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OPENSEQ.org
1I1Q
Genes: A B A+B
Length: 512 186 640
Sequences: 3934 16212 1961
Seq/Len: 7.68 87.16 3.06
MirrorTree (Pazo et al. 2001) 0.36
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.03 2.29
2 0.01 0.03 2.42
5 0.01 0.03 2.56
10 0.01 0.04 2.68
20 0.01 0.05 2.81
100 0.03 0.12 3.06
∞ 0.13 0.20 3.80
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
254_A 99_Q 4.02 1.00 1.00
375_P 21_R 2.56 1.00 1.00
484_L 100_I 2.43 1.00 1.00
250_K 99_Q 2.21 1.00 0.99
370_A 18_D 1.95 0.99 0.98
155_E 31_R 1.93 0.99 0.98
253_R 99_Q 1.63 0.98 0.94
251_A 58_G 1.48 0.95 0.89
359_L 126_A 1.41 0.93 0.86
359_L 168_L 1.40 0.93 0.85
485_D 104_K 1.23 0.86 0.74
375_P 17_A 0.98 0.63 0.47
256_E 62_E 0.97 0.61 0.46
256_E 58_G 0.94 0.57 0.42
405_H 68_E 0.87 0.49 0.34
422_L 126_A 0.81 0.43 0.28
404_R 21_R 0.79 0.39 0.25
375_P 27_V 0.78 0.39 0.25
241_F 125_V 0.76 0.36 0.22
386_V 177_E 0.75 0.35 0.22
254_A 59_V 0.75 0.35 0.21
373_C 89_I 0.75 0.35 0.21
383_L 167_I 0.74 0.34 0.20
260_V 14_W 0.74 0.34 0.20
400_V 20_L 0.74 0.33 0.20
253_R 100_I 0.73 0.33 0.20
241_F 93_Y 0.72 0.32 0.19
401_G 89_I 0.72 0.32 0.19
428_V 31_R 0.72 0.32 0.19
446_G 27_V 0.72 0.31 0.18
389_Y 170_T 0.71 0.31 0.18
308_L 65_C 0.70 0.30 0.17
177_L 51_L 0.69 0.29 0.16
156_A 34_I 0.69 0.29 0.16
446_G 126_A 0.68 0.28 0.16
489_Q 121_N 0.68 0.28 0.15
412_A 146_M 0.67 0.27 0.15
372_I 43_L 0.67 0.27 0.15
415_A 176_L 0.67 0.27 0.15
17_P 13_T 0.67 0.26 0.14
317_I 53_L 0.65 0.24 0.13
399_V 82_I 0.64 0.24 0.13
247_Q 47_K 0.64 0.23 0.12
452_F 47_K 0.63 0.23 0.12
456_G 53_L 0.63 0.23 0.12
412_A 169_T 0.63 0.23 0.12
258_F 169_T 0.63 0.23 0.12
127_Q 162_F 0.63 0.22 0.12
384_T 126_A 0.62 0.22 0.11
243_A 117_A 0.62 0.22 0.11
175_E 16_L 0.62 0.22 0.11
57_I 150_V 0.62 0.22 0.11
199_R 115_M 0.62 0.21 0.11
452_F 72_R 0.61 0.21 0.11
506_I 93_Y 0.61 0.21 0.11
247_Q 117_A 0.61 0.21 0.11
296_D 42_R 0.61 0.21 0.10
291_F 147_V 0.61 0.21 0.10
365_A 50_V 0.61 0.21 0.10
147_A 116_F 0.61 0.21 0.10
201_K 145_G 0.60 0.20 0.10
501_A 126_A 0.60 0.20 0.10
215_L 39_L 0.60 0.20 0.10
404_R 117_A 0.60 0.20 0.10
495_T 16_L 0.60 0.20 0.10
446_G 58_G 0.59 0.20 0.10
279_V 82_I 0.59 0.20 0.10
371_R 137_L 0.59 0.20 0.10
44_D 2_D 0.59 0.20 0.10
263_S 14_W 0.59 0.20 0.10
402_E 108_I 0.58 0.19 0.09
356_S 18_D 0.58 0.19 0.09
355_L 124_P 0.58 0.19 0.09
240_A 45_T 0.58 0.19 0.09
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)
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