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OPENSEQ.org
ProBA_GREMLIN
Genes: A B A+B
Length: 417 367 781
Sequences: 17595 1893 1727
Seq/Len: 42.19 5.16 2.21
MirrorTree (Pazo et al. 2001) 0.13
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 0.03 0.07 1.12
2 0.04 0.07 1.22
5 0.04 0.07 1.30
10 0.06 0.07 1.35
20 0.08 0.07 1.41
100 0.14 0.07 1.64
∞ 0.21 0.08 2.20
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
213_S 257_A 0.92 0.46 0.00
155_T 264_N 0.92 0.46 0.00
50_V 366_T 0.87 0.41 0.00
365_Y 105_R 0.87 0.40 0.00
251_S 169_T 0.78 0.31 0.00
140_V 293_S 0.77 0.30 0.00
251_S 114_F 0.77 0.30 0.00
220_G 15_V 0.75 0.28 0.00
240_K 323_I 0.75 0.28 0.00
48_Q 303_V 0.72 0.26 0.00
302_V 303_V 0.72 0.26 0.00
17_A 242_I 0.71 0.25 0.00
26_R 301_K 0.71 0.25 0.00
291_L 132_V 0.71 0.25 0.00
261_V 301_K 0.68 0.22 0.00
15_K 323_I 0.68 0.22 0.00
363_A 117_A 0.68 0.22 0.00
145_G 34_Q 0.67 0.21 0.00
257_E 74_L 0.66 0.21 0.00
73_L 242_I 0.66 0.21 0.00
17_A 359_V 0.65 0.20 0.00
243_V 365_I 0.65 0.20 0.00
415_I 110_D 0.64 0.19 0.00
231_E 184_Q 0.64 0.19 0.00
341_S 105_R 0.64 0.19 0.00
283_T 166_L 0.64 0.19 0.00
213_S 39_H 0.63 0.19 0.00
87_A 343_S 0.63 0.19 0.00
112_L 344_Q 0.63 0.19 0.00
77_A 42_G 0.63 0.18 0.00
408_I 208_G 0.62 0.18 0.00
187_M 132_V 0.62 0.18 0.00
277_M 301_K 0.62 0.18 0.00
343_A 81_S 0.62 0.18 0.00
341_S 21_R 0.62 0.17 0.00
26_R 133_I 0.61 0.17 0.00
255_T 286_A 0.61 0.17 0.00
219_T 15_V 0.61 0.17 0.00
38_Q 300_I 0.61 0.17 0.00
52_D 9_V 0.61 0.17 0.00
48_Q 282_E 0.61 0.17 0.00
321_K 32_V 0.60 0.17 0.00
8_A 359_V 0.60 0.17 0.00
11_Q 336_R 0.60 0.16 0.00
166_C 269_I 0.59 0.16 0.00
10_K 101_M 0.59 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)
ID Seq/Len Name Options I_Prob Status
10653 2.21 ProBA_GREMLIN Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8607 1.42 ProBA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
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