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OPENSEQ.org
BvnA_SSBvnB_PCP
Genes: A B A+B
Length: 442 92 493
Sequences: 11712 35173 183
Seq/Len: 26.5 382.32 0.37
MirrorTree (Pazo et al. 2001) 0.21
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 0.00 0.85 0.09
2 0.00 0.85 0.14
5 0.00 0.85 0.34
10 0.00 0.85 0.56
20 0.00 0.85 0.74
100 0.03 0.85 1.28
∞ 0.11 0.85 3.53
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
262_A 39_E 1.28 0.32 0.00
389_T 39_E 1.20 0.28 0.00
405_V 44_E 1.13 0.24 0.00
244_G 29_M 1.08 0.22 0.00
327_M 64_A 1.08 0.21 0.00
386_V 63_G 1.06 0.21 0.00
101_L 71_L 1.03 0.19 0.00
343_V 23_R 1.02 0.18 0.00
109_R 22_V 0.98 0.17 0.00
265_D 29_M 0.97 0.17 0.00
81_G 31_P 0.96 0.16 0.00
242_S 25_Q 0.95 0.16 0.00
168_E 71_L 0.94 0.16 0.00
295_V 58_K 0.94 0.15 0.00
187_H 83_L 0.92 0.15 0.00
175_A 36_F 0.92 0.15 0.00
230_A 29_M 0.91 0.14 0.00
295_V 35_E 0.89 0.14 0.00
330_R 62_E 0.89 0.14 0.00
201_L 83_L 0.89 0.14 0.00
152_A 54_R 0.87 0.13 0.00
301_I 29_M 0.87 0.13 0.00
83_A 77_L 0.86 0.13 0.00
303_L 19_Y 0.85 0.12 0.00
102_F 55_M 0.84 0.12 0.00
262_A 52_M 0.84 0.12 0.00
268_K 31_P 0.83 0.12 0.00
230_A 77_L 0.83 0.12 0.00
168_E 29_M 0.82 0.12 0.00
135_V 40_Q 0.82 0.12 0.00
223_R 58_K 0.82 0.12 0.00
395_G 63_G 0.81 0.11 0.00
279_A 26_I 0.81 0.11 0.00
412_E 48_N 0.81 0.11 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 (0.85 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
10954 0.37 BvnA_SSBvnB_PCP Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done
10952 0 BvnA_SSBvnB_PCP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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