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cIm_L_2 1_440_cyt1_2_human
Genes: A B A+B
Length: 440 325 688
Sequences: 19180 747 188
Seq/Len: 43.59 2.3 0.27
MirrorTree (Pazo et al. 2001) 0.11
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 0.65 0.02 0.00
2 0.71 0.02 0.00
5 0.87 0.02 0.00
10 0.87 0.02 0.01
20 0.87 0.02 0.01
100 0.87 0.02 0.04
∞ 0.87 0.02 0.25
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
194_N 145_A 1.36 0.31 0.00
39_I 255_F 1.11 0.19 0.00
36_V 127_M 1.10 0.18 0.00
45_I 73_G 1.08 0.18 0.00
368_L 293_L 1.08 0.17 0.00
329_I 248_I 1.03 0.16 0.00
74_T 154_V 1.03 0.16 0.00
188_W 127_M 0.96 0.13 0.00
204_L 245_A 0.93 0.13 0.00
16_I 179_Y 0.93 0.13 0.00
343_S 143_D 0.93 0.12 0.00
13_T 282_H 0.93 0.12 0.00
431_L 169_G 0.91 0.12 0.00
298_I 186_R 0.91 0.12 0.00
276_L 246_P 0.91 0.12 0.00
373_L 298_L 0.90 0.12 0.00
98_W 78_L 0.90 0.12 0.00
345_S 271_C 0.90 0.12 0.00
76_L 127_M 0.90 0.12 0.00
189_F 123_S 0.89 0.11 0.00
138_F 226_S 0.89 0.11 0.00
210_L 190_N 0.89 0.11 0.00
76_L 197_L 0.89 0.11 0.00
195_S 105_L 0.89 0.11 0.00
411_I 70_G 0.88 0.11 0.00
176_R 97_S 0.86 0.11 0.00
17_P 104_S 0.86 0.11 0.00
374_T 213_S 0.86 0.11 0.00
310_L 169_G 0.86 0.11 0.00
189_F 309_H 0.86 0.11 0.00
375_I 221_P 0.86 0.11 0.00
289_A 248_I 0.86 0.11 0.00
44_F 293_L 0.85 0.10 0.00
57_L 130_V 0.84 0.10 0.00
391_S 193_L 0.83 0.10 0.00
398_T 282_H 0.83 0.10 0.00
420_S 300_V 0.83 0.10 0.00
9_T 308_R 0.83 0.10 0.00
189_F 154_V 0.83 0.10 0.00
201_M 312_S 0.82 0.10 0.00
413_L 248_I 0.82 0.10 0.00
271_P 143_D 0.82 0.10 0.00
399_A 221_P 0.82 0.10 0.00
209_S 310_K 0.81 0.10 0.00
86_S 132_Y 0.81 0.09 0.00
134_A 115_Q 0.81 0.09 0.00
25_N 105_L 0.81 0.09 0.00
20_L 148_L 0.81 0.09 0.00
23_L 143_D 0.80 0.09 0.00
326_F 298_L 0.80 0.09 0.00
69_A 182_S 0.80 0.09 0.00
20_L 256_D 0.80 0.09 0.00
280_L 299_L 0.80 0.09 0.00
383_M 160_E 0.80 0.09 0.00
375_I 153_E 0.80 0.09 0.00
291_C 114_F 0.80 0.09 0.00
283_I 220_E 0.80 0.09 0.00
189_F 145_A 0.79 0.09 0.00
305_S 274_L 0.79 0.09 0.00
66_W 143_D 0.79 0.09 0.00
42_S 200_I 0.79 0.09 0.00
102_E 286_K 0.79 0.09 0.00
358_K 144_E 0.79 0.09 0.00
45_I 87_L 0.78 0.09 0.00
403_Y 141_T 0.78 0.09 0.00
399_A 293_L 0.78 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.87 > 0.4) of paralogs.
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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