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OPENSEQ.org
TREM1-PGLYRP1
Genes: A B A+B
Length: 196 234 385
Sequences: 2800 1407 55
Seq/Len: 14.29 6.01 0.14
MirrorTree (Pazo et al. 2001) 0.05
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 0.01 0.12 0.00
2 0.01 0.13 0.00
5 0.01 0.14 0.00
10 0.01 0.15 0.01
20 0.01 0.15 0.01
100 0.01 0.17 0.04
∞ 0.03 0.18 0.13
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
172_D 207_V 1.78 0.39 0.00
193_Y 207_V 1.58 0.29 0.00
93_V 207_V 1.53 0.27 0.00
107_E 107_D 1.49 0.25 0.00
59_V 207_V 1.33 0.19 0.00
96_N 98_V 1.30 0.18 0.00
167_L 154_I 1.29 0.18 0.00
145_I 205_N 1.24 0.16 0.00
107_E 55_W 1.17 0.14 0.00
135_Y 136_G 1.09 0.12 0.00
84_H 162_L 1.08 0.12 0.00
93_V 68_A 1.07 0.12 0.00
178_S 114_V 1.05 0.11 0.00
61_H 162_L 1.04 0.11 0.00
162_R 195_V 1.03 0.11 0.00
128_G 109_G 1.01 0.10 0.00
141_T 192_L 1.01 0.10 0.00
107_E 111_Y 1.01 0.10 0.00
99_I 137_F 1.01 0.10 0.00
39_W 111_Y 0.96 0.09 0.00
133_G 111_Y 0.96 0.09 0.00
98_L 107_D 0.96 0.09 0.00
39_W 55_W 0.96 0.09 0.00
133_G 55_W 0.96 0.09 0.00
111_W 107_D 0.95 0.09 0.00
129_I 137_F 0.95 0.09 0.00
110_G 41_C 0.94 0.09 0.00
145_I 194_N 0.94 0.09 0.00
165_Y 131_L 0.91 0.09 0.00
97_F 162_L 0.91 0.09 0.00
96_N 88_E 0.91 0.08 0.00
193_Y 73_P 0.91 0.08 0.00
39_W 107_D 0.89 0.08 0.00
133_G 107_D 0.89 0.08 0.00
59_V 94_G 0.89 0.08 0.00
53_P 34_G 0.89 0.08 0.00
81_Q 109_G 0.89 0.08 0.00
96_N 147_S 0.88 0.08 0.00
35_P 103_L 0.88 0.08 0.00
105_V 221_F 0.87 0.08 0.00
41_A 131_L 0.87 0.08 0.00
85_M 189_E 0.87 0.08 0.00
122_W 203_V 0.86 0.08 0.00
161_L 193_T 0.86 0.08 0.00
110_G 113_C 0.86 0.08 0.00
151_L 137_F 0.86 0.08 0.00
57_V 31_L 0.86 0.08 0.00
123_N 41_C 0.86 0.08 0.00
123_N 34_G 0.86 0.08 0.00
89_G 103_L 0.86 0.08 0.00
150_G 65_K 0.85 0.08 0.00
145_I 115_I 0.85 0.07 0.00
59_V 203_V 0.85 0.07 0.00
59_V 137_F 0.84 0.07 0.00
80_V 68_A 0.84 0.07 0.00
131_F 85_I 0.84 0.07 0.00
135_Y 107_D 0.84 0.07 0.00
81_Q 41_C 0.84 0.07 0.00
191_P 92_D 0.84 0.07 0.00
84_H 41_C 0.84 0.07 0.00
173_V 163_C 0.83 0.07 0.00
36_R 37_L 0.83 0.07 0.00
191_P 103_L 0.82 0.07 0.00
125_M 11_W 0.82 0.07 0.00
189_N 180_T 0.82 0.07 0.00
69_T 59_R 0.82 0.07 0.00
145_I 36_T 0.81 0.07 0.00
92_D 111_Y 0.81 0.07 0.00
108_G 111_Y 0.81 0.07 0.00
179_P 111_Y 0.81 0.07 0.00
92_D 55_W 0.81 0.07 0.00
108_G 55_W 0.81 0.07 0.00
179_P 55_W 0.81 0.07 0.00
159_G 187_D 0.81 0.07 0.00
156_V 185_T 0.81 0.07 0.00
27_P 12_M 0.80 0.07 0.00
50_L 86_I 0.80 0.07 0.00
151_L 39_V 0.80 0.07 0.00
156_V 137_F 0.80 0.07 0.00
140_P 131_L 0.80 0.07 0.00
78_R 24_L 0.80 0.07 0.00
112_N 85_I 0.80 0.07 0.00
101_E 137_F 0.80 0.07 0.00
107_E 154_I 0.80 0.07 0.00
35_P 173_T 0.80 0.07 0.00
37_N 86_I 0.80 0.07 0.00
81_Q 133_V 0.79 0.07 0.00
140_P 111_Y 0.79 0.07 0.00
191_P 211_A 0.79 0.07 0.00
80_V 134_T 0.79 0.07 0.00
36_R 206_I 0.79 0.07 0.00
95_Y 55_W 0.79 0.07 0.00
110_G 109_G 0.79 0.07 0.00
184_Y 30_E 0.78 0.07 0.00
36_R 163_C 0.78 0.07 0.00
27_P 10_L 0.78 0.07 0.00
99_I 168_S 0.78 0.07 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
11946 0 PGRP-S TREM1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
10463 0.14 TREM1-PGLYRP1 Δgene:(0, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
10462 0.03 TREM1-PGLYRP1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
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