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OPENSEQ.org
pengfei
Genes: A B A+B
Length: 317 153 459
Sequences: 4454 2834 110
Seq/Len: 14.05 18.52 0.24
MirrorTree (Pazo et al. 2001) 0.33
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 0.03 0.35 0.08
2 0.04 0.39 0.09
5 0.05 0.42 0.13
10 0.05 0.43 0.17
20 0.05 0.44 0.23
100 0.06 0.45 0.37
∞ 0.07 0.48 0.55
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
258_Y 136_L 1.62 0.44 0.00
269_A 90_K 1.60 0.42 0.00
285_D 17_S 1.52 0.37 0.00
72_N 42_I 1.39 0.30 0.00
181_V 82_A 1.28 0.24 0.00
85_L 72_Y 1.21 0.21 0.00
273_K 72_Y 1.19 0.20 0.00
79_T 119_F 1.13 0.18 0.00
33_Y 117_D 1.12 0.18 0.00
85_L 73_E 1.12 0.18 0.00
230_V 42_I 1.11 0.17 0.00
99_I 110_D 1.09 0.17 0.00
26_P 93_L 1.07 0.16 0.00
18_L 101_L 1.07 0.16 0.00
240_I 43_D 1.07 0.16 0.00
35_I 84_D 1.05 0.15 0.00
164_Q 23_L 1.05 0.15 0.00
258_Y 119_F 1.05 0.15 0.00
234_S 58_S 1.04 0.15 0.00
184_Q 140_C 1.03 0.15 0.00
230_V 129_L 1.03 0.14 0.00
15_Y 141_D 1.03 0.14 0.00
37_V 127_T 1.02 0.14 0.00
109_Q 46_Q 1.02 0.14 0.00
168_L 95_S 1.00 0.14 0.00
251_D 59_L 1.00 0.14 0.00
201_N 145_V 1.00 0.14 0.00
298_I 116_E 0.99 0.13 0.00
122_I 16_P 0.99 0.13 0.00
196_S 82_A 0.99 0.13 0.00
285_D 51_Q 0.99 0.13 0.00
228_R 118_S 0.98 0.13 0.00
28_K 80_A 0.98 0.13 0.00
205_S 77_E 0.98 0.13 0.00
260_G 136_L 0.97 0.13 0.00
236_L 89_A 0.97 0.13 0.00
15_Y 92_F 0.97 0.13 0.00
181_V 147_S 0.95 0.12 0.00
304_L 48_S 0.95 0.12 0.00
237_G 125_I 0.95 0.12 0.00
236_L 117_D 0.95 0.12 0.00
258_Y 70_G 0.95 0.12 0.00
48_V 45_A 0.94 0.12 0.00
224_K 6_I 0.94 0.12 0.00
18_L 4_H 0.94 0.12 0.00
233_E 108_A 0.93 0.12 0.00
35_I 59_L 0.93 0.12 0.00
118_D 89_A 0.92 0.12 0.00
259_Y 81_D 0.92 0.12 0.00
285_D 21_Q 0.92 0.12 0.00
191_Q 86_L 0.92 0.12 0.00
96_D 93_L 0.91 0.11 0.00
118_D 106_S 0.91 0.11 0.00
231_V 120_E 0.91 0.11 0.00
270_G 119_F 0.90 0.11 0.00
275_V 117_D 0.90 0.11 0.00
128_D 101_L 0.90 0.11 0.00
161_V 122_P 0.90 0.11 0.00
69_G 146_I 0.89 0.11 0.00
16_Q 139_L 0.89 0.11 0.00
150_G 75_C 0.89 0.11 0.00
157_G 75_C 0.89 0.11 0.00
220_G 75_C 0.89 0.11 0.00
240_I 68_L 0.89 0.11 0.00
195_T 38_G 0.89 0.11 0.00
6_V 145_V 0.88 0.11 0.00
234_S 39_Q 0.88 0.10 0.00
124_R 113_G 0.88 0.10 0.00
99_I 74_T 0.88 0.10 0.00
280_Y 14_R 0.88 0.10 0.00
152_V 71_R 0.87 0.10 0.00
202_I 127_T 0.87 0.10 0.00
241_N 146_I 0.87 0.10 0.00
311_Y 44_I 0.86 0.10 0.00
214_E 119_F 0.86 0.10 0.00
156_F 81_D 0.86 0.10 0.00
226_Y 145_V 0.86 0.10 0.00
64_A 114_T 0.86 0.10 0.00
226_Y 129_L 0.86 0.10 0.00
49_A 150_L 0.86 0.10 0.00
240_I 49_A 0.86 0.10 0.00
96_D 25_S 0.85 0.10 0.00
48_V 86_L 0.85 0.10 0.00
20_E 111_G 0.85 0.10 0.00
288_K 136_L 0.85 0.10 0.00
152_V 111_G 0.85 0.10 0.00
304_L 33_D 0.85 0.10 0.00
18_L 88_Q 0.84 0.10 0.00
152_V 94_T 0.84 0.10 0.00
258_Y 69_K 0.84 0.10 0.00
269_A 125_I 0.83 0.10 0.00
63_Y 139_L 0.83 0.09 0.00
34_V 59_L 0.83 0.09 0.00
234_S 120_E 0.83 0.09 0.00
273_K 17_S 0.82 0.09 0.00
236_L 96_G 0.82 0.09 0.00
289_A 114_T 0.82 0.09 0.00
193_T 108_A 0.82 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.44 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
8229 0.41 pengfei Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8081 0.24 pengfei Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.00 Done
8066 0.21 tt Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
8065 0.27 tt Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
8064 0.22 test Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
8063 0.26 ss Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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