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OPENSEQ.org
LCB2_ORM1_Pfam
Genes: A B A+B
Length: 360 136 494
Sequences: 4982 234 55
Seq/Len: 13.84 1.72 0.11
MirrorTree (Pazo et al. 2001) 0.12
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 0.03 0.03 0.00
2 0.04 0.03 0.00
5 0.04 0.03 0.00
10 0.04 0.03 0.00
20 0.04 0.03 0.00
100 0.05 0.04 0.02
∞ 0.15 0.04 0.11
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
37_G 15_I 1.70 0.29 0.00
171_C 34_T 1.49 0.21 0.00
175_I 101_V 1.25 0.14 0.00
167_K 51_Y 1.25 0.14 0.00
173_L 69_Y 1.21 0.13 0.00
303_L 80_D 1.21 0.13 0.00
191_V 51_Y 1.14 0.12 0.00
156_L 56_L 1.11 0.11 0.00
330_Y 101_V 1.10 0.11 0.00
266_Q 21_I 1.10 0.11 0.00
56_A 32_G 1.09 0.11 0.00
101_G 130_P 1.07 0.10 0.00
71_Y 123_G 1.06 0.10 0.00
167_K 26_F 1.06 0.10 0.00
63_D 25_L 1.05 0.10 0.00
144_I 132_T 1.05 0.10 0.00
55_V 135_L 1.02 0.09 0.00
183_A 21_I 1.01 0.09 0.00
304_L 7_V 1.01 0.09 0.00
85_K 30_F 1.00 0.09 0.00
117_M 9_Q 0.98 0.09 0.00
163_V 45_T 0.98 0.09 0.00
156_L 51_Y 0.98 0.09 0.00
292_V 48_I 0.98 0.09 0.00
99_R 73_T 0.97 0.09 0.00
21_T 88_R 0.97 0.09 0.00
168_K 80_D 0.97 0.09 0.00
36_G 51_Y 0.97 0.09 0.00
360_V 81_E 0.97 0.09 0.00
56_A 31_P 0.96 0.08 0.00
360_V 9_Q 0.96 0.08 0.00
271_L 87_S 0.96 0.08 0.00
45_T 52_V 0.95 0.08 0.00
242_S 73_T 0.95 0.08 0.00
89_I 45_T 0.95 0.08 0.00
161_K 102_S 0.95 0.08 0.00
101_G 106_A 0.94 0.08 0.00
117_M 60_T 0.93 0.08 0.00
113_K 7_V 0.92 0.08 0.00
351_E 118_F 0.92 0.08 0.00
191_V 11_G 0.92 0.08 0.00
345_S 38_S 0.92 0.08 0.00
16_S 4_A 0.92 0.08 0.00
122_K 51_Y 0.91 0.07 0.00
185_G 1_N 0.90 0.07 0.00
188_G 1_N 0.90 0.07 0.00
274_I 51_Y 0.89 0.07 0.00
168_K 91_L 0.89 0.07 0.00
258_I 48_I 0.89 0.07 0.00
202_V 21_I 0.89 0.07 0.00
187_T 101_V 0.89 0.07 0.00
360_V 83_L 0.89 0.07 0.00
341_R 130_P 0.89 0.07 0.00
309_S 63_D 0.88 0.07 0.00
230_L 42_T 0.88 0.07 0.00
55_V 17_V 0.88 0.07 0.00
62_E 97_A 0.88 0.07 0.00
56_A 130_P 0.87 0.07 0.00
7_S 109_D 0.87 0.07 0.00
272_Q 42_T 0.87 0.07 0.00
177_E 43_N 0.87 0.07 0.00
177_E 129_L 0.87 0.07 0.00
254_S 115_W 0.87 0.07 0.00
191_V 5_T 0.87 0.07 0.00
334_P 33_V 0.87 0.07 0.00
126_E 90_F 0.87 0.07 0.00
202_V 101_V 0.86 0.07 0.00
204_I 54_F 0.86 0.07 0.00
305_L 21_I 0.86 0.07 0.00
110_R 26_F 0.86 0.07 0.00
349_T 63_D 0.85 0.07 0.00
286_Q 26_F 0.85 0.07 0.00
159_L 51_Y 0.85 0.07 0.00
220_I 30_F 0.84 0.07 0.00
342_F 131_V 0.84 0.07 0.00
191_V 69_Y 0.84 0.07 0.00
292_V 42_T 0.84 0.07 0.00
110_R 87_S 0.84 0.07 0.00
230_L 6_W 0.84 0.07 0.00
63_D 8_D 0.83 0.07 0.00
241_E 51_Y 0.83 0.07 0.00
15_Q 27_Y 0.83 0.07 0.00
242_S 92_I 0.83 0.07 0.00
89_I 88_R 0.83 0.06 0.00
66_V 58_K 0.83 0.06 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
13505 0.38 LCB2_ORM1_Pfam_1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
13503 0.11 LCB2_ORM1_Pfam Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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