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cytb_40_cIV_B_20_human
Genes: A B A+B
Length: 378 227 598
Sequences: 3773 4343 1461
Seq/Len: 9.98 19.13 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 0.19
5 0.02 0.01 0.56
10 0.02 0.01 1.70
20 0.02 0.01 1.82
100 0.02 0.02 1.91
∞ 0.02 0.07 2.41
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 1.27 0.83 0.12
322_Q 12_A 1.12 0.71 0.07
283_S 144_L 1.06 0.65 0.06
119_L 76_I 0.96 0.54 0.04
234_L 215_P 0.95 0.53 0.04
252_D 205_S 0.95 0.52 0.04
102_L 68_L 0.94 0.52 0.04
355_S 4_A 0.89 0.46 0.04
364_I 36_F 0.87 0.43 0.03
164_I 76_I 0.86 0.42 0.03
173_P 88_D 0.86 0.42 0.03
318_R 4_A 0.86 0.42 0.03
140_F 14_S 0.85 0.41 0.03
57_P 138_V 0.85 0.41 0.03
121_L 41_A 0.85 0.41 0.03
343_V 97_I 0.81 0.37 0.03
248_D 156_S 0.81 0.37 0.03
211_I 43_F 0.81 0.36 0.03
316_M 32_F 0.80 0.36 0.03
82_L 155_T 0.80 0.36 0.03
188_I 32_F 0.79 0.34 0.02
331_D 99_S 0.79 0.34 0.02
37_L 86_M 0.78 0.33 0.02
308_H 8_G 0.78 0.33 0.02
173_P 67_I 0.78 0.33 0.02
304_I 95_L 0.78 0.33 0.02
158_T 152_M 0.78 0.33 0.02
330_A 150_I 0.77 0.33 0.02
94_L 184_F 0.77 0.32 0.02
345_Y 192_Y 0.77 0.32 0.02
179_F 38_V 0.76 0.31 0.02
66_I 165_V 0.76 0.31 0.02
101_G 138_V 0.76 0.31 0.02
353_V 126_L 0.76 0.31 0.02
49_L 95_L 0.76 0.31 0.02
334_I 172_T 0.75 0.30 0.02
21_L 205_S 0.75 0.30 0.02
155_Y 35_C 0.75 0.30 0.02
193_A 110_Y 0.74 0.30 0.02
221_H 175_I 0.74 0.29 0.02
189_I 150_I 0.74 0.29 0.02
246_S 165_V 0.73 0.29 0.02
181_F 21_I 0.73 0.28 0.02
105_G 214_I 0.73 0.28 0.02
292_L 39_L 0.73 0.28 0.02
340_G 58_A 0.72 0.28 0.02
115_I 184_F 0.72 0.28 0.02
347_F 137_D 0.72 0.27 0.02
239_L 13_T 0.72 0.27 0.02
33_F 33_L 0.72 0.27 0.02
329_A 34_I 0.71 0.27 0.02
42_I 92_D 0.71 0.26 0.02
332_L 155_T 0.70 0.26 0.02
245_F 150_I 0.70 0.26 0.02
13_L 95_L 0.70 0.26 0.02
47_T 9_L 0.70 0.25 0.02
58_D 13_T 0.70 0.25 0.02
46_T 165_V 0.70 0.25 0.02
353_V 192_Y 0.70 0.25 0.02
192_L 152_M 0.70 0.25 0.02
55_Y 107_T 0.70 0.25 0.02
361_T 37_L 0.70 0.25 0.02
129_M 3_H 0.70 0.25 0.02
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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