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OPENSEQ.org
cI_F_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 431 263 668
Sequences: 2638 973 401
Seq/Len: 6.12 3.7 0.6
MirrorTree (Pazo et al. 2001) 0.20
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 0.01 0.01
2 0.01 0.01 0.01
5 0.01 0.01 0.01
10 0.02 0.01 0.01
20 0.03 0.01 0.02
100 0.05 0.01 0.07
∞ 0.14 0.01 0.58
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
363_M 257_K 1.28 0.44 0.00
377_D 230_V 1.03 0.26 0.00
121_A 240_V 1.01 0.25 0.00
140_I 52_Q 0.99 0.24 0.00
301_N 46_Q 0.99 0.24 0.00
363_M 74_D 0.99 0.24 0.00
249_V 52_Q 0.98 0.23 0.00
218_V 43_D 0.96 0.22 0.00
111_I 236_I 0.95 0.21 0.00
214_S 40_G 0.94 0.21 0.00
302_A 65_R 0.91 0.19 0.00
249_V 148_I 0.91 0.19 0.00
384_K 250_K 0.90 0.19 0.00
226_A 209_A 0.90 0.19 0.00
113_S 54_Y 0.89 0.18 0.00
186_K 42_F 0.89 0.18 0.00
260_S 255_P 0.89 0.18 0.00
36_I 63_G 0.89 0.18 0.00
383_T 95_T 0.89 0.18 0.00
209_V 250_K 0.88 0.18 0.00
271_G 241_L 0.88 0.18 0.00
149_L 236_I 0.86 0.17 0.00
47_M 52_Q 0.86 0.17 0.00
250_N 201_T 0.85 0.17 0.00
283_A 63_G 0.85 0.17 0.00
101_D 236_I 0.85 0.16 0.00
227_E 67_V 0.84 0.16 0.00
250_N 45_H 0.84 0.16 0.00
47_M 163_G 0.84 0.16 0.00
297_E 236_I 0.84 0.16 0.00
41_D 124_S 0.83 0.16 0.00
25_K 242_A 0.83 0.16 0.00
47_M 236_I 0.83 0.16 0.00
226_A 244_L 0.83 0.16 0.00
231_S 19_A 0.83 0.16 0.00
271_G 180_A 0.83 0.15 0.00
118_A 246_Y 0.83 0.15 0.00
271_G 81_P 0.82 0.15 0.00
190_P 241_L 0.82 0.15 0.00
183_L 240_V 0.82 0.15 0.00
145_D 101_E 0.81 0.15 0.00
116_M 226_D 0.81 0.15 0.00
24_K 156_A 0.81 0.15 0.00
251_T 109_D 0.80 0.14 0.00
277_G 190_L 0.80 0.14 0.00
320_C 214_A 0.80 0.14 0.00
259_M 244_L 0.80 0.14 0.00
260_S 115_S 0.79 0.14 0.00
44_I 234_S 0.79 0.14 0.00
218_V 157_V 0.79 0.14 0.00
386_V 47_L 0.79 0.14 0.00
297_E 235_V 0.79 0.14 0.00
405_L 161_Y 0.79 0.14 0.00
164_L 51_L 0.78 0.14 0.00
268_E 42_F 0.78 0.14 0.00
284_V 69_L 0.78 0.14 0.00
312_L 81_P 0.78 0.13 0.00
125_I 235_V 0.77 0.13 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
3024 0.6 cI_F_4_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2795 0.6 cI_F_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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