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OPENSEQ.org
1
Genes: A B A+B
Length: 295 331 589
Sequences: 1695 1146 921
Seq/Len: 5.75 3.46 1.56
MirrorTree (Pazo et al. 2001) 0.45
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 0.00 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.12
10 0.01 0.00 0.46
20 0.01 0.00 0.63
100 0.02 0.01 1.02
∞ 0.11 0.05 1.47
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
154_H 133_I 1.54 0.89 0.28
95_F 277_N 1.21 0.67 0.11
50_N 300_Q 1.08 0.54 0.07
79_L 255_D 1.04 0.49 0.06
99_R 280_Q 0.96 0.41 0.05
185_V 50_K 0.96 0.41 0.05
203_A 141_Q 0.95 0.40 0.05
169_G 235_L 0.94 0.39 0.04
147_M 97_I 0.93 0.38 0.04
42_I 29_L 0.93 0.38 0.04
240_C 53_T 0.91 0.36 0.04
46_I 212_E 0.91 0.36 0.04
224_A 36_A 0.90 0.35 0.04
71_T 311_I 0.90 0.35 0.04
119_D 54_D 0.90 0.35 0.04
54_I 161_I 0.88 0.33 0.03
61_I 47_I 0.87 0.32 0.03
265_L 286_L 0.87 0.32 0.03
80_A 93_L 0.87 0.32 0.03
47_V 175_L 0.86 0.32 0.03
91_Q 291_A 0.85 0.30 0.03
150_E 29_L 0.85 0.30 0.03
265_L 20_D 0.84 0.30 0.03
132_L 103_T 0.84 0.29 0.03
200_A 268_P 0.84 0.29 0.03
147_M 75_E 0.82 0.28 0.03
90_R 263_L 0.82 0.28 0.03
198_L 252_Q 0.82 0.28 0.03
151_I 13_L 0.82 0.28 0.03
64_L 51_Q 0.81 0.28 0.03
186_H 289_D 0.81 0.27 0.03
253_A 289_D 0.81 0.27 0.03
236_K 145_I 0.79 0.26 0.02
213_I 276_R 0.78 0.25 0.02
238_M 145_I 0.78 0.25 0.02
223_L 290_L 0.78 0.25 0.02
35_V 262_A 0.78 0.25 0.02
89_S 72_N 0.78 0.25 0.02
85_L 176_T 0.78 0.25 0.02
144_E 283_A 0.78 0.24 0.02
69_K 143_A 0.78 0.24 0.02
23_G 270_L 0.77 0.24 0.02
79_L 222_D 0.77 0.24 0.02
247_S 310_L 0.77 0.24 0.02
161_P 167_V 0.76 0.23 0.02
248_N 229_I 0.76 0.23 0.02
61_I 233_M 0.76 0.23 0.02
149_E 12_I 0.76 0.23 0.02
228_R 94_L 0.76 0.23 0.02
225_T 311_I 0.76 0.23 0.02
248_N 63_A 0.76 0.23 0.02
119_D 10_S 0.76 0.23 0.02
238_M 91_S 0.75 0.22 0.02
53_A 33_E 0.75 0.22 0.02
191_A 122_I 0.75 0.22 0.02
150_E 92_S 0.75 0.22 0.02
44_A 50_K 0.74 0.22 0.02
185_V 298_L 0.74 0.22 0.02
35_V 255_D 0.74 0.22 0.02
163_N 156_D 0.74 0.22 0.02
220_I 8_D 0.74 0.22 0.02
130_L 237_E 0.74 0.22 0.02
57_T 108_E 0.74 0.21 0.02
47_V 8_D 0.74 0.21 0.02
30_Q 215_I 0.74 0.21 0.02
29_Y 201_E 0.74 0.21 0.02
46_I 34_V 0.73 0.21 0.02
135_S 279_S 0.73 0.21 0.02
277_E 139_R 0.73 0.21 0.02
224_A 290_L 0.73 0.21 0.02
227_L 284_D 0.73 0.21 0.02
131_R 286_L 0.73 0.21 0.02
42_I 142_A 0.73 0.21 0.02
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
10914 1.56 1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.28 Done - Shared
9357 2.41 motA fliG salty jh Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.32 Done
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