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OPENSEQ.org
PPI - 2nd (truncated)
Genes: A B A+B
Length: 281 166 436
Sequences: 35117 27821 566
Seq/Len: 124.97 167.6 1.3
MirrorTree (Pazo et al. 2001) 0.15
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 0.08 0.08 0.05
2 0.09 0.09 0.09
5 0.12 0.12 0.19
10 0.16 0.16 0.33
20 0.20 0.19 0.56
100 0.30 0.29 1.11
∞ 0.33 0.32 1.27
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
111_V 49_S 1.28 0.67 0.01
204_V 47_L 1.15 0.55 0.00
135_I 121_I 1.04 0.44 0.00
271_I 110_M 1.03 0.43 0.00
39_P 152_V 0.96 0.37 0.00
181_L 121_I 0.91 0.32 0.00
278_N 7_V 0.91 0.32 0.00
83_I 1_A 0.91 0.32 0.00
77_A 35_V 0.88 0.29 0.00
252_G 113_A 0.87 0.29 0.00
61_G 55_V 0.87 0.28 0.00
21_I 49_S 0.85 0.27 0.00
210_N 140_V 0.84 0.26 0.00
194_F 119_A 0.84 0.26 0.00
77_A 7_V 0.84 0.26 0.00
203_Q 47_L 0.84 0.26 0.00
181_L 146_D 0.82 0.25 0.00
174_S 146_D 0.82 0.25 0.00
8_V 140_V 0.82 0.25 0.00
114_V 125_S 0.81 0.24 0.00
56_G 163_V 0.81 0.24 0.00
30_V 37_V 0.81 0.24 0.00
30_V 161_L 0.81 0.24 0.00
125_G 117_N 0.80 0.23 0.00
182_W 154_T 0.80 0.23 0.00
181_L 35_V 0.80 0.23 0.00
178_T 161_L 0.79 0.22 0.00
111_V 45_E 0.78 0.22 0.00
223_L 163_V 0.78 0.22 0.00
251_H 28_L 0.78 0.22 0.00
210_N 154_T 0.77 0.21 0.00
4_H 91_L 0.77 0.21 0.00
133_L 119_A 0.75 0.20 0.00
92_P 28_L 0.74 0.20 0.00
6_G 8_R 0.74 0.19 0.00
181_L 27_N 0.74 0.19 0.00
76_S 165_S 0.73 0.19 0.00
135_I 49_S 0.73 0.19 0.00
115_S 33_K 0.73 0.19 0.00
277_D 49_S 0.73 0.18 0.00
81_H 28_L 0.73 0.18 0.00
274_V 69_Q 0.72 0.18 0.00
114_V 156_S 0.72 0.18 0.00
65_S 56_I 0.72 0.18 0.00
135_I 58_L 0.72 0.18 0.00
228_L 140_V 0.72 0.18 0.00
179_V 130_I 0.71 0.17 0.00
30_V 166_I 0.71 0.17 0.00
223_L 162_R 0.71 0.17 0.00
170_L 58_L 0.71 0.17 0.00
165_Y 47_L 0.70 0.17 0.00
29_D 49_S 0.70 0.17 0.00
114_V 33_K 0.70 0.17 0.00
175_A 98_V 0.70 0.17 0.00
215_A 96_E 0.70 0.17 0.00
128_A 154_T 0.70 0.17 0.00
30_V 155_L 0.70 0.17 0.00
74_L 32_T 0.69 0.17 0.00
135_I 128_Q 0.69 0.17 0.00
209_H 149_G 0.69 0.17 0.00
49_N 133_F 0.69 0.17 0.00
24_K 111_A 0.69 0.17 0.00
102_T 156_S 0.69 0.17 0.00
108_T 49_S 0.69 0.16 0.00
16_Q 140_V 0.69 0.16 0.00
124_F 35_V 0.69 0.16 0.00
260_D 9_I 0.69 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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.292), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
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