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OPENSEQ.org
cI_2_4_cI_4_4_tt
Genes: A B A+B
Length: 181 409 562
Sequences: 2539 3475 1161
Seq/Len: 14.03 8.5 2.07
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 0.01 1.22
2 0.00 0.01 1.33
5 0.01 0.03 1.55
10 0.01 0.04 1.58
20 0.02 0.05 1.60
100 0.04 0.06 1.68
∞ 0.10 0.13 1.97
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
4_F 47_L 0.99 0.52 0.00
136_V 258_E 0.97 0.50 0.00
28_M 55_V 0.95 0.47 0.00
10_F 390_V 0.91 0.43 0.00
125_L 119_I 0.90 0.42 0.00
106_I 28_L 0.89 0.41 0.00
60_V 399_S 0.85 0.37 0.00
103_T 48_S 0.80 0.31 0.00
77_K 268_E 0.79 0.31 0.00
158_R 116_I 0.79 0.31 0.00
126_G 64_T 0.79 0.30 0.00
77_K 288_K 0.78 0.30 0.00
146_T 98_A 0.78 0.30 0.00
158_R 48_S 0.78 0.30 0.00
134_I 394_V 0.78 0.29 0.00
136_V 407_V 0.77 0.29 0.00
138_D 96_A 0.76 0.28 0.00
33_R 221_V 0.74 0.26 0.00
103_T 107_A 0.74 0.26 0.00
72_F 182_L 0.73 0.25 0.00
64_A 246_Y 0.73 0.25 0.00
133_V 91_F 0.73 0.25 0.00
96_L 296_R 0.73 0.25 0.00
125_L 270_G 0.72 0.25 0.00
141_Y 52_V 0.72 0.24 0.00
25_A 321_M 0.71 0.24 0.00
69_Y 405_G 0.71 0.24 0.00
112_T 263_D 0.71 0.24 0.00
82_V 391_P 0.71 0.23 0.00
115_G 106_G 0.70 0.23 0.00
70_Y 344_V 0.70 0.23 0.00
139_E 65_G 0.70 0.23 0.00
9_D 291_K 0.69 0.22 0.00
45_R 75_Y 0.69 0.22 0.00
68_S 315_H 0.69 0.22 0.00
40_W 389_Q 0.69 0.22 0.00
137_N 99_L 0.69 0.22 0.00
155_A 53_L 0.68 0.21 0.00
42_R 131_V 0.67 0.21 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
4824 2.07 cI_2_4_cI_4_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4823 1.58 cI_2_40_cI_4_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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