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OPENSEQ.org
LCB2_ORM1_Pfam_1
Genes: A B A+B
Length: 360 136 482
Sequences: 55236 239 182
Seq/Len: 153.43 1.76 0.38
MirrorTree (Pazo et al. 2001) 0.24
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 0.03 0.00
2 0.07 0.03 0.00
5 0.09 0.03 0.01
10 0.11 0.03 0.02
20 0.14 0.03 0.04
100 0.24 0.04 0.17
∞ 0.29 0.04 0.37
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
81_F 45_T 1.11 0.23 0.00
356_L 97_A 1.00 0.18 0.00
341_R 95_P 1.00 0.18 0.00
173_L 133_H 0.96 0.17 0.00
114_H 52_V 0.96 0.16 0.00
227_I 60_T 0.93 0.15 0.00
301_I 22_L 0.91 0.15 0.00
26_E 34_T 0.90 0.14 0.00
154_G 136_R 0.90 0.14 0.00
112_F 21_I 0.89 0.14 0.00
176_D 55_H 0.89 0.14 0.00
176_D 61_P 0.89 0.14 0.00
176_D 76_E 0.89 0.14 0.00
176_D 77_Q 0.89 0.14 0.00
176_D 128_K 0.89 0.14 0.00
341_R 3_N 0.89 0.14 0.00
109_V 34_T 0.89 0.14 0.00
55_V 126_V 0.88 0.14 0.00
257_T 51_Y 0.88 0.14 0.00
328_V 24_K 0.88 0.14 0.00
176_D 59_G 0.87 0.13 0.00
252_I 126_V 0.86 0.13 0.00
301_I 17_V 0.86 0.13 0.00
104_L 19_I 0.86 0.13 0.00
357_L 52_V 0.85 0.13 0.00
91_D 107_H 0.85 0.12 0.00
49_I 106_A 0.85 0.12 0.00
162_L 131_V 0.84 0.12 0.00
303_L 50_S 0.84 0.12 0.00
250_Q 101_V 0.84 0.12 0.00
301_I 74_M 0.83 0.12 0.00
88_V 21_I 0.83 0.12 0.00
281_L 115_W 0.82 0.12 0.00
303_L 17_V 0.82 0.12 0.00
75_A 34_T 0.82 0.12 0.00
102_V 63_D 0.81 0.12 0.00
281_L 110_L 0.81 0.11 0.00
249_A 60_T 0.81 0.11 0.00
153_E 63_D 0.81 0.11 0.00
89_I 135_L 0.81 0.11 0.00
318_M 51_Y 0.81 0.11 0.00
137_R 80_D 0.80 0.11 0.00
118_V 50_S 0.80 0.11 0.00
84_K 121_T 0.80 0.11 0.00
314_F 30_F 0.80 0.11 0.00
110_R 48_I 0.79 0.11 0.00
280_Y 45_T 0.79 0.11 0.00
86_C 63_D 0.78 0.11 0.00
226_I 132_T 0.78 0.10 0.00
116_D 26_F 0.78 0.10 0.00
64_A 48_I 0.78 0.10 0.00
254_S 121_T 0.78 0.10 0.00
318_M 19_I 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
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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