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OPENSEQ.org
SH2-KD(Linker)
Genes: A B A+B
Length: 120 259 373
Sequences: 1325 80416 351
Seq/Len: 11.04 310.49 0.94
MirrorTree (Pazo et al. 2001) 0.76
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 0.06 0.11 0.95
2 0.06 0.14 0.96
5 0.07 0.17 1.01
10 0.08 0.21 1.08
20 0.08 0.25 1.15
100 0.09 0.32 1.36
∞ 0.12 0.34 1.38
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
116_E 144_R 1.51 0.76 0.02
82_H 13_F 1.46 0.72 0.01
117_I 73_I 1.46 0.72 0.01
2_Y 135_V 1.37 0.66 0.01
95_Y 127_C 1.34 0.63 0.01
2_Y 44_E 1.32 0.61 0.01
81_Y 199_E 1.30 0.59 0.01
75_I 127_C 1.27 0.57 0.01
29_S 71_F 1.22 0.52 0.01
80_N 95_T 1.20 0.50 0.01
36_T 200_R 1.18 0.48 0.01
88_G 49_M 1.18 0.48 0.01
81_Y 216_L 1.17 0.48 0.01
82_H 127_C 1.14 0.45 0.01
10_Q 47_K 1.12 0.43 0.01
66_L 161_V 1.11 0.42 0.01
116_E 8_L 1.09 0.40 0.01
81_Y 183_F 1.08 0.39 0.01
26_V 252_L 1.08 0.39 0.01
66_L 146_V 1.05 0.37 0.01
12_E 175_S 1.05 0.37 0.01
118_D 62_G 1.04 0.36 0.01
56_V 130_N 1.03 0.35 0.00
59_T 19_G 1.03 0.35 0.00
64_Y 81_C 1.03 0.35 0.00
88_G 58_V 1.03 0.35 0.00
33_G 158_K 1.03 0.35 0.00
12_E 109_M 1.02 0.34 0.00
81_Y 44_E 1.01 0.34 0.00
39_V 13_F 1.01 0.34 0.00
64_Y 85_Y 1.01 0.33 0.00
15_L 90_R 1.00 0.33 0.00
26_V 100_E 1.00 0.33 0.00
80_N 182_A 0.99 0.32 0.00
6_M 210_I 0.98 0.31 0.00
20_K 81_C 0.96 0.30 0.00
39_V 138_S 0.96 0.29 0.00
40_F 122_L 0.95 0.29 0.00
1_W 187_M 0.95 0.29 0.00
82_H 118_L 0.95 0.28 0.00
117_I 2_L 0.94 0.28 0.00
23_G 118_L 0.94 0.28 0.00
9_S 137_V 0.93 0.28 0.00
75_I 238_A 0.93 0.27 0.00
66_L 216_L 0.92 0.27 0.00
117_I 74_T 0.92 0.27 0.00
82_H 169_L 0.91 0.26 0.00
115_W 4_F 0.91 0.26 0.00
79_I 112_L 0.91 0.26 0.00
76_P 73_I 0.91 0.26 0.00
108_A 48_V 0.90 0.25 0.00
67_A 48_V 0.90 0.25 0.00
94_K 191_Y 0.90 0.25 0.00
15_L 234_W 0.90 0.25 0.00
8_R 46_A 0.89 0.25 0.00
30_S 190_I 0.89 0.25 0.00
3_S 62_G 0.89 0.25 0.00
89_L 206_T 0.89 0.24 0.00
74_T 8_L 0.88 0.24 0.00
67_A 117_F 0.88 0.24 0.00
39_V 112_L 0.88 0.24 0.00
115_W 50_M 0.87 0.23 0.00
38_S 56_K 0.86 0.23 0.00
87_A 116_Q 0.86 0.23 0.00
26_V 188_W 0.86 0.23 0.00
78_L 85_Y 0.86 0.23 0.00
52_R 35_G 0.86 0.23 0.00
36_T 40_D 0.86 0.23 0.00
34_K 123_A 0.86 0.23 0.00
54_Y 10_T 0.85 0.22 0.00
10_Q 161_V 0.85 0.22 0.00
119_P 69_P 0.85 0.22 0.00
119_P 15_V 0.84 0.22 0.00
113_G 50_M 0.84 0.21 0.00
22_G 189_E 0.83 0.21 0.00
22_G 197_P 0.83 0.21 0.00
79_I 76_Y 0.83 0.21 0.00
72_F 210_I 0.83 0.21 0.00
26_V 95_T 0.83 0.21 0.00
93_L 122_L 0.83 0.20 0.00
52_R 61_Y 0.83 0.20 0.00
92_R 185_V 0.82 0.20 0.00
69_K 229_I 0.82 0.20 0.00
116_E 16_V 0.82 0.20 0.00
30_S 200_R 0.82 0.20 0.00
54_Y 234_W 0.82 0.20 0.00
24_F 57_L 0.81 0.20 0.00
57_C 183_F 0.81 0.20 0.00
23_G 105_V 0.81 0.20 0.00
91_S 55_E 0.81 0.20 0.00
25_I 187_M 0.81 0.19 0.00
28_D 187_M 0.80 0.19 0.00
66_L 199_E 0.80 0.19 0.00
64_Y 217_Y 0.80 0.19 0.00
119_P 164_S 0.80 0.19 0.00
10_Q 137_V 0.80 0.19 0.00
26_V 116_Q 0.80 0.19 0.00
56_V 42_F 0.80 0.19 0.00
9_S 192_S 0.79 0.19 0.00
33_G 240_E 0.79 0.18 0.00
35_Y 2_L 0.79 0.18 0.00
4_K 83_L 0.79 0.18 0.00
54_Y 198_Y 0.79 0.18 0.00
57_C 73_I 0.79 0.18 0.00
99_Q 102_C 0.78 0.18 0.00
39_V 41_E 0.78 0.18 0.00
97_V 64_C 0.78 0.18 0.00
23_G 251_I 0.78 0.18 0.00
2_Y 137_V 0.78 0.18 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
5761 0.94 SH2-KD(Linker) Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
5755 0.24 complex_btk Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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