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OPENSEQ.org
cI_2_40_cI_4_40_tt
Genes: A B A+B
Length: 181 409 566
Sequences: 1903 1636 895
Seq/Len: 10.51 4 1.58
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 0.00 0.00 1.18
2 0.00 0.00 1.28
5 0.01 0.00 1.31
10 0.01 0.01 1.32
20 0.01 0.01 1.32
100 0.02 0.01 1.35
∞ 0.04 0.05 1.52
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
136_V 258_E 1.14 0.60 0.00
4_F 47_L 1.11 0.57 0.00
149_R 98_A 1.06 0.52 0.00
34_V 97_Y 1.00 0.46 0.00
10_F 390_V 0.99 0.45 0.00
64_A 182_L 0.99 0.44 0.00
136_V 407_V 0.97 0.42 0.00
118_S 296_R 0.95 0.41 0.00
154_L 290_I 0.93 0.39 0.00
116_L 52_V 0.93 0.38 0.00
42_R 131_V 0.90 0.35 0.00
106_I 28_L 0.90 0.35 0.00
125_L 270_G 0.89 0.34 0.00
105_G 106_G 0.88 0.34 0.00
65_S 224_I 0.88 0.33 0.00
115_G 235_T 0.87 0.33 0.00
162_R 285_E 0.87 0.33 0.00
104_L 239_L 0.87 0.32 0.00
63_V 266_L 0.85 0.31 0.00
96_L 296_R 0.85 0.31 0.00
25_A 321_M 0.84 0.30 0.00
127_S 103_K 0.84 0.30 0.00
158_R 48_S 0.83 0.29 0.00
91_A 390_V 0.83 0.29 0.00
129_H 169_H 0.83 0.29 0.00
40_W 145_P 0.82 0.28 0.00
60_V 399_S 0.82 0.28 0.00
70_Y 250_K 0.82 0.28 0.00
86_L 33_Q 0.81 0.27 0.00
28_M 218_A 0.81 0.27 0.00
171_K 134_G 0.80 0.27 0.00
133_V 390_V 0.80 0.26 0.00
158_R 106_G 0.79 0.26 0.00
123_E 321_M 0.79 0.25 0.00
137_N 126_L 0.78 0.25 0.00
116_L 159_L 0.78 0.25 0.00
65_S 53_L 0.77 0.24 0.00
69_Y 405_G 0.77 0.24 0.00
134_I 394_V 0.76 0.24 0.00
138_D 264_V 0.76 0.24 0.00
109_G 180_E 0.76 0.23 0.00
68_S 315_H 0.76 0.23 0.00
126_G 109_V 0.76 0.23 0.00
69_Y 276_M 0.76 0.23 0.00
104_L 369_K 0.76 0.23 0.00
154_L 203_E 0.75 0.23 0.00
11_L 116_I 0.75 0.23 0.00
28_M 260_Y 0.75 0.23 0.00
32_R 297_L 0.75 0.23 0.00
96_L 20_E 0.75 0.22 0.00
105_G 44_M 0.75 0.22 0.00
139_E 65_G 0.74 0.22 0.00
26_A 321_M 0.74 0.22 0.00
65_S 233_G 0.74 0.22 0.00
99_Y 395_A 0.74 0.22 0.00
11_L 134_G 0.74 0.22 0.00
137_N 225_P 0.74 0.22 0.00
127_S 224_I 0.73 0.21 0.00
29_P 330_H 0.73 0.21 0.00
64_A 141_G 0.73 0.21 0.00
112_T 263_D 0.73 0.21 0.00
159_A 239_L 0.73 0.21 0.00
73_V 226_P 0.73 0.21 0.00
149_R 106_G 0.73 0.21 0.00
70_Y 301_P 0.72 0.21 0.00
39_G 359_S 0.72 0.21 0.00
125_L 119_I 0.72 0.21 0.00
158_R 116_I 0.72 0.21 0.00
42_R 143_L 0.72 0.20 0.00
94_E 269_R 0.72 0.20 0.00
112_T 23_T 0.72 0.20 0.00
34_V 264_V 0.72 0.20 0.00
150_L 274_D 0.71 0.20 0.00
12_E 156_I 0.71 0.20 0.00
103_T 107_A 0.71 0.20 0.00
99_Y 241_A 0.71 0.20 0.00
5_D 201_I 0.71 0.20 0.00
147_R 386_K 0.71 0.20 0.00
98_D 231_D 0.71 0.20 0.00
65_S 345_P 0.71 0.20 0.00
93_A 323_A 0.70 0.20 0.00
86_L 264_V 0.70 0.19 0.00
41_I 206_A 0.70 0.19 0.00
131_A 57_P 0.70 0.19 0.00
4_F 113_A 0.70 0.19 0.00
142_V 44_M 0.70 0.19 0.00
113_P 227_E 0.70 0.19 0.00
82_V 172_Y 0.70 0.19 0.00
47_E 194_L 0.70 0.19 0.00
155_A 221_V 0.69 0.19 0.00
127_S 398_A 0.69 0.19 0.00
146_T 266_L 0.69 0.19 0.00
126_G 80_T 0.69 0.19 0.00
134_I 162_W 0.69 0.19 0.00
26_A 40_V 0.69 0.19 0.00
85_T 159_L 0.69 0.18 0.00
69_Y 270_G 0.69 0.18 0.00
126_G 407_V 0.69 0.18 0.00
135_Q 348_S 0.69 0.18 0.00
96_L 386_K 0.69 0.18 0.00
40_W 65_G 0.68 0.18 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
4824 2.07 cI_2_4_cI_4_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4823 1.58 cI_2_40_cI_4_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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