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OPENSEQ.org
Karl
Genes: A B A+B
Length: 244 848 919
Sequences: 168 3514 70
Seq/Len: 0.69 4.14 0.08
MirrorTree (Pazo et al. 2001) 0.09
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 0.01 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.00
100 0.01 0.03 0.00
∞ 0.04 0.13 0.06
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
104_P 277_N 1.24 0.12 0.00
182_A 234_V 1.20 0.11 0.00
30_Q 780_E 1.15 0.10 0.00
118_H 519_I 1.15 0.10 0.00
11_V 392_D 1.11 0.09 0.00
137_D 175_G 1.09 0.09 0.00
108_N 277_N 1.09 0.09 0.00
182_A 252_L 1.08 0.09 0.00
198_I 624_F 1.05 0.09 0.00
68_K 137_Q 1.04 0.08 0.00
226_R 166_S 1.04 0.08 0.00
173_I 519_I 1.03 0.08 0.00
175_F 279_R 1.01 0.08 0.00
142_A 233_I 1.00 0.08 0.00
198_I 166_S 1.00 0.08 0.00
104_P 704_H 0.98 0.07 0.00
137_D 717_I 0.97 0.07 0.00
39_D 247_L 0.97 0.07 0.00
27_P 201_M 0.97 0.07 0.00
136_A 605_E 0.96 0.07 0.00
73_T 249_T 0.96 0.07 0.00
97_E 330_K 0.95 0.07 0.00
231_L 277_N 0.95 0.07 0.00
213_G 489_G 0.95 0.07 0.00
127_P 794_I 0.94 0.07 0.00
73_T 201_M 0.93 0.07 0.00
162_L 620_S 0.93 0.07 0.00
68_K 351_T 0.93 0.07 0.00
226_R 243_K 0.93 0.07 0.00
65_E 85_K 0.93 0.07 0.00
110_I 377_S 0.92 0.07 0.00
231_L 301_A 0.92 0.07 0.00
225_E 787_E 0.92 0.07 0.00
207_L 620_S 0.92 0.07 0.00
101_R 381_A 0.92 0.07 0.00
104_P 605_E 0.90 0.07 0.00
121_R 169_L 0.90 0.07 0.00
226_R 126_K 0.89 0.06 0.00
29_E 234_V 0.88 0.06 0.00
229_A 298_A 0.88 0.06 0.00
37_A 780_E 0.87 0.06 0.00
102_F 529_S 0.87 0.06 0.00
224_A 176_R 0.86 0.06 0.00
212_D 201_M 0.86 0.06 0.00
180_K 362_L 0.86 0.06 0.00
198_I 753_D 0.86 0.06 0.00
84_K 252_L 0.86 0.06 0.00
145_L 283_I 0.85 0.06 0.00
27_P 505_T 0.85 0.06 0.00
140_G 87_V 0.85 0.06 0.00
102_F 169_L 0.85 0.06 0.00
177_T 254_S 0.85 0.06 0.00
43_E 586_H 0.85 0.06 0.00
58_R 377_S 0.84 0.06 0.00
102_F 277_N 0.84 0.06 0.00
36_I 519_I 0.84 0.06 0.00
187_F 726_E 0.84 0.06 0.00
223_D 301_A 0.84 0.06 0.00
32_T 527_A 0.84 0.06 0.00
214_D 351_T 0.84 0.06 0.00
225_E 180_A 0.83 0.06 0.00
49_I 377_S 0.83 0.06 0.00
216_P 133_R 0.83 0.06 0.00
137_D 523_D 0.83 0.06 0.00
131_L 750_E 0.82 0.06 0.00
182_A 137_Q 0.82 0.06 0.00
111_V 787_E 0.82 0.06 0.00
39_D 346_Q 0.82 0.06 0.00
43_E 425_D 0.82 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
9734 0.08 ClpC2 vs ClpC1 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.00 Done
9726 0.08 Karl Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.00 Done
9724 0.08 ClpC2 vs ClpC1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
9714 0 ClpC2 vs ClpC1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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