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OPENSEQ.org
ABAR9_PP2C50 (A, 30-200) (B, 60-380)
Genes: A B A+B
Length: 171 321 475
Sequences: 265 2777 133
Seq/Len: 1.55 8.65 0.28
MirrorTree (Pazo et al. 2001) 0.14
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 0.10 0.05 0.00
2 0.10 0.06 0.01
5 0.11 0.06 0.02
10 0.11 0.06 0.04
20 0.11 0.06 0.05
100 0.12 0.08 0.14
∞ 0.27 0.14 0.27
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
90_H 167_C 1.38 0.32 0.00
88_N 236_A 1.32 0.29 0.00
88_N 154_V 1.21 0.24 0.00
63_S 157_A 1.09 0.18 0.00
92_L 244_L 1.06 0.17 0.00
95_R 245_A 0.99 0.15 0.00
104_K 311_I 0.98 0.14 0.00
164_L 50_L 0.98 0.14 0.00
64_V 260_K 0.97 0.14 0.00
100_D 214_S 0.97 0.14 0.00
97_V 284_E 0.94 0.13 0.00
151_K 108_C 0.94 0.13 0.00
45_L 246_S 0.93 0.13 0.00
26_I 161_D 0.91 0.12 0.00
159_E 314_I 0.91 0.12 0.00
31_H 104_V 0.91 0.12 0.00
18_C 244_L 0.91 0.12 0.00
21_A 56_G 0.91 0.12 0.00
57_G 254_S 0.90 0.12 0.00
112_V 150_C 0.90 0.12 0.00
88_N 7_T 0.90 0.12 0.00
64_V 300_R 0.89 0.12 0.00
3_E 314_I 0.89 0.12 0.00
26_I 143_T 0.89 0.12 0.00
88_N 50_L 0.88 0.12 0.00
118_D 291_A 0.86 0.11 0.00
140_D 65_E 0.86 0.11 0.00
64_V 102_D 0.86 0.11 0.00
68_N 147_A 0.85 0.11 0.00
94_V 147_A 0.85 0.11 0.00
58_N 262_A 0.83 0.10 0.00
118_D 262_A 0.83 0.10 0.00
97_V 173_V 0.83 0.10 0.00
149_L 182_D 0.82 0.10 0.00
94_V 56_G 0.82 0.10 0.00
39_R 55_F 0.82 0.10 0.00
19_S 223_F 0.81 0.10 0.00
164_L 311_I 0.81 0.10 0.00
22_V 58_F 0.81 0.10 0.00
112_V 79_S 0.81 0.10 0.00
58_N 106_T 0.80 0.10 0.00
95_R 269_W 0.80 0.09 0.00
151_K 188_A 0.80 0.09 0.00
91_I 263_R 0.79 0.09 0.00
39_R 210_A 0.79 0.09 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
10622 0.28 ABAR9_PP2C50 (A, 30-200) (B, 60-380) Δgene:(1, ∞) A:(1E-60, 4) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10621 0.28 ABAR9_PP2C50 (A, 30-200) (B, 60-380) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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