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OPENSEQ.org
cI_1_4_cI_9_4_tt
Genes: A B A+B
Length: 438 182 578
Sequences: 2611 870 497
Seq/Len: 5.96 4.78 0.86
MirrorTree (Pazo et al. 2001) 0.70
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 0.00
2 0.01 0.00 0.03
5 0.01 0.01 0.57
10 0.02 0.01 0.61
20 0.03 0.01 0.61
100 0.05 0.01 0.67
∞ 0.14 0.02 0.80
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
205_F 58_L 1.18 0.46 0.00
57_V 24_V 1.15 0.43 0.00
51_D 29_A 1.11 0.39 0.00
34_R 82_S 1.07 0.36 0.00
268_M 2_T 1.06 0.35 0.00
77_S 131_Y 1.05 0.35 0.00
355_K 70_V 1.05 0.35 0.00
392_P 24_V 0.99 0.30 0.00
138_Y 149_E 0.96 0.28 0.00
272_F 105_E 0.95 0.27 0.00
343_N 46_H 0.94 0.27 0.00
135_R 135_D 0.93 0.26 0.00
29_L 15_K 0.91 0.25 0.00
223_T 35_P 0.90 0.24 0.00
253_Q 91_Y 0.90 0.24 0.00
401_P 47_P 0.89 0.23 0.00
214_K 100_F 0.89 0.23 0.00
314_E 47_P 0.89 0.23 0.00
39_E 20_K 0.88 0.22 0.00
268_M 37_F 0.87 0.22 0.00
45_L 6_L 0.87 0.22 0.00
236_D 10_L 0.87 0.22 0.00
157_Y 54_I 0.86 0.22 0.00
91_C 10_L 0.86 0.22 0.00
28_T 134_E 0.86 0.21 0.00
238_F 54_I 0.86 0.21 0.00
157_Y 127_S 0.86 0.21 0.00
106_I 70_V 0.86 0.21 0.00
418_K 134_E 0.85 0.21 0.00
287_I 119_F 0.85 0.21 0.00
122_G 74_E 0.85 0.21 0.00
134_V 54_I 0.84 0.20 0.00
260_R 20_K 0.84 0.20 0.00
141_A 96_L 0.83 0.20 0.00
166_D 128_D 0.83 0.19 0.00
249_M 119_F 0.83 0.19 0.00
237_W 100_F 0.82 0.19 0.00
53_V 106_E 0.81 0.18 0.00
171_L 6_L 0.81 0.18 0.00
302_F 112_A 0.81 0.18 0.00
119_I 6_L 0.81 0.18 0.00
40_T 100_F 0.80 0.18 0.00
421_Y 113_I 0.80 0.18 0.00
93_A 58_L 0.80 0.18 0.00
296_S 68_I 0.80 0.18 0.00
235_A 11_G 0.80 0.18 0.00
146_E 113_I 0.79 0.17 0.00
138_Y 135_D 0.78 0.17 0.00
108_E 42_V 0.78 0.17 0.00
419_D 73_A 0.78 0.17 0.00
36_G 41_H 0.78 0.17 0.00
43_R 125_E 0.78 0.17 0.00
177_A 100_F 0.77 0.17 0.00
100_S 136_M 0.77 0.17 0.00
370_L 48_N 0.77 0.16 0.00
276_I 116_G 0.76 0.16 0.00
226_S 111_G 0.76 0.16 0.00
287_I 106_E 0.76 0.16 0.00
186_T 147_R 0.76 0.16 0.00
311_M 52_K 0.76 0.16 0.00
270_T 2_T 0.75 0.15 0.00
290_I 70_V 0.75 0.15 0.00
235_A 145_P 0.75 0.15 0.00
19_A 24_V 0.75 0.15 0.00
260_R 4_K 0.75 0.15 0.00
384_V 90_V 0.74 0.15 0.00
106_I 60_A 0.74 0.15 0.00
329_I 16_Y 0.74 0.15 0.00
177_A 135_D 0.74 0.15 0.00
361_E 93_I 0.74 0.15 0.00
115_I 145_P 0.74 0.15 0.00
412_G 43_L 0.74 0.15 0.00
56_E 74_E 0.74 0.15 0.00
142_A 54_I 0.73 0.15 0.00
218_I 15_K 0.73 0.15 0.00
115_I 8_Q 0.73 0.15 0.00
225_A 121_M 0.73 0.14 0.00
318_A 33_L 0.73 0.14 0.00
431_V 10_L 0.72 0.14 0.00
57_V 19_S 0.72 0.14 0.00
117_G 93_I 0.72 0.14 0.00
149_I 7_A 0.72 0.14 0.00
74_L 103_L 0.72 0.14 0.00
399_F 75_N 0.72 0.14 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
4925 0.86 cI_1_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4924 1.21 cI_1_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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