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OPENSEQ.org
ClpC2 vs ClpC1
Genes: A B A+B
Length: 244 848 932
Sequences: 168 3514 70
Seq/Len: 0.69 4.14 0.08
MirrorTree (Pazo et al. 2001) 0.06
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 0.01
∞ 0.04 0.13 0.06
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
18_D 519_I 1.43 0.16 0.00
73_T 713_I 1.17 0.10 0.00
231_L 622_V 1.15 0.10 0.00
102_F 752_S 1.14 0.10 0.00
157_R 644_D 1.13 0.10 0.00
164_P 283_I 1.11 0.09 0.00
99_F 332_I 1.11 0.09 0.00
96_E 277_N 1.09 0.09 0.00
142_A 499_L 1.06 0.09 0.00
198_I 735_I 1.06 0.09 0.00
65_E 249_T 1.06 0.09 0.00
219_R 512_E 1.05 0.08 0.00
65_E 225_V 1.05 0.08 0.00
73_T 252_L 1.03 0.08 0.00
104_P 292_L 1.03 0.08 0.00
44_I 718_V 1.03 0.08 0.00
32_T 423_E 1.02 0.08 0.00
43_E 767_V 1.02 0.08 0.00
227_F 489_G 1.01 0.08 0.00
44_I 735_I 1.00 0.08 0.00
136_A 605_E 0.99 0.08 0.00
138_T 174_F 0.99 0.08 0.00
121_R 201_M 0.98 0.07 0.00
65_E 85_K 0.98 0.07 0.00
160_V 740_N 0.98 0.07 0.00
227_F 793_E 0.97 0.07 0.00
43_E 695_Q 0.97 0.07 0.00
142_A 233_I 0.95 0.07 0.00
193_L 123_V 0.93 0.07 0.00
209_D 489_G 0.93 0.07 0.00
97_E 403_I 0.93 0.07 0.00
198_I 336_A 0.92 0.07 0.00
231_L 300_G 0.92 0.07 0.00
119_D 663_I 0.92 0.07 0.00
49_I 620_S 0.91 0.07 0.00
198_I 184_E 0.91 0.07 0.00
160_V 300_G 0.91 0.07 0.00
127_P 704_H 0.90 0.07 0.00
101_R 252_L 0.90 0.07 0.00
32_T 460_Q 0.90 0.06 0.00
206_A 663_I 0.90 0.06 0.00
154_D 247_L 0.90 0.06 0.00
138_T 777_I 0.89 0.06 0.00
206_A 620_S 0.89 0.06 0.00
228_E 233_I 0.89 0.06 0.00
128_D 717_I 0.88 0.06 0.00
73_T 723_T 0.88 0.06 0.00
38_A 624_F 0.88 0.06 0.00
198_I 512_E 0.88 0.06 0.00
42_G 233_I 0.88 0.06 0.00
37_A 93_R 0.88 0.06 0.00
145_L 283_I 0.87 0.06 0.00
32_T 381_A 0.87 0.06 0.00
90_P 301_A 0.87 0.06 0.00
65_E 344_P 0.87 0.06 0.00
211_E 489_G 0.87 0.06 0.00
43_E 453_K 0.86 0.06 0.00
194_G 499_L 0.86 0.06 0.00
214_D 717_I 0.86 0.06 0.00
206_A 98_L 0.86 0.06 0.00
234_A 747_M 0.86 0.06 0.00
110_I 488_L 0.86 0.06 0.00
30_Q 780_E 0.86 0.06 0.00
164_P 481_D 0.85 0.06 0.00
87_D 235_H 0.85 0.06 0.00
89_D 390_I 0.85 0.06 0.00
83_P 166_S 0.85 0.06 0.00
39_D 279_R 0.84 0.06 0.00
222_V 111_G 0.84 0.06 0.00
223_D 133_R 0.84 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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