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OPENSEQ.org
cIm_L_20_1_440_cyt1_2_human
Genes: A B A+B
Length: 440 325 638
Sequences: 8233 747 158
Seq/Len: 18.71 2.3 0.25
MirrorTree (Pazo et al. 2001) 0.05
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.00
100 0.01 0.02 0.02
∞ 0.04 0.02 0.21
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
375_I 238_P 1.21 0.22 0.00
206_A 267_A 1.20 0.21 0.00
134_A 232_Y 1.19 0.21 0.00
383_M 154_V 1.19 0.21 0.00
134_A 115_Q 1.18 0.20 0.00
191_L 86_D 1.16 0.20 0.00
201_M 105_L 1.10 0.18 0.00
227_L 138_V 1.08 0.17 0.00
206_A 310_K 1.06 0.16 0.00
402_S 141_T 1.05 0.16 0.00
93_A 299_L 1.04 0.15 0.00
182_F 251_D 1.03 0.15 0.00
420_S 176_P 1.00 0.14 0.00
69_A 154_V 0.99 0.14 0.00
77_S 73_G 0.98 0.14 0.00
180_I 177_K 0.97 0.13 0.00
134_A 228_R 0.97 0.13 0.00
315_V 213_S 0.97 0.13 0.00
94_L 169_G 0.96 0.13 0.00
384_P 102_L 0.96 0.13 0.00
102_E 312_S 0.94 0.12 0.00
137_L 197_L 0.94 0.12 0.00
276_L 107_H 0.94 0.12 0.00
375_I 288_M 0.94 0.12 0.00
260_L 298_L 0.93 0.12 0.00
286_L 294_M 0.93 0.12 0.00
276_L 182_S 0.93 0.12 0.00
162_A 282_H 0.93 0.12 0.00
227_L 132_Y 0.92 0.12 0.00
93_A 81_A 0.92 0.12 0.00
262_R 144_E 0.92 0.12 0.00
213_L 282_H 0.91 0.12 0.00
228_G 138_V 0.91 0.12 0.00
138_F 126_S 0.90 0.11 0.00
74_T 160_E 0.89 0.11 0.00
77_S 245_A 0.89 0.11 0.00
365_T 261_A 0.88 0.11 0.00
113_N 267_A 0.88 0.11 0.00
203_L 81_A 0.88 0.11 0.00
68_W 304_Y 0.88 0.11 0.00
169_I 282_H 0.88 0.11 0.00
390_Y 312_S 0.88 0.11 0.00
283_I 232_Y 0.88 0.11 0.00
375_I 239_G 0.88 0.11 0.00
324_L 305_T 0.87 0.11 0.00
203_L 277_A 0.87 0.10 0.00
228_G 281_E 0.87 0.10 0.00
414_I 129_F 0.86 0.10 0.00
291_C 169_G 0.86 0.10 0.00
364_K 227_L 0.86 0.10 0.00
78_L 293_L 0.86 0.10 0.00
396_I 138_V 0.85 0.10 0.00
412_T 74_L 0.85 0.10 0.00
267_A 237_F 0.84 0.10 0.00
227_L 266_I 0.84 0.10 0.00
283_I 154_V 0.84 0.10 0.00
385_F 208_E 0.84 0.10 0.00
217_L 182_S 0.84 0.10 0.00
102_E 314_L 0.84 0.10 0.00
212_P 310_K 0.84 0.10 0.00
286_L 126_S 0.84 0.10 0.00
371_T 127_M 0.84 0.10 0.00
82_L 94_Y 0.83 0.10 0.00
420_S 132_Y 0.83 0.10 0.00
218_L 193_L 0.83 0.10 0.00
215_G 68_A 0.83 0.10 0.00
218_L 235_P 0.83 0.10 0.00
207_N 137_G 0.83 0.10 0.00
140_L 175_F 0.82 0.09 0.00
396_I 145_A 0.82 0.09 0.00
259_L 172_F 0.82 0.09 0.00
216_L 171_L 0.82 0.09 0.00
375_I 299_L 0.82 0.09 0.00
376_G 301_P 0.82 0.09 0.00
134_A 295_M 0.82 0.09 0.00
114_I 132_Y 0.82 0.09 0.00
202_A 314_L 0.81 0.09 0.00
105_L 96_W 0.81 0.09 0.00
94_L 206_G 0.81 0.09 0.00
204_L 69_A 0.81 0.09 0.00
93_A 179_Y 0.81 0.09 0.00
275_T 254_E 0.81 0.09 0.00
62_I 310_K 0.81 0.09 0.00
227_L 109_S 0.81 0.09 0.00
181_G 286_K 0.80 0.09 0.00
121_L 246_P 0.80 0.09 0.00
138_F 118_K 0.80 0.09 0.00
230_H 181_N 0.80 0.09 0.00
402_S 188_A 0.80 0.09 0.00
63_I 294_M 0.79 0.09 0.00
293_L 220_E 0.79 0.09 0.00
375_I 143_D 0.79 0.09 0.00
82_L 115_Q 0.79 0.09 0.00
358_K 267_A 0.79 0.09 0.00
263_F 105_L 0.79 0.09 0.00
414_I 294_M 0.79 0.09 0.00
363_L 272_T 0.79 0.09 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
5746 0.25 cIm_L_20_1_440_cyt1_2_human Δgene:(1, ∞) A:(1E-20, 1) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5743 0.27 cIm_L_2 1_440_cyt1_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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