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OPENSEQ.org
ClpC1ClpC2_redo
Genes: A B A+B
Length: 848 252 1052
Sequences: 3457 167 64
Seq/Len: 4.08 0.66 0.06
MirrorTree (Pazo et al. 2001) -0.03
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.00 0.00
20 0.03 0.00 0.00
100 0.04 0.00 0.01
∞ 0.12 0.01 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
332_I 96_F 1.33 0.11 0.00
454_E 195_I 1.27 0.10 0.00
233_I 219_V 1.26 0.10 0.00
201_M 65_D 1.24 0.10 0.00
735_I 195_I 1.24 0.10 0.00
718_V 73_T 1.21 0.10 0.00
283_I 70_M 1.20 0.09 0.00
283_I 148_I 1.20 0.09 0.00
280_G 110_A 1.20 0.09 0.00
301_A 70_M 1.19 0.09 0.00
736_S 22_R 1.17 0.09 0.00
690_Y 172_F 1.17 0.09 0.00
135_R 200_L 1.17 0.09 0.00
717_I 125_D 1.15 0.09 0.00
747_M 231_T 1.14 0.08 0.00
131_L 140_T 1.13 0.08 0.00
108_I 130_G 1.12 0.08 0.00
710_L 134_D 1.10 0.08 0.00
53_G 118_A 1.09 0.08 0.00
585_F 110_A 1.09 0.08 0.00
662_L 43_E 1.08 0.08 0.00
710_L 191_G 1.08 0.08 0.00
130_E 177_R 1.08 0.08 0.00
794_V 94_Q 1.07 0.08 0.00
803_D 130_G 1.06 0.07 0.00
535_T 195_I 1.06 0.07 0.00
519_I 32_S 1.06 0.07 0.00
11_R 226_A 1.05 0.07 0.00
390_I 140_T 1.05 0.07 0.00
565_A 191_G 1.05 0.07 0.00
420_D 27_V 1.05 0.07 0.00
301_A 69_S 1.03 0.07 0.00
516_K 219_V 1.03 0.07 0.00
5_F 229_I 1.02 0.07 0.00
126_K 157_V 1.02 0.07 0.00
332_I 55_Q 1.02 0.07 0.00
450_L 100_T 1.01 0.07 0.00
435_K 151_A 1.01 0.07 0.00
289_L 101_P 1.01 0.07 0.00
798_Q 107_V 1.00 0.07 0.00
761_K 117_A 1.00 0.07 0.00
307_I 87_A 1.00 0.07 0.00
580_I 110_A 1.00 0.07 0.00
627_I 151_A 0.99 0.07 0.00
6_T 33_D 0.99 0.07 0.00
180_A 163_V 0.99 0.07 0.00
5_F 143_L 0.99 0.07 0.00
135_R 172_F 0.98 0.07 0.00
505_T 29_D 0.98 0.07 0.00
197_I 194_Y 0.98 0.07 0.00
197_I 198_E 0.98 0.07 0.00
526_K 109_A 0.98 0.07 0.00
225_V 195_I 0.97 0.07 0.00
166_S 170_I 0.97 0.06 0.00
197_I 102_R 0.97 0.06 0.00
783_D 105_N 0.97 0.06 0.00
564_K 156_A 0.96 0.06 0.00
87_V 219_V 0.96 0.06 0.00
292_L 90_L 0.96 0.06 0.00
158_R 230_T 0.96 0.06 0.00
225_V 26_D 0.96 0.06 0.00
585_F 181_E 0.96 0.06 0.00
174_F 170_I 0.95 0.06 0.00
460_Q 226_A 0.95 0.06 0.00
225_V 73_T 0.95 0.06 0.00
336_A 195_I 0.95 0.06 0.00
501_E 232_L 0.95 0.06 0.00
627_I 110_A 0.95 0.06 0.00
537_A 150_I 0.95 0.06 0.00
578_I 198_E 0.94 0.06 0.00
804_V 144_Q 0.94 0.06 0.00
509_R 143_L 0.94 0.06 0.00
744_S 170_I 0.94 0.06 0.00
710_L 194_Y 0.94 0.06 0.00
91_S 107_V 0.94 0.06 0.00
789_I 118_A 0.94 0.06 0.00
518_I 208_E 0.94 0.06 0.00
248_Y 121_E 0.94 0.06 0.00
462_A 132_L 0.94 0.06 0.00
111_G 219_V 0.93 0.06 0.00
762_R 195_I 0.93 0.06 0.00
656_D 191_G 0.93 0.06 0.00
231_Q 81_F 0.93 0.06 0.00
650_G 194_Y 0.93 0.06 0.00
187_L 168_Q 0.93 0.06 0.00
417_A 223_R 0.93 0.06 0.00
87_V 109_A 0.92 0.06 0.00
462_A 153_L 0.92 0.06 0.00
27_Y 11_V 0.92 0.06 0.00
430_E 143_L 0.92 0.06 0.00
245_K 224_A 0.92 0.06 0.00
244_D 27_V 0.92 0.06 0.00
502_A 112_N 0.92 0.06 0.00
332_I 103_A 0.92 0.06 0.00
762_R 73_T 0.92 0.06 0.00
523_D 121_E 0.92 0.06 0.00
622_V 228_L 0.91 0.06 0.00
735_I 21_K 0.91 0.06 0.00
758_L 113_A 0.91 0.06 0.00
662_L 219_V 0.91 0.06 0.00
203_V 101_P 0.91 0.06 0.00
292_L 219_V 0.91 0.06 0.00
244_D 137_A 0.91 0.06 0.00
33_I 177_R 0.91 0.06 0.00
316_E 191_G 0.91 0.06 0.00
535_T 70_M 0.90 0.06 0.00
357_E 120_S 0.90 0.06 0.00
784_Q 68_K 0.90 0.06 0.00
686_G 175_P 0.90 0.06 0.00
527_A 114_A 0.90 0.06 0.00
12_V 107_V 0.90 0.06 0.00
273_L 186_E 0.90 0.06 0.00
605_E 108_V 0.90 0.06 0.00
523_D 141_A 0.89 0.06 0.00
122_Q 186_E 0.89 0.06 0.00
425_D 172_F 0.89 0.06 0.00
435_K 157_V 0.88 0.06 0.00
637_S 43_E 0.88 0.06 0.00
595_F 33_D 0.88 0.06 0.00
716_I 164_T 0.88 0.06 0.00
674_S 146_Q 0.88 0.06 0.00
297_A 144_Q 0.88 0.06 0.00
286_I 136_A 0.88 0.06 0.00
674_S 220_D 0.88 0.06 0.00
254_S 219_V 0.88 0.06 0.00
744_S 230_T 0.88 0.06 0.00
67_I 19_A 0.88 0.06 0.00
528_V 216_R 0.88 0.06 0.00
300_G 109_A 0.88 0.06 0.00
529_S 11_V 0.88 0.06 0.00
326_D 81_F 0.88 0.06 0.00
585_F 170_I 0.88 0.06 0.00
87_V 19_A 0.87 0.06 0.00
813_G 109_A 0.87 0.06 0.00
674_S 123_T 0.87 0.06 0.00
794_V 89_T 0.87 0.06 0.00
95_A 90_L 0.87 0.05 0.00
585_F 221_K 0.87 0.05 0.00
301_A 167_P 0.87 0.05 0.00
217_E 130_G 0.86 0.05 0.00
313_A 130_G 0.86 0.05 0.00
686_G 195_I 0.86 0.05 0.00
229_L 113_A 0.86 0.05 0.00
425_D 122_I 0.86 0.05 0.00
14_V 195_I 0.86 0.05 0.00
450_L 191_G 0.86 0.05 0.00
537_A 179_V 0.86 0.05 0.00
174_F 65_D 0.86 0.05 0.00
387_D 104_R 0.86 0.05 0.00
280_G 211_D 0.86 0.05 0.00
330_K 177_R 0.86 0.05 0.00
272_V 24_H 0.86 0.05 0.00
514_L 217_S 0.85 0.05 0.00
497_F 22_R 0.85 0.05 0.00
662_L 119_S 0.85 0.05 0.00
57_E 32_S 0.85 0.05 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
3403 0.07 ClpC1ClpC2_redo Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3396 0.06 ClpC1ClpC2_redo Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3394 0 ClpC1ClpC2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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