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OPENSEQ.org
ClpC1ClpC2_redo
Genes: A B A+B
Length: 848 252 1049
Sequences: 3457 188 69
Seq/Len: 4.08 0.75 0.07
MirrorTree (Pazo et al. 2001) 0.14
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 0.01 0.01
∞ 0.12 0.02 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
717_I 125_D 1.37 0.13 0.00
718_V 73_T 1.34 0.13 0.00
578_I 162_A 1.33 0.12 0.00
710_L 191_G 1.32 0.12 0.00
201_M 65_D 1.29 0.12 0.00
280_G 110_A 1.29 0.12 0.00
516_K 219_V 1.25 0.11 0.00
283_I 148_I 1.21 0.10 0.00
519_I 231_T 1.20 0.10 0.00
301_A 70_M 1.18 0.10 0.00
454_E 195_I 1.15 0.09 0.00
690_Y 172_F 1.15 0.09 0.00
135_R 200_L 1.14 0.09 0.00
735_I 195_I 1.14 0.09 0.00
585_F 110_A 1.12 0.09 0.00
486_E 26_D 1.12 0.09 0.00
300_G 109_A 1.10 0.09 0.00
336_A 195_I 1.08 0.08 0.00
519_I 102_R 1.07 0.08 0.00
620_S 154_R 1.07 0.08 0.00
460_Q 226_A 1.07 0.08 0.00
351_T 107_V 1.06 0.08 0.00
272_V 24_H 1.06 0.08 0.00
332_I 96_F 1.06 0.08 0.00
501_E 232_L 1.05 0.08 0.00
686_G 195_I 1.04 0.08 0.00
355_T 101_P 1.03 0.08 0.00
585_F 181_E 1.03 0.08 0.00
710_L 134_D 1.02 0.07 0.00
505_T 29_D 1.02 0.07 0.00
28_I 122_I 1.02 0.07 0.00
697_V 125_D 1.01 0.07 0.00
768_L 73_T 1.01 0.07 0.00
565_A 191_G 1.01 0.07 0.00
747_M 27_V 1.01 0.07 0.00
764_F 224_A 1.01 0.07 0.00
663_I 166_P 1.00 0.07 0.00
282_I 130_G 0.99 0.07 0.00
64_E 128_L 0.99 0.07 0.00
519_I 32_S 0.98 0.07 0.00
736_S 22_R 0.98 0.07 0.00
301_A 69_S 0.97 0.07 0.00
744_S 170_I 0.97 0.07 0.00
390_I 140_T 0.97 0.07 0.00
233_I 219_V 0.97 0.07 0.00
578_I 198_E 0.97 0.07 0.00
564_K 156_A 0.97 0.07 0.00
702_K 153_L 0.96 0.07 0.00
591_A 27_V 0.96 0.07 0.00
662_L 43_E 0.96 0.07 0.00
509_R 143_L 0.96 0.07 0.00
108_I 25_S 0.96 0.07 0.00
355_T 172_F 0.96 0.07 0.00
131_L 140_T 0.96 0.07 0.00
489_G 219_V 0.95 0.07 0.00
6_T 160_P 0.95 0.07 0.00
716_I 164_T 0.95 0.07 0.00
225_V 195_I 0.95 0.07 0.00
380_V 160_P 0.95 0.07 0.00
135_R 172_F 0.94 0.07 0.00
87_V 219_V 0.94 0.07 0.00
744_S 230_T 0.94 0.07 0.00
528_V 216_R 0.94 0.07 0.00
462_A 153_L 0.94 0.07 0.00
686_G 175_P 0.94 0.07 0.00
435_K 151_A 0.94 0.07 0.00
764_F 23_V 0.94 0.07 0.00
387_D 133_T 0.93 0.07 0.00
242_L 147_E 0.93 0.07 0.00
462_A 132_L 0.93 0.06 0.00
233_I 143_L 0.93 0.06 0.00
187_L 162_A 0.93 0.06 0.00
482_E 125_D 0.93 0.06 0.00
67_I 19_A 0.93 0.06 0.00
504_T 38_A 0.93 0.06 0.00
519_I 18_N 0.92 0.06 0.00
786_S 195_I 0.92 0.06 0.00
434_E 203_A 0.91 0.06 0.00
697_V 156_A 0.91 0.06 0.00
332_I 55_Q 0.91 0.06 0.00
574_D 191_G 0.91 0.06 0.00
87_V 132_L 0.91 0.06 0.00
752_T 164_T 0.91 0.06 0.00
362_L 43_E 0.91 0.06 0.00
313_A 130_G 0.90 0.06 0.00
519_I 168_Q 0.90 0.06 0.00
234_V 135_P 0.90 0.06 0.00
174_F 65_D 0.90 0.06 0.00
588_R 130_G 0.90 0.06 0.00
759_L 177_R 0.90 0.06 0.00
126_K 157_V 0.90 0.06 0.00
390_I 224_A 0.90 0.06 0.00
166_S 138_L 0.89 0.06 0.00
529_S 11_V 0.89 0.06 0.00
95_A 227_D 0.89 0.06 0.00
273_L 147_E 0.89 0.06 0.00
580_I 110_A 0.89 0.06 0.00
331_Y 65_D 0.89 0.06 0.00
282_I 132_L 0.88 0.06 0.00
187_L 172_F 0.88 0.06 0.00
172_D 191_G 0.88 0.06 0.00
14_V 195_I 0.88 0.06 0.00
57_E 32_S 0.88 0.06 0.00
27_Y 11_V 0.87 0.06 0.00
229_L 113_A 0.87 0.06 0.00
718_V 118_A 0.87 0.06 0.00
783_D 105_N 0.87 0.06 0.00
765_D 77_A 0.87 0.06 0.00
564_K 23_V 0.87 0.06 0.00
156_G 43_E 0.87 0.06 0.00
131_L 216_R 0.87 0.06 0.00
67_I 226_A 0.87 0.06 0.00
6_T 33_D 0.86 0.06 0.00
668_L 86_E 0.86 0.06 0.00
761_K 117_A 0.86 0.06 0.00
283_I 70_M 0.86 0.06 0.00
732_D 127_L 0.86 0.06 0.00
752_T 230_T 0.86 0.06 0.00
715_D 115_H 0.86 0.06 0.00
69_Q 18_N 0.85 0.06 0.00
203_V 101_P 0.85 0.06 0.00
357_E 120_S 0.85 0.06 0.00
387_D 104_R 0.85 0.06 0.00
537_A 150_I 0.85 0.06 0.00
729_R 89_T 0.85 0.06 0.00
245_K 224_A 0.85 0.06 0.00
226_V 218_G 0.85 0.06 0.00
494_I 153_L 0.85 0.06 0.00
547_G 218_G 0.85 0.06 0.00
593_R 218_G 0.85 0.06 0.00
299_E 106_A 0.84 0.06 0.00
747_M 231_T 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
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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