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OPENSEQ.org
cI_H_40_cytb_40_human
Genes: A B A+B
Length: 318 378 690
Sequences: 5631 4493 3628
Seq/Len: 17.71 11.89 5.26
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 1.93
2 0.00 0.00 2.31
5 0.00 0.00 2.79
10 0.00 0.00 3.07
20 0.00 0.00 4.32
100 0.00 0.00 4.43
∞ 0.01 0.00 5.21
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
237_L 42_I 0.97 0.78 0.02
184_M 82_L 0.96 0.77 0.02
118_W 292_L 0.93 0.73 0.01
3_M 320_L 0.91 0.71 0.01
232_I 232_L 0.91 0.71 0.01
116_I 52_A 0.89 0.69 0.01
105_I 23_T 0.83 0.61 0.01
45_L 348_T 0.83 0.61 0.01
41_G 45_I 0.81 0.57 0.01
205_S 21_L 0.80 0.56 0.01
69_T 45_I 0.80 0.56 0.01
109_S 257_T 0.79 0.55 0.01
84_L 241_T 0.79 0.55 0.01
106_L 188_I 0.79 0.55 0.01
270_F 8_N 0.78 0.54 0.01
139_T 253_P 0.78 0.53 0.01
205_S 37_L 0.78 0.53 0.01
108_T 307_L 0.77 0.53 0.01
217_A 176_T 0.77 0.52 0.01
107_A 102_L 0.77 0.51 0.01
198_F 47_T 0.76 0.51 0.01
109_S 322_Q 0.76 0.50 0.01
11_V 82_L 0.75 0.50 0.01
265_L 365_L 0.75 0.49 0.01
77_L 61_T 0.74 0.48 0.01
241_I 233_L 0.74 0.48 0.01
298_L 320_L 0.74 0.47 0.01
151_L 352_Q 0.73 0.47 0.01
269_L 364_I 0.73 0.46 0.01
102_L 324_L 0.73 0.46 0.01
146_L 189_I 0.73 0.46 0.01
152_S 286_N 0.73 0.46 0.01
97_N 92_I 0.73 0.46 0.01
175_L 360_T 0.72 0.45 0.01
216_A 318_R 0.72 0.45 0.01
41_G 185_L 0.72 0.45 0.01
241_I 42_I 0.72 0.45 0.01
203_G 21_L 0.72 0.45 0.01
213_I 303_M 0.71 0.44 0.01
297_T 197_L 0.71 0.43 0.01
306_S 107_F 0.71 0.43 0.01
127_Y 62_A 0.71 0.43 0.01
291_K 189_I 0.71 0.43 0.01
203_G 277_A 0.70 0.42 0.01
280_F 52_A 0.70 0.41 0.01
87_T 180_T 0.69 0.41 0.01
83_L 173_P 0.69 0.41 0.01
266_L 292_L 0.69 0.41 0.01
266_L 185_L 0.69 0.41 0.01
73_T 13_L 0.69 0.41 0.01
273_I 185_L 0.69 0.41 0.01
217_A 242_L 0.69 0.41 0.01
118_W 181_F 0.68 0.40 0.01
18_A 32_N 0.68 0.39 0.01
152_S 81_Y 0.67 0.38 0.01
90_P 57_P 0.67 0.38 0.01
183_M 114_N 0.67 0.38 0.01
93_N 226_I 0.67 0.38 0.01
276_A 315_M 0.67 0.38 0.01
71_Y 185_L 0.67 0.37 0.01
259_F 119_L 0.67 0.37 0.01
154_L 164_I 0.67 0.37 0.01
95_L 120_L 0.66 0.37 0.01
97_N 89_M 0.66 0.37 0.01
48_P 134_P 0.66 0.37 0.01
16_A 119_L 0.66 0.36 0.01
246_T 192_L 0.66 0.36 0.01
147_A 107_F 0.66 0.36 0.01
284_Q 318_R 0.65 0.36 0.01
222_L 294_L 0.65 0.36 0.01
247_Y 79_I 0.65 0.35 0.01
77_L 245_F 0.65 0.35 0.01
32_Q 245_F 0.65 0.35 0.01
200_L 373_E 0.65 0.35 0.01
239_T 47_T 0.65 0.34 0.01
201_A 261_P 0.64 0.34 0.01
198_F 72_D 0.64 0.34 0.01
166_I 242_L 0.64 0.33 0.01
231_I 325_Y 0.64 0.33 0.01
201_A 252_D 0.64 0.33 0.01
6_L 49_L 0.64 0.33 0.01
29_G 216_D 0.63 0.33 0.01
101_G 72_D 0.63 0.33 0.01
11_V 249_L 0.63 0.33 0.01
243_L 41_L 0.63 0.33 0.01
264_L 238_S 0.63 0.33 0.01
149_I 289_G 0.63 0.33 0.01
156_M 75_Y 0.63 0.33 0.01
62_K 333_L 0.63 0.33 0.01
135_A 276_F 0.63 0.33 0.01
240_T 239_L 0.63 0.32 0.01
81_I 78_I 0.63 0.32 0.01
261_T 368_T 0.63 0.32 0.01
285_L 85_N 0.63 0.32 0.01
4_A 47_T 0.62 0.32 0.01
293_F 30_W 0.62 0.32 0.01
238_T 75_Y 0.62 0.32 0.01
269_L 332_L 0.62 0.32 0.01
137_A 210_G 0.62 0.31 0.01
238_T 79_I 0.62 0.31 0.01
302_M 230_L 0.62 0.31 0.01
96_V 244_L 0.62 0.31 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
5781 5.33 cI_H_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.02 Done - Shared
5621 5.26 cI_H_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.02 Done - Shared
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