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cytb_40_cIV_B_40_human
Genes: A B A+B
Length: 378 227 598
Sequences: 3773 4352 1462
Seq/Len: 9.98 19.17 2.44
MirrorTree (Pazo et al. 2001) 0.74
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 0.02 0.01 0.12
2 0.02 0.01 0.18
5 0.02 0.01 0.56
10 0.02 0.01 1.69
20 0.02 0.01 1.81
100 0.02 0.02 1.91
∞ 0.02 0.07 2.42
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
37_L 205_S 1.23 0.80 0.07
283_S 144_L 1.11 0.70 0.05
322_Q 12_A 1.09 0.68 0.05
252_D 205_S 0.96 0.54 0.03
119_L 76_I 0.93 0.50 0.03
355_S 4_A 0.92 0.49 0.03
156_I 47_T 0.91 0.48 0.03
211_I 43_F 0.90 0.46 0.03
164_I 76_I 0.89 0.45 0.02
173_P 88_D 0.89 0.45 0.02
234_L 215_P 0.88 0.44 0.02
140_F 14_S 0.86 0.42 0.02
316_M 32_F 0.86 0.42 0.02
57_P 138_V 0.85 0.40 0.02
189_I 150_I 0.84 0.39 0.02
94_L 184_F 0.83 0.39 0.02
102_L 68_L 0.82 0.38 0.02
248_D 156_S 0.82 0.37 0.02
78_I 160_L 0.81 0.36 0.02
13_L 95_L 0.80 0.36 0.02
302_A 156_S 0.80 0.35 0.02
318_R 4_A 0.80 0.35 0.02
155_Y 35_C 0.79 0.34 0.02
261_P 67_I 0.78 0.34 0.02
66_I 165_V 0.78 0.34 0.02
121_L 41_A 0.78 0.34 0.02
101_G 138_V 0.78 0.33 0.02
193_A 110_Y 0.77 0.32 0.02
179_F 38_V 0.77 0.32 0.02
292_L 39_L 0.77 0.32 0.01
82_L 68_L 0.76 0.32 0.01
304_I 95_L 0.76 0.31 0.01
343_V 97_I 0.76 0.31 0.01
258_L 26_H 0.75 0.30 0.01
353_V 126_L 0.75 0.30 0.01
274_F 162_S 0.75 0.30 0.01
223_Y 155_T 0.74 0.30 0.01
173_P 67_I 0.74 0.29 0.01
82_L 155_T 0.74 0.29 0.01
246_S 165_V 0.73 0.28 0.01
297_S 34_I 0.73 0.28 0.01
37_L 86_M 0.73 0.28 0.01
221_H 175_I 0.73 0.28 0.01
153_I 67_I 0.73 0.28 0.01
308_H 8_G 0.73 0.28 0.01
239_L 30_I 0.73 0.28 0.01
342_P 61_M 0.73 0.28 0.01
55_Y 37_L 0.73 0.28 0.01
334_I 172_T 0.72 0.28 0.01
364_I 36_F 0.72 0.28 0.01
331_D 99_S 0.72 0.28 0.01
55_Y 107_T 0.72 0.27 0.01
355_S 30_I 0.72 0.27 0.01
245_F 150_I 0.72 0.27 0.01
197_L 211_L 0.72 0.27 0.01
33_F 33_L 0.71 0.27 0.01
39_A 97_I 0.71 0.26 0.01
99_G 119_N 0.71 0.26 0.01
105_G 214_I 0.71 0.26 0.01
362_I 133_L 0.70 0.26 0.01
332_L 155_T 0.70 0.26 0.01
129_M 3_H 0.70 0.26 0.01
239_L 13_T 0.70 0.26 0.01
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
5399 2.44 cytb_40_cIV_B_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.04 Done - Shared
5398 2.44 cytb_40_cIV_B_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.12 Done - Shared
5397 2.45 cytb_20_cIV_B_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5396 1.92 cytb_80_cIV_B_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5395 2.44 cytb_40_cIV_B_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.06 Done - Shared
5392 2.44 cytb_40_cIV_B_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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