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OPENSEQ.org
SH2(NoLink)-KD-0-0
Genes: A B A+B
Length: 98 259 351
Sequences: 1577 80416 306
Seq/Len: 16.09 310.49 0.87
MirrorTree (Pazo et al. 2001) 0.72
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 0.88
2 0.06 0.14 0.90
5 0.07 0.17 0.99
10 0.08 0.21 1.17
20 0.08 0.25 1.35
100 0.10 0.32 1.74
∞ 0.13 0.34 1.78
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
82_H 13_F 1.51 0.74 0.01
82_H 127_C 1.41 0.66 0.01
12_E 175_S 1.35 0.61 0.01
82_H 169_L 1.30 0.57 0.01
2_Y 44_E 1.28 0.55 0.01
78_L 85_Y 1.24 0.52 0.01
64_Y 81_C 1.23 0.50 0.01
15_L 90_R 1.19 0.47 0.00
81_Y 216_L 1.17 0.46 0.00
95_Y 127_C 1.14 0.43 0.00
66_L 161_V 1.09 0.38 0.00
9_S 137_V 1.08 0.38 0.00
26_V 100_E 1.08 0.38 0.00
90_I 168_V 1.08 0.37 0.00
75_I 127_C 1.07 0.37 0.00
56_V 249_S 1.07 0.37 0.00
26_V 188_W 1.07 0.36 0.00
24_F 57_L 1.06 0.36 0.00
23_G 251_I 1.05 0.35 0.00
67_A 101_M 1.04 0.35 0.00
2_Y 135_V 1.03 0.34 0.00
81_Y 199_E 1.03 0.34 0.00
82_H 118_L 1.03 0.33 0.00
92_R 154_S 1.02 0.33 0.00
36_T 200_R 1.02 0.33 0.00
92_R 207_A 1.02 0.32 0.00
29_S 71_F 1.00 0.31 0.00
24_F 43_I 1.00 0.31 0.00
66_L 146_V 1.00 0.31 0.00
12_E 109_M 0.99 0.30 0.00
88_G 49_M 0.97 0.29 0.00
3_S 62_G 0.97 0.29 0.00
83_Q 47_K 0.97 0.29 0.00
33_G 158_K 0.97 0.29 0.00
4_K 83_L 0.96 0.28 0.00
3_S 188_W 0.96 0.28 0.00
54_Y 10_T 0.94 0.27 0.00
51_I 230_M 0.93 0.26 0.00
81_Y 203_N 0.93 0.26 0.00
60_P 243_T 0.93 0.26 0.00
39_V 13_F 0.93 0.26 0.00
52_R 35_G 0.92 0.25 0.00
39_V 41_E 0.92 0.25 0.00
94_K 191_Y 0.92 0.25 0.00
35_Y 2_L 0.92 0.25 0.00
54_Y 234_W 0.91 0.24 0.00
81_Y 155_V 0.91 0.24 0.00
51_I 15_V 0.91 0.24 0.00
75_I 91_H 0.90 0.24 0.00
3_S 123_A 0.90 0.24 0.00
39_V 112_L 0.90 0.24 0.00
67_A 48_V 0.89 0.23 0.00
7_T 191_Y 0.89 0.23 0.00
31_K 64_C 0.88 0.23 0.00
30_S 190_I 0.88 0.23 0.00
58_S 210_I 0.88 0.22 0.00
30_S 200_R 0.88 0.22 0.00
81_Y 183_F 0.87 0.22 0.00
7_T 178_S 0.87 0.22 0.00
80_N 95_T 0.86 0.22 0.00
30_S 50_M 0.86 0.21 0.00
3_S 143_S 0.86 0.21 0.00
10_Q 47_K 0.86 0.21 0.00
23_G 118_L 0.85 0.21 0.00
15_L 234_W 0.85 0.21 0.00
11_A 113_E 0.85 0.21 0.00
15_L 98_L 0.85 0.21 0.00
76_P 229_I 0.84 0.20 0.00
4_K 162_R 0.84 0.20 0.00
10_Q 161_V 0.84 0.20 0.00
89_L 161_V 0.84 0.20 0.00
14_L 50_M 0.84 0.20 0.00
97_V 64_C 0.84 0.20 0.00
76_P 73_I 0.84 0.20 0.00
22_G 179_D 0.83 0.20 0.00
22_G 189_E 0.83 0.20 0.00
22_G 197_P 0.83 0.20 0.00
33_G 175_S 0.83 0.20 0.00
55_V 64_C 0.83 0.20 0.00
74_T 8_L 0.83 0.20 0.00
1_W 109_M 0.83 0.19 0.00
64_Y 29_I 0.82 0.19 0.00
52_R 61_Y 0.82 0.19 0.00
34_K 123_A 0.82 0.19 0.00
68_E 63_V 0.82 0.19 0.00
35_Y 78_A 0.82 0.19 0.00
65_Y 110_E 0.82 0.19 0.00
98_S 251_I 0.81 0.19 0.00
56_V 42_F 0.81 0.19 0.00
53_H 149_D 0.81 0.19 0.00
65_Y 147_L 0.81 0.19 0.00
87_A 33_K 0.81 0.18 0.00
50_V 29_I 0.81 0.18 0.00
37_V 127_C 0.81 0.18 0.00
25_I 187_M 0.80 0.18 0.00
91_S 204_S 0.80 0.18 0.00
23_G 12_Q 0.80 0.18 0.00
59_T 19_G 0.80 0.18 0.00
3_S 149_D 0.79 0.18 0.00
82_H 90_R 0.79 0.17 0.00
3_S 125_R 0.78 0.17 0.00
38_S 56_K 0.78 0.17 0.00
67_A 192_S 0.78 0.17 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
5762 0.87 SH2(NoLink)-KD-0-0 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
5759 0.33 SH2(NoLink)-KD Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5758 0.06 SH2(NoLink)-KD Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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