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OPENSEQ.org
4Y0Y_10_inf
Genes: A B A+B
Length: 216 51 267
Sequences: 14597 2483 155
Seq/Len: 67.58 48.69 0.58
MirrorTree (Pazo et al. 2001) 0.01
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.19 0.18 0.02
2 0.20 0.19 0.02
5 0.21 0.21 0.04
10 0.22 0.22 0.10
20 0.23 0.22 0.19
100 0.25 0.23 0.45
∞ 0.29 0.25 0.58
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
28_S 31_Y 1.40 0.53 0.00
76_Y 45_E 1.23 0.40 0.00
124_T 45_E 1.17 0.35 0.00
133_D 19_Y 1.16 0.34 0.00
173_C 39_N 1.07 0.28 0.00
100_V 24_G 1.02 0.25 0.00
90_L 31_Y 1.01 0.24 0.00
139_K 41_F 0.99 0.23 0.00
12_V 33_G 0.96 0.22 0.00
140_A 43_S 0.93 0.20 0.00
197_C 17_Y 0.93 0.20 0.00
31_N 19_Y 0.92 0.19 0.00
25_C 33_G 0.91 0.19 0.00
64_F 41_F 0.91 0.19 0.00
204_G 33_G 0.90 0.18 0.00
141_P 19_Y 0.89 0.18 0.00
103_I 22_K 0.89 0.18 0.00
14_Y 48_M 0.88 0.17 0.00
206_Y 37_K 0.87 0.17 0.00
178_G 26_C 0.86 0.17 0.00
72_V 49_R 0.86 0.17 0.00
198_A 19_Y 0.85 0.16 0.00
190_I 8_G 0.85 0.16 0.00
214_S 5_P 0.85 0.16 0.00
163_A 43_S 0.83 0.15 0.00
208_K 2_L 0.81 0.15 0.00
149_K 45_E 0.80 0.14 0.00
187_L 12_A 0.79 0.14 0.00
206_Y 40_N 0.79 0.14 0.00
195_S 43_S 0.78 0.13 0.00
186_K 29_F 0.78 0.13 0.00
161_F 20_N 0.78 0.13 0.00
180_P 19_Y 0.78 0.13 0.00
178_G 47_C 0.76 0.12 0.00
190_I 49_R 0.75 0.12 0.00
93_A 20_N 0.74 0.12 0.00
212_Y 22_K 0.74 0.12 0.00
143_L 32_G 0.74 0.12 0.00
92_S 12_A 0.74 0.12 0.00
18_L 10_C 0.73 0.12 0.00
173_C 47_C 0.73 0.12 0.00
69_K 45_E 0.73 0.12 0.00
67_A 28_T 0.73 0.12 0.00
49_R 16_R 0.72 0.11 0.00
24_F 18_F 0.72 0.11 0.00
178_G 51_C 0.72 0.11 0.00
120_G 47_C 0.72 0.11 0.00
173_C 37_K 0.72 0.11 0.00
85_I 19_Y 0.72 0.11 0.00
54_N 7_T 0.72 0.11 0.00
182_V 24_G 0.71 0.11 0.00
213_V 20_N 0.71 0.11 0.00
50_L 13_R 0.71 0.11 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
11600 0.58 4Y0Y_10_inf Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11597 0.64 4Y0Y_6_inf Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11596 0.67 4Y0Y_4_inf Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11594 0.68 4Y0Y_2_inf Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11564 0.2 4Y0Y_4_20 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11545 0.19 4Y0Y_10_20 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11478 0.2 4Y0Y_6_20 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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