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OPENSEQ.org
cI_1_4_cI_4_4_tt
Genes: A B A+B
Length: 438 409 818
Sequences: 2611 3475 1181
Seq/Len: 5.96 8.5 1.44
MirrorTree (Pazo et al. 2001) 0.56
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 0.01 0.03
2 0.01 0.01 0.71
5 0.01 0.03 0.95
10 0.02 0.04 0.98
20 0.03 0.05 1.00
100 0.05 0.06 1.09
∞ 0.14 0.13 1.39
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
177_A 221_V 0.97 0.40 0.00
131_Y 28_L 0.92 0.35 0.00
270_T 109_V 0.85 0.29 0.00
30_D 346_T 0.84 0.28 0.00
223_T 385_C 0.82 0.27 0.00
330_L 194_L 0.81 0.26 0.00
115_I 390_V 0.81 0.26 0.00
142_A 226_P 0.79 0.24 0.00
58_K 262_F 0.78 0.24 0.00
131_Y 357_I 0.76 0.22 0.00
425_A 221_V 0.76 0.22 0.00
173_V 75_Y 0.75 0.22 0.00
131_Y 48_S 0.75 0.21 0.00
270_T 162_W 0.74 0.21 0.00
25_G 101_V 0.73 0.20 0.00
122_G 136_G 0.73 0.20 0.00
72_T 99_L 0.72 0.20 0.00
146_E 96_A 0.72 0.19 0.00
278_E 219_R 0.72 0.19 0.00
379_G 246_Y 0.71 0.19 0.00
223_T 185_E 0.71 0.19 0.00
149_I 194_L 0.71 0.19 0.00
258_V 288_K 0.71 0.19 0.00
181_I 256_G 0.71 0.18 0.00
53_V 218_A 0.71 0.18 0.00
342_W 52_V 0.70 0.18 0.00
238_F 205_E 0.70 0.18 0.00
238_F 79_I 0.70 0.18 0.00
224_L 370_V 0.70 0.18 0.00
57_V 120_L 0.70 0.18 0.00
57_V 133_L 0.69 0.18 0.00
407_V 390_V 0.69 0.18 0.00
274_E 108_V 0.69 0.18 0.00
211_L 375_F 0.69 0.18 0.00
90_I 224_I 0.69 0.17 0.00
107_L 106_G 0.69 0.17 0.00
40_T 159_L 0.69 0.17 0.00
414_L 28_L 0.69 0.17 0.00
254_I 274_D 0.68 0.17 0.00
344_L 280_I 0.68 0.17 0.00
16_T 120_L 0.68 0.17 0.00
218_I 192_K 0.68 0.17 0.00
120_L 120_L 0.66 0.16 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
4826 1.08 cI_1_40_cI_4_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4825 1.44 cI_1_4_cI_4_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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