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OPENSEQ.org
cIm_L_20_1_440_isp_2_human
Genes: A B A+B
Length: 440 274 618
Sequences: 8233 609 178
Seq/Len: 18.71 2.22 0.29
MirrorTree (Pazo et al. 2001) 0.19
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.01 0.00 0.02
∞ 0.04 0.00 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
211_T 130_K 1.25 0.26 0.00
304_F 216_V 1.18 0.23 0.00
164_A 114_S 1.17 0.22 0.00
194_N 92_R 1.08 0.18 0.00
91_P 272_I 1.07 0.18 0.00
260_L 216_V 1.06 0.18 0.00
399_A 120_V 1.05 0.17 0.00
369_T 96_V 1.04 0.17 0.00
378_L 104_R 1.04 0.17 0.00
225_A 106_S 1.03 0.17 0.00
257_I 69_G 1.03 0.16 0.00
337_A 130_K 1.02 0.16 0.00
386_L 204_R 1.01 0.16 0.00
375_I 185_E 1.01 0.16 0.00
141_F 119_G 1.01 0.15 0.00
205_N 272_I 0.98 0.15 0.00
282_A 91_Y 0.96 0.14 0.00
94_L 91_Y 0.95 0.14 0.00
348_H 127_Y 0.95 0.14 0.00
142_I 65_V 0.94 0.13 0.00
77_S 114_S 0.93 0.13 0.00
423_S 123_V 0.93 0.13 0.00
311_G 263_Y 0.92 0.13 0.00
309_Q 229_G 0.91 0.13 0.00
164_A 245_A 0.91 0.12 0.00
406_A 165_M 0.90 0.12 0.00
375_I 162_G 0.90 0.12 0.00
157_W 65_V 0.90 0.12 0.00
376_G 248_R 0.89 0.12 0.00
219_A 129_A 0.89 0.12 0.00
386_L 131_N 0.88 0.12 0.00
387_T 123_V 0.88 0.12 0.00
130_I 168_K 0.87 0.11 0.00
240_P 229_G 0.86 0.11 0.00
69_A 184_I 0.86 0.11 0.00
195_S 130_K 0.86 0.11 0.00
139_Q 247_G 0.85 0.11 0.00
218_L 90_E 0.85 0.11 0.00
148_G 272_I 0.84 0.10 0.00
364_K 144_A 0.83 0.10 0.00
275_T 92_R 0.83 0.10 0.00
415_A 120_V 0.83 0.10 0.00
199_Q 184_I 0.82 0.10 0.00
186_L 87_D 0.82 0.10 0.00
377_S 74_A 0.82 0.10 0.00
92_V 140_M 0.82 0.10 0.00
265_P 67_S 0.82 0.10 0.00
384_P 247_G 0.82 0.10 0.00
130_I 257_N 0.81 0.10 0.00
218_L 88_F 0.81 0.10 0.00
329_I 266_T 0.81 0.10 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)
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