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OPENSEQ.org
SH2(NoLink)-KD
Genes: A B A+B
Length: 98 259 347
Sequences: 1577 80416 116
Seq/Len: 16.09 310.49 0.33
MirrorTree (Pazo et al. 2001) 0.11
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 0.03
2 0.06 0.14 0.06
5 0.07 0.17 0.15
10 0.08 0.21 0.32
20 0.08 0.25 0.51
100 0.10 0.32 0.89
∞ 0.13 0.34 0.94
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
35_Y 187_M 1.68 0.57 0.00
75_I 143_S 1.26 0.29 0.00
81_Y 20_K 1.25 0.29 0.00
26_V 127_C 1.24 0.28 0.00
25_I 123_A 1.11 0.21 0.00
37_V 187_M 1.08 0.20 0.00
15_L 75_E 1.04 0.18 0.00
79_I 55_E 1.04 0.18 0.00
35_Y 102_C 1.04 0.18 0.00
93_L 184_G 1.02 0.17 0.00
2_Y 72_I 1.00 0.17 0.00
22_G 197_P 1.00 0.17 0.00
81_Y 70_I 0.99 0.16 0.00
38_S 249_S 0.98 0.16 0.00
24_F 104_D 0.98 0.16 0.00
7_T 8_L 0.98 0.16 0.00
34_K 243_T 0.98 0.16 0.00
61_Q 244_F 0.98 0.16 0.00
26_V 8_L 0.97 0.15 0.00
2_Y 231_Y 0.95 0.15 0.00
96_P 166_P 0.95 0.15 0.00
79_I 19_G 0.90 0.13 0.00
6_M 140_F 0.89 0.13 0.00
30_S 32_I 0.89 0.13 0.00
74_T 78_A 0.89 0.13 0.00
9_S 108_A 0.88 0.12 0.00
2_Y 247_L 0.87 0.12 0.00
56_V 17_K 0.87 0.12 0.00
82_H 174_F 0.85 0.12 0.00
40_F 195_K 0.83 0.11 0.00
21_E 29_I 0.83 0.11 0.00
72_F 164_S 0.83 0.11 0.00
38_S 165_P 0.83 0.11 0.00
64_Y 114_S 0.82 0.11 0.00
31_K 127_C 0.82 0.11 0.00
15_L 86_L 0.82 0.11 0.00
79_I 36_S 0.82 0.11 0.00
37_V 141_G 0.82 0.11 0.00
25_I 122_L 0.81 0.11 0.00
13_Q 58_V 0.81 0.11 0.00
96_P 184_G 0.81 0.10 0.00
61_Q 72_I 0.81 0.10 0.00
96_P 187_M 0.80 0.10 0.00
33_G 54_H 0.80 0.10 0.00
96_P 126_N 0.80 0.10 0.00
81_Y 173_K 0.80 0.10 0.00
93_L 139_D 0.80 0.10 0.00
34_K 81_C 0.80 0.10 0.00
81_Y 228_T 0.79 0.10 0.00
15_L 203_N 0.79 0.10 0.00
74_T 148_D 0.79 0.10 0.00
71_L 20_K 0.79 0.10 0.00
62_S 178_S 0.79 0.10 0.00
93_L 126_N 0.79 0.10 0.00
96_P 72_I 0.79 0.10 0.00
71_L 62_G 0.79 0.10 0.00
74_T 170_M 0.78 0.10 0.00
38_S 73_I 0.78 0.10 0.00
31_K 246_I 0.78 0.10 0.00
27_R 241_R 0.78 0.10 0.00
10_Q 191_Y 0.78 0.10 0.00
52_R 57_L 0.78 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)
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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