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OPENSEQ.org
3rko_2_D_F
Genes: A B A+B
Length: 485 184 574
Sequences: 11137 2185 1726
Seq/Len: 22.96 11.88 3.01
MirrorTree (Pazo et al. 2001) 0.47
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 0.33 0.02 0.16
2 0.42 0.02 2.12
5 0.49 0.02 2.46
10 0.50 0.02 2.57
20 0.51 0.02 2.58
100 0.51 0.03 2.63
∞ 0.51 0.05 2.71
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
468_G 62_A 1.00 0.65 0.01
367_W 58_V 0.96 0.60 0.01
114_L 29_L 0.95 0.59 0.01
213_G 56_I 0.93 0.56 0.01
122_A 135_G 0.93 0.56 0.01
138_P 72_M 0.93 0.56 0.01
272_V 13_I 0.93 0.56 0.01
222_P 142_E 0.93 0.56 0.01
367_W 40_S 0.90 0.53 0.01
130_L 73_M 0.90 0.53 0.01
356_A 74_L 0.89 0.52 0.01
133_E 72_M 0.89 0.52 0.01
467_L 52_G 0.88 0.50 0.01
453_G 154_V 0.86 0.48 0.01
178_Y 35_S 0.86 0.47 0.01
149_Q 159_G 0.86 0.47 0.01
312_A 129_V 0.85 0.47 0.01
225_L 29_L 0.85 0.46 0.01
174_M 137_Y 0.84 0.45 0.01
64_T 102_I 0.84 0.45 0.01
426_L 63_I 0.84 0.45 0.01
134_L 57_I 0.83 0.44 0.01
285_N 43_F 0.83 0.44 0.01
74_M 145_S 0.83 0.44 0.01
224_H 156_F 0.83 0.44 0.01
462_L 105_V 0.83 0.44 0.01
215_G 39_I 0.82 0.43 0.01
221_V 45_S 0.81 0.42 0.01
422_L 33_I 0.80 0.40 0.00
161_I 54_L 0.79 0.39 0.00
298_L 156_F 0.79 0.39 0.00
422_L 21_T 0.78 0.38 0.00
173_G 141_V 0.78 0.38 0.00
188_A 3_F 0.78 0.38 0.00
124_H 28_A 0.78 0.37 0.00
465_L 117_Q 0.77 0.37 0.00
294_I 137_Y 0.77 0.37 0.00
465_L 50_F 0.77 0.37 0.00
232_Q 150_A 0.76 0.36 0.00
215_G 26_V 0.76 0.36 0.00
134_L 70_V 0.76 0.36 0.00
459_I 20_I 0.76 0.36 0.00
436_A 16_T 0.76 0.35 0.00
416_V 162_E 0.75 0.35 0.00
316_L 43_F 0.75 0.34 0.00
89_T 122_T 0.75 0.34 0.00
113_A 130_G 0.75 0.34 0.00
296_R 21_T 0.74 0.34 0.00
444_A 58_V 0.74 0.34 0.00
206_G 97_A 0.74 0.33 0.00
264_G 129_V 0.74 0.33 0.00
110_L 64_M 0.73 0.33 0.00
379_M 63_I 0.73 0.32 0.00
114_L 30_L 0.72 0.32 0.00
397_Y 73_M 0.72 0.31 0.00
280_S 73_M 0.72 0.31 0.00
131_G 64_M 0.72 0.31 0.00
350_P 150_A 0.72 0.31 0.00
208_G 132_T 0.72 0.31 0.00
130_L 130_G 0.72 0.31 0.00
316_L 20_I 0.72 0.31 0.00
163_S 124_I 0.71 0.30 0.00
365_L 139_L 0.71 0.30 0.00
161_I 154_V 0.71 0.30 0.00
294_I 11_I 0.71 0.30 0.00
411_V 146_M 0.71 0.30 0.00
397_Y 130_G 0.71 0.30 0.00
204_L 158_V 0.71 0.30 0.00
146_A 19_V 0.71 0.30 0.00
173_G 103_M 0.70 0.30 0.00
258_F 74_L 0.70 0.29 0.00
121_N 74_L 0.70 0.29 0.00
291_Q 74_L 0.70 0.29 0.00
180_Q 129_V 0.70 0.29 0.00
402_G 33_I 0.70 0.29 0.00
284_G 63_I 0.70 0.29 0.00
216_F 5_F 0.70 0.29 0.00
158_K 72_M 0.70 0.29 0.00
124_H 5_F 0.70 0.29 0.00
410_L 45_S 0.69 0.29 0.00
229_D 72_M 0.69 0.28 0.00
87_T 49_Y 0.69 0.28 0.00
350_P 54_L 0.69 0.28 0.00
157_I 159_G 0.69 0.28 0.00
174_M 156_F 0.69 0.28 0.00
225_L 141_V 0.69 0.28 0.00
326_V 28_A 0.69 0.28 0.00
122_A 71_V 0.68 0.28 0.00
257_L 73_M 0.68 0.28 0.00
412_G 23_T 0.68 0.28 0.00
156_S 25_P 0.68 0.27 0.00
349_S 154_V 0.68 0.27 0.00
350_P 8_C 0.68 0.27 0.00
464_V 102_I 0.68 0.27 0.00
373_A 153_V 0.68 0.27 0.00
426_L 145_S 0.68 0.27 0.00
222_P 64_M 0.68 0.27 0.00
284_G 43_F 0.67 0.27 0.00
170_L 111_I 0.67 0.27 0.00
285_N 151_G 0.67 0.26 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 A, there is a high ratio (0.51 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
7432 3.01 3rko_2_D_F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
2404 2.27 cI_D_F Δgene:(1, ∞) A:(1E-40, 1) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
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