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OPENSEQ.org
LCB1_ORM1_Pfam
Genes: A B A+B
Length: 401 136 506
Sequences: 17206 234 89
Seq/Len: 42.91 1.72 0.18
MirrorTree (Pazo et al. 2001) 0.23
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 0.04 0.03 0.00
2 0.04 0.03 0.00
5 0.04 0.03 0.00
10 0.05 0.03 0.01
20 0.06 0.03 0.01
100 0.12 0.04 0.03
∞ 0.20 0.04 0.17
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
167_N 97_A 1.34 0.23 0.00
156_L 56_L 1.28 0.20 0.00
167_N 51_Y 1.16 0.16 0.00
55_L 56_L 1.13 0.15 0.00
104_L 23_L 1.09 0.14 0.00
164_K 63_D 1.07 0.13 0.00
196_N 80_D 1.05 0.13 0.00
123_L 21_I 1.05 0.13 0.00
276_L 115_W 1.04 0.13 0.00
392_E 118_F 1.04 0.13 0.00
112_F 63_D 1.03 0.12 0.00
165_L 69_Y 1.03 0.12 0.00
165_L 54_F 1.00 0.12 0.00
125_N 66_G 1.00 0.12 0.00
303_L 51_Y 0.98 0.11 0.00
173_L 7_V 0.96 0.11 0.00
245_P 125_V 0.95 0.10 0.00
57_Q 51_Y 0.94 0.10 0.00
231_Q 42_T 0.94 0.10 0.00
164_K 88_R 0.93 0.10 0.00
394_L 101_V 0.93 0.10 0.00
167_N 27_Y 0.92 0.10 0.00
154_G 136_R 0.92 0.10 0.00
76_S 42_T 0.92 0.10 0.00
123_L 51_Y 0.91 0.10 0.00
229_L 34_T 0.90 0.10 0.00
382_K 130_P 0.89 0.09 0.00
49_Y 63_D 0.89 0.09 0.00
176_D 55_H 0.89 0.09 0.00
176_D 59_G 0.89 0.09 0.00
176_D 61_P 0.89 0.09 0.00
176_D 76_E 0.89 0.09 0.00
176_D 77_Q 0.89 0.09 0.00
176_D 95_P 0.89 0.09 0.00
176_D 128_K 0.89 0.09 0.00
257_K 58_K 0.88 0.09 0.00
253_S 25_L 0.88 0.09 0.00
13_Q 14_I 0.88 0.09 0.00
22_E 37_W 0.88 0.09 0.00
399_E 93_S 0.87 0.09 0.00
112_F 101_V 0.87 0.09 0.00
84_R 17_V 0.87 0.09 0.00
303_L 131_V 0.87 0.09 0.00
400_S 97_A 0.86 0.09 0.00
16_A 27_Y 0.86 0.09 0.00
63_G 8_D 0.85 0.09 0.00
173_L 69_Y 0.85 0.09 0.00
162_L 115_W 0.85 0.09 0.00
171_F 34_T 0.85 0.08 0.00
269_L 44_M 0.85 0.08 0.00
384_C 42_T 0.84 0.08 0.00
264_D 56_L 0.84 0.08 0.00
28_I 69_Y 0.83 0.08 0.00
395_K 34_T 0.83 0.08 0.00
31_Y 7_V 0.82 0.08 0.00
191_L 51_Y 0.82 0.08 0.00
301_L 69_Y 0.82 0.08 0.00
264_D 45_T 0.82 0.08 0.00
226_V 45_T 0.82 0.08 0.00
80_A 63_D 0.81 0.08 0.00
156_L 125_V 0.81 0.08 0.00
227_M 90_F 0.81 0.08 0.00
126_E 82_T 0.81 0.08 0.00
108_T 30_F 0.80 0.08 0.00
304_Q 7_V 0.80 0.08 0.00
176_D 3_N 0.80 0.08 0.00
36_C 82_T 0.80 0.08 0.00
395_K 123_G 0.80 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
13504 0.18 LCB1_ORM1_Pfam_1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
13502 0.18 LCB1_ORM1_Pfam Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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