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OPENSEQ.org
cI_H_4_cytb_4_human
Genes: A B A+B
Length: 318 378 690
Sequences: 6355 4516 3675
Seq/Len: 19.98 11.95 5.33
MirrorTree (Pazo et al. 2001) 0.77
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 1.94
2 0.00 0.00 2.32
5 0.00 0.00 2.79
10 0.00 0.00 3.07
20 0.00 0.00 4.33
100 0.00 0.00 4.45
∞ 0.03 0.00 5.28
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
184_M 82_L 0.97 0.78 0.02
232_I 232_L 0.96 0.77 0.02
106_L 188_I 0.94 0.75 0.01
11_V 82_L 0.92 0.72 0.01
105_I 23_T 0.91 0.71 0.01
237_L 42_I 0.91 0.71 0.01
116_I 52_A 0.89 0.69 0.01
45_L 348_T 0.88 0.67 0.01
270_F 8_N 0.81 0.58 0.01
84_L 241_T 0.80 0.57 0.01
109_S 322_Q 0.80 0.56 0.01
41_G 45_I 0.79 0.56 0.01
118_W 292_L 0.78 0.54 0.01
41_G 185_L 0.78 0.53 0.01
175_L 360_T 0.77 0.52 0.01
109_S 257_T 0.76 0.51 0.01
146_L 189_I 0.76 0.51 0.01
97_N 92_I 0.76 0.51 0.01
240_T 239_L 0.75 0.50 0.01
297_T 197_L 0.75 0.49 0.01
77_L 61_T 0.74 0.48 0.01
83_L 173_P 0.74 0.48 0.01
203_G 21_L 0.73 0.47 0.01
152_S 81_Y 0.73 0.47 0.01
217_A 176_T 0.73 0.47 0.01
69_T 45_I 0.73 0.46 0.01
273_I 185_L 0.72 0.45 0.01
139_T 253_P 0.72 0.45 0.01
11_V 249_L 0.72 0.45 0.01
280_F 314_S 0.72 0.45 0.01
107_A 102_L 0.71 0.44 0.01
4_A 47_T 0.71 0.44 0.01
280_F 52_A 0.71 0.44 0.01
151_L 352_Q 0.71 0.44 0.01
70_L 102_L 0.71 0.44 0.01
306_S 107_F 0.71 0.43 0.01
260_V 189_I 0.71 0.43 0.01
203_G 277_A 0.71 0.43 0.01
217_A 79_I 0.70 0.43 0.01
127_Y 62_A 0.70 0.42 0.01
298_L 320_L 0.70 0.42 0.01
261_T 368_T 0.70 0.42 0.01
73_T 13_L 0.70 0.42 0.01
205_S 21_L 0.69 0.42 0.01
62_K 333_L 0.69 0.41 0.01
18_A 32_N 0.69 0.41 0.01
213_I 303_M 0.69 0.41 0.01
243_L 10_L 0.69 0.41 0.01
152_S 286_N 0.69 0.41 0.01
101_G 72_D 0.69 0.40 0.01
217_A 242_L 0.68 0.40 0.01
167_T 353_V 0.68 0.40 0.01
77_L 245_F 0.68 0.40 0.01
154_L 164_I 0.68 0.39 0.01
147_A 107_F 0.68 0.39 0.01
247_Y 79_I 0.68 0.39 0.01
48_P 134_P 0.68 0.39 0.01
93_N 226_I 0.68 0.39 0.01
269_L 332_L 0.67 0.38 0.01
77_L 298_I 0.67 0.38 0.01
291_K 189_I 0.67 0.38 0.01
205_S 37_L 0.67 0.38 0.01
222_L 294_L 0.67 0.38 0.01
243_L 295_L 0.67 0.38 0.01
266_L 185_L 0.67 0.38 0.01
198_F 47_T 0.67 0.38 0.01
182_A 156_I 0.67 0.38 0.01
293_F 96_L 0.67 0.38 0.01
198_F 72_D 0.66 0.37 0.01
129_L 119_L 0.66 0.37 0.01
171_H 360_T 0.66 0.37 0.01
196_T 181_F 0.66 0.37 0.01
150_L 237_L 0.66 0.36 0.01
4_A 189_I 0.66 0.36 0.01
118_W 181_F 0.66 0.36 0.01
183_M 114_N 0.65 0.36 0.01
175_L 303_M 0.65 0.36 0.01
16_A 119_L 0.65 0.35 0.01
239_T 47_T 0.65 0.35 0.01
176_L 356_V 0.65 0.35 0.01
269_L 328_L 0.65 0.35 0.01
178_S 218_I 0.65 0.35 0.01
119_S 266_P 0.65 0.35 0.01
129_L 298_I 0.65 0.35 0.01
23_T 295_L 0.65 0.35 0.01
175_L 364_I 0.65 0.35 0.01
175_L 194_T 0.65 0.35 0.01
3_M 320_L 0.65 0.35 0.01
203_G 252_D 0.64 0.35 0.01
30_Y 5_R 0.64 0.35 0.01
197_P 83_H 0.64 0.34 0.01
81_I 114_N 0.64 0.34 0.01
132_A 198_L 0.64 0.34 0.01
116_I 190_A 0.64 0.34 0.01
191_A 90_F 0.64 0.34 0.01
243_L 41_L 0.64 0.33 0.01
264_L 153_I 0.63 0.33 0.01
129_L 328_L 0.63 0.33 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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