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OPENSEQ.org
cIm_M_4_1_cyt1_2_human
Genes: A B A+B
Length: 459 325 651
Sequences: 9265 747 151
Seq/Len: 20.19 2.3 0.23
MirrorTree (Pazo et al. 2001) 0.01
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 0.18 0.02 0.00
2 0.18 0.02 0.00
5 0.20 0.02 0.00
10 0.20 0.02 0.00
20 0.20 0.02 0.00
100 0.20 0.02 0.02
∞ 0.22 0.02 0.19
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
164_L 96_W 1.56 0.39 0.00
115_L 137_G 1.55 0.38 0.00
351_L 138_V 1.43 0.31 0.00
382_L 127_M 1.25 0.22 0.00
337_T 211_V 1.24 0.22 0.00
295_A 190_N 1.17 0.19 0.00
73_L 132_Y 1.16 0.19 0.00
383_V 245_A 1.12 0.17 0.00
360_L 271_C 1.10 0.16 0.00
73_L 109_S 1.10 0.16 0.00
115_L 138_V 1.09 0.16 0.00
258_A 105_L 1.07 0.15 0.00
385_T 213_S 1.07 0.15 0.00
414_T 200_I 1.07 0.15 0.00
383_V 130_V 1.06 0.15 0.00
222_E 96_W 1.05 0.15 0.00
238_L 136_V 1.04 0.15 0.00
416_W 192_A 1.04 0.15 0.00
405_L 268_K 1.02 0.14 0.00
75_L 144_E 1.01 0.14 0.00
266_L 208_E 1.00 0.13 0.00
351_L 303_V 0.97 0.13 0.00
73_L 176_P 0.97 0.13 0.00
305_T 242_I 0.97 0.12 0.00
267_W 174_Y 0.97 0.12 0.00
266_L 199_Y 0.97 0.12 0.00
187_S 221_P 0.95 0.12 0.00
261_F 310_K 0.95 0.12 0.00
64_P 170_K 0.95 0.12 0.00
392_T 256_D 0.95 0.12 0.00
162_I 260_P 0.95 0.12 0.00
175_N 310_K 0.94 0.12 0.00
397_G 293_L 0.94 0.12 0.00
419_L 237_F 0.94 0.12 0.00
164_L 127_M 0.94 0.12 0.00
414_T 313_V 0.93 0.12 0.00
393_L 267_A 0.93 0.11 0.00
348_L 176_P 0.92 0.11 0.00
348_L 109_S 0.92 0.11 0.00
72_L 197_L 0.92 0.11 0.00
321_L 295_M 0.92 0.11 0.00
253_L 299_L 0.92 0.11 0.00
262_L 254_E 0.92 0.11 0.00
382_L 315_K 0.92 0.11 0.00
146_G 310_K 0.91 0.11 0.00
69_T 107_H 0.91 0.11 0.00
234_V 137_G 0.91 0.11 0.00
314_I 145_A 0.91 0.11 0.00
312_A 221_P 0.91 0.11 0.00
69_T 98_H 0.91 0.11 0.00
361_L 105_L 0.91 0.11 0.00
84_L 283_D 0.90 0.11 0.00
143_L 94_Y 0.90 0.11 0.00
101_S 294_M 0.90 0.11 0.00
385_T 208_E 0.89 0.11 0.00
337_T 201_V 0.89 0.11 0.00
80_S 91_P 0.89 0.10 0.00
309_F 154_V 0.89 0.10 0.00
407_S 201_V 0.89 0.10 0.00
79_A 132_Y 0.89 0.10 0.00
270_I 264_S 0.88 0.10 0.00
85_S 297_A 0.88 0.10 0.00
299_T 292_M 0.88 0.10 0.00
400_M 290_L 0.87 0.10 0.00
383_V 298_L 0.87 0.10 0.00
64_P 295_M 0.87 0.10 0.00
141_E 96_W 0.87 0.10 0.00
164_L 200_I 0.87 0.10 0.00
312_A 248_I 0.86 0.10 0.00
109_T 98_H 0.86 0.10 0.00
360_L 72_A 0.86 0.10 0.00
80_S 179_Y 0.86 0.10 0.00
124_T 221_P 0.85 0.10 0.00
65_L 191_G 0.85 0.10 0.00
358_W 299_L 0.85 0.10 0.00
162_I 186_R 0.84 0.10 0.00
107_I 314_L 0.84 0.10 0.00
395_L 245_A 0.84 0.10 0.00
270_I 282_H 0.84 0.09 0.00
124_T 301_P 0.84 0.09 0.00
418_S 260_P 0.84 0.09 0.00
111_T 232_Y 0.84 0.09 0.00
165_I 304_Y 0.84 0.09 0.00
262_L 229_E 0.83 0.09 0.00
305_T 290_L 0.83 0.09 0.00
115_L 105_L 0.83 0.09 0.00
313_V 87_L 0.83 0.09 0.00
386_F 157_G 0.82 0.09 0.00
312_A 268_K 0.82 0.09 0.00
357_F 107_H 0.82 0.09 0.00
312_A 70_G 0.82 0.09 0.00
80_S 140_Y 0.81 0.09 0.00
58_S 70_G 0.81 0.09 0.00
304_Q 266_I 0.81 0.09 0.00
351_L 242_I 0.81 0.09 0.00
124_T 87_L 0.81 0.09 0.00
267_W 95_P 0.80 0.09 0.00
337_T 140_Y 0.80 0.09 0.00
243_M 308_R 0.80 0.09 0.00
415_Q 126_S 0.80 0.09 0.00
301_I 293_L 0.80 0.09 0.00
93_K 209_D 0.80 0.09 0.00
374_N 202_R 0.80 0.09 0.00
175_N 80_S 0.80 0.09 0.00
396_T 142_E 0.80 0.09 0.00
282_L 300_V 0.80 0.09 0.00
115_L 145_A 0.80 0.09 0.00
379_L 315_K 0.80 0.09 0.00
386_F 158_P 0.80 0.09 0.00
109_T 186_R 0.79 0.08 0.00
143_L 157_G 0.79 0.08 0.00
421_H 306_I 0.79 0.08 0.00
295_A 309_H 0.79 0.08 0.00
387_S 105_L 0.79 0.08 0.00
222_E 190_N 0.79 0.08 0.00
84_L 171_L 0.79 0.08 0.00
158_L 180_P 0.79 0.08 0.00
263_V 243_A 0.78 0.08 0.00
360_L 308_R 0.78 0.08 0.00
270_I 132_Y 0.78 0.08 0.00
262_L 308_R 0.78 0.08 0.00
70_T 160_E 0.78 0.08 0.00
262_L 105_L 0.78 0.08 0.00
97_S 264_S 0.78 0.08 0.00
140_P 232_Y 0.78 0.08 0.00
256_H 277_A 0.78 0.08 0.00
442_S 150_A 0.78 0.08 0.00
309_F 200_I 0.77 0.08 0.00
317_I 170_K 0.77 0.08 0.00
282_L 281_E 0.77 0.08 0.00
317_I 282_H 0.77 0.08 0.00
308_S 247_P 0.77 0.08 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
5740 0.23 cIm_M_4_1_cyt1_2_human Δgene:(1, ∞) A:(1E-04, 1) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5736 0.21 cIm_M_20_1_cyt1_2_human Δgene:(1, ∞) A:(1E-20, 1) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5732 0.08 cIm_M_60_1_cyt1_2_human Δgene:(1, ∞) A:(1E-60, 1) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5731 0 cIm_M_60_1_cyt1_2_human Δgene:(1, ∞) A:(1E-60, 1) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
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