 0.10 0.00
61_L 251_R 0.95 0.10 0.00
289_E 119_T 0.95 0.10 0.00
137_G 94_R 0.95 0.10 0.00
396_R 192_E 0.95 0.10 0.00
330_F 114_F 0.94 0.10 0.00
71_I 270_D 0.94 0.10 0.00
336_A 124_V 0.94 0.10 0.00
407_S 235_Y 0.94 0.10 0.00
291_I 207_K 0.93 0.10 0.00
186_V 185_I 0.93 0.10 0.00
397_P 249_R 0.92 0.09 0.00
86_T 267_T 0.92 0.09 0.00
217_K 246_A 0.92 0.09 0.00
258_R 263_T 0.91 0.09 0.00
73_T 126_V 0.91 0.09 0.00
165_R 67_A 0.90 0.09 0.00
250_G 147_V 0.90 0.09 0.00
441_M 273_I 0.90 0.09 0.00
245_I 269_D 0.89 0.09 0.00
384_N 93_R 0.89 0.09 0.00
353_D 124_V 0.89 0.09 0.00
55_K 167_A 0.89 0.09 0.00
396_R 171_R 0.88 0.09 0.00
142_A 174_P 0.88 0.09 0.00
147_I 147_V 0.88 0.09 0.00
201_T 152_K 0.88 0.09 0.00
122_L 193_L 0.87 0.08 0.00
289_E 177_V 0.87 0.08 0.00
441_M 124_V 0.87 0.08 0.00
247_R 155_I 0.86 0.08 0.00
269_I 105_R 0.86 0.08 0.00
176_N 135_T 0.85 0.08 0.00
73_T 85_K 0.85 0.08 0.00
318_I 173_K 0.85 0.08 0.00
245_I 143_A 0.85 0.08 0.00
73_T 93_R 0.85 0.08 0.00
250_G 66_V 0.85 0.08 0.00
176_N 77_V 0.84 0.08 0.00
366_K 213_I 0.84 0.08 0.00
441_M 166_M 0.84 0.08 0.00
387_M 154_E 0.84 0.08 0.00
182_Y 185_I 0.84 0.08 0.00
363_E 94_R 0.84 0.08 0.00
414_T 241_G 0.84 0.08 0.00
232_T 173_K 0.83 0.08 0.00
67_I 199_P 0.83 0.08 0.00
386_V 188_E 0.83 0.08 0.00
318_I 67_A 0.83 0.08 0.00
136_G 95_L 0.83 0.08 0.00
149_I 201_H 0.82 0.08 0.00
445_A 248_G 0.82 0.08 0.00
285_V 172_G 0.82 0.08 0.00
266_L 120_G 0.82 0.08 0.00
255_G 108_S 0.82 0.08 0.00
398_A 267_T 0.82 0.08 0.00
176_N 269_D 0.82 0.07 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
5856 0.16 cIp_1_4_isp_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5855 0.16 cIp_1_4_isp_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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