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OPENSEQ.org
cIV_A_4_cI_H_10_Pdenitr
Genes: A B A+B
Length: 538 345 835
Sequences: 4477 4774 2466
Seq/Len: 8.32 13.84 2.95
MirrorTree (Pazo et al. 2001) 0.48
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 0.01 0.00 0.10
2 0.01 0.00 0.53
5 0.02 0.00 0.68
10 0.03 0.01 1.05
20 0.03 0.01 1.68
100 0.05 0.02 1.90
∞ 0.08 0.05 2.79
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
104_I 242_L 0.96 0.60 0.00
527_F 308_R 0.96 0.59 0.00
354_K 121_F 0.94 0.57 0.00
414_Y 144_F 0.94 0.56 0.00
132_S 40_I 0.93 0.56 0.00
432_H 180_I 0.92 0.55 0.00
492_F 131_V 0.92 0.55 0.00
357_M 101_V 0.91 0.54 0.00
410_A 87_A 0.89 0.51 0.00
18_L 143_P 0.88 0.50 0.00
106_A 147_S 0.84 0.44 0.00
48_Y 21_A 0.83 0.44 0.00
416_I 257_L 0.81 0.42 0.00
359_W 225_S 0.81 0.41 0.00
29_I 117_I 0.81 0.41 0.00
355_T 180_I 0.80 0.40 0.00
486_F 84_Y 0.80 0.40 0.00
381_P 225_S 0.79 0.39 0.00
181_A 161_L 0.79 0.38 0.00
382_L 44_V 0.78 0.38 0.00
389_T 147_S 0.78 0.38 0.00
254_I 262_F 0.78 0.38 0.00
131_A 148_L 0.78 0.37 0.00
301_I 204_L 0.78 0.37 0.00
130_V 126_L 0.77 0.37 0.00
413_Y 141_K 0.77 0.37 0.00
459_Y 223_A 0.77 0.36 0.00
213_W 125_S 0.77 0.36 0.00
326_L 84_Y 0.77 0.36 0.00
527_F 28_G 0.77 0.36 0.00
432_H 110_M 0.76 0.36 0.00
189_L 207_V 0.76 0.35 0.00
102_L 95_A 0.76 0.35 0.00
298_A 117_I 0.76 0.35 0.00
39_M 318_S 0.76 0.35 0.00
166_A 54_G 0.75 0.34 0.00
378_S 167_G 0.75 0.34 0.00
298_A 98_A 0.75 0.34 0.00
316_M 251_M 0.74 0.33 0.00
24_G 259_S 0.74 0.33 0.00
333_V 261_L 0.74 0.33 0.00
7_F 197_P 0.74 0.33 0.00
344_A 241_L 0.74 0.33 0.00
127_A 179_A 0.73 0.32 0.00
213_W 246_G 0.73 0.32 0.00
382_L 23_I 0.73 0.32 0.00
523_P 265_G 0.73 0.32 0.00
178_I 27_M 0.73 0.32 0.00
273_I 100_V 0.73 0.32 0.00
369_V 40_I 0.73 0.32 0.00
106_A 218_F 0.73 0.32 0.00
27_G 112_N 0.73 0.32 0.00
432_H 120_I 0.72 0.31 0.00
510_H 202_V 0.72 0.31 0.00
466_F 165_I 0.72 0.31 0.00
364_L 160_S 0.72 0.31 0.00
484_F 150_S 0.72 0.31 0.00
501_V 55_P 0.71 0.30 0.00
320_Q 291_F 0.71 0.30 0.00
483_S 221_V 0.71 0.30 0.00
207_S 246_G 0.71 0.30 0.00
483_S 233_T 0.71 0.30 0.00
359_W 223_A 0.71 0.29 0.00
90_A 233_T 0.71 0.29 0.00
351_I 16_L 0.70 0.29 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
3464 2.96 cIV_A_6_cI_H_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3463 2.95 cIV_A_4_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3462 2.98 cIV_A_6_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3446 2.95 cIV_A_6_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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