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OPENSEQ.org
FAK
Genes: A B A+B
Length: 552 287 801
Sequences: 1021 3438 657
Seq/Len: 1.85 11.98 0.82
MirrorTree (Pazo et al. 2001) 0.41
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 0.11
2 0.01 0.03 0.14
5 0.01 0.03 0.14
10 0.01 0.04 0.15
20 0.01 0.05 0.18
100 0.01 0.09 0.32
∞ 0.01 0.19 0.78
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
386_A 35_G 1.09 0.37 0.00
413_V 75_E 1.04 0.33 0.00
306_A 130_I 1.02 0.32 0.00
388_I 277_I 0.99 0.29 0.00
104_I 5_V 0.97 0.27 0.00
413_V 149_L 0.96 0.27 0.00
423_T 11_S 0.95 0.27 0.00
418_I 23_I 0.95 0.26 0.00
386_A 138_D 0.94 0.26 0.00
91_F 94_I 0.93 0.25 0.00
162_E 144_E 0.92 0.24 0.00
507_T 5_V 0.91 0.23 0.00
409_E 32_L 0.90 0.23 0.00
522_I 129_V 0.89 0.23 0.00
388_I 115_P 0.88 0.21 0.00
105_D 195_D 0.87 0.21 0.00
530_F 3_I 0.86 0.21 0.00
56_V 160_L 0.85 0.20 0.00
72_S 167_N 0.84 0.20 0.00
111_K 230_I 0.84 0.20 0.00
111_K 35_G 0.84 0.19 0.00
387_I 63_S 0.83 0.19 0.00
295_G 174_I 0.83 0.19 0.00
430_G 190_V 0.82 0.19 0.00
72_S 195_D 0.82 0.19 0.00
440_A 90_L 0.82 0.19 0.00
186_S 145_I 0.82 0.19 0.00
109_F 107_M 0.82 0.18 0.00
470_D 15_Q 0.82 0.18 0.00
98_L 144_E 0.82 0.18 0.00
94_F 19_K 0.82 0.18 0.00
415_T 32_L 0.81 0.18 0.00
169_E 266_I 0.81 0.18 0.00
526_M 116_V 0.81 0.18 0.00
393_K 198_I 0.81 0.18 0.00
483_S 11_S 0.81 0.18 0.00
51_S 28_L 0.81 0.18 0.00
461_K 22_N 0.81 0.18 0.00
415_T 118_S 0.81 0.18 0.00
375_V 72_H 0.81 0.18 0.00
34_Y 203_K 0.81 0.18 0.00
413_V 281_N 0.81 0.18 0.00
65_G 72_H 0.80 0.17 0.00
30_A 30_I 0.80 0.17 0.00
434_L 11_S 0.80 0.17 0.00
531_E 232_I 0.80 0.17 0.00
281_V 90_L 0.80 0.17 0.00
458_R 79_A 0.79 0.17 0.00
336_E 277_I 0.79 0.17 0.00
348_I 86_I 0.79 0.17 0.00
186_S 162_V 0.79 0.17 0.00
306_A 174_I 0.79 0.17 0.00
10_F 44_M 0.78 0.17 0.00
292_F 61_T 0.78 0.16 0.00
384_K 38_H 0.78 0.16 0.00
315_E 186_K 0.78 0.16 0.00
137_K 67_I 0.78 0.16 0.00
470_D 245_L 0.77 0.16 0.00
12_E 266_I 0.77 0.16 0.00
94_F 266_I 0.77 0.16 0.00
415_T 48_E 0.76 0.16 0.00
350_K 237_N 0.76 0.16 0.00
470_D 220_E 0.76 0.16 0.00
506_L 184_L 0.76 0.16 0.00
413_V 276_G 0.76 0.15 0.00
7_G 184_L 0.76 0.15 0.00
350_K 86_I 0.76 0.15 0.00
13_M 203_K 0.75 0.15 0.00
72_S 93_G 0.75 0.15 0.00
186_S 135_L 0.75 0.15 0.00
199_L 86_I 0.75 0.15 0.00
388_I 142_I 0.75 0.15 0.00
388_I 118_S 0.75 0.15 0.00
453_I 166_K 0.74 0.15 0.00
165_L 85_V 0.74 0.15 0.00
372_E 164_D 0.74 0.15 0.00
372_E 190_V 0.74 0.14 0.00
260_R 265_V 0.74 0.14 0.00
189_K 203_K 0.74 0.14 0.00
340_I 55_Q 0.74 0.14 0.00
340_I 37_N 0.74 0.14 0.00
172_P 232_I 0.74 0.14 0.00
156_I 134_D 0.74 0.14 0.00
508_I 11_S 0.74 0.14 0.00
29_D 178_Q 0.73 0.14 0.00
295_G 30_I 0.73 0.14 0.00
45_M 60_P 0.73 0.14 0.00
293_T 89_H 0.73 0.14 0.00
338_A 153_R 0.73 0.14 0.00
5_I 179_A 0.73 0.14 0.00
29_D 264_P 0.73 0.14 0.00
378_I 2_K 0.73 0.14 0.00
18_A 178_Q 0.73 0.14 0.00
28_V 146_L 0.73 0.14 0.00
522_I 55_Q 0.73 0.14 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
9072 0.82 FAK Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9071 0.19 FAK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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