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OPENSEQ.org
TnnC_I
Genes: A B A+B
Length: 210 161 358
Sequences: 146 10373 59
Seq/Len: 0.7 64.43 0.16
MirrorTree (Pazo et al. 2001) 0.01
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 0.11 0.08 0.01
2 0.11 0.10 0.01
5 0.11 0.12 0.01
10 0.12 0.13 0.02
20 0.12 0.14 0.04
100 0.12 0.19 0.10
∞ 0.14 0.22 0.16
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
64_E 70_G 1.33 0.21 0.00
93_L 110_G 1.32 0.20 0.00
115_E 110_G 1.26 0.18 0.00
205_K 14_E 1.08 0.13 0.00
91_E 52_P 0.99 0.11 0.00
37_K 102_R 0.98 0.10 0.00
7_A 112_I 0.97 0.10 0.00
72_K 67_D 0.96 0.10 0.00
91_E 157_M 0.95 0.10 0.00
91_E 13_T 0.94 0.10 0.00
58_K 128_I 0.92 0.09 0.00
60_E 135_E 0.92 0.09 0.00
3_E 128_I 0.89 0.09 0.00
171_A 140_G 0.89 0.09 0.00
105_D 73_D 0.88 0.09 0.00
95_D 127_T 0.88 0.09 0.00
4_S 95_E 0.87 0.08 0.00
115_E 121_L 0.86 0.08 0.00
21_R 74_F 0.86 0.08 0.00
7_A 36_I 0.84 0.08 0.00
196_D 148_I 0.84 0.08 0.00
29_Y 30_G 0.84 0.08 0.00
72_K 105_D 0.83 0.08 0.00
107_V 153_F 0.83 0.08 0.00
36_K 33_D 0.82 0.07 0.00
93_L 36_I 0.82 0.07 0.00
12_Q 78_L 0.82 0.07 0.00
72_K 42_G 0.82 0.07 0.00
69_R 140_G 0.81 0.07 0.00
39_S 53_T 0.81 0.07 0.00
14_A 22_A 0.80 0.07 0.00
32_E 117_L 0.80 0.07 0.00
114_V 110_G 0.80 0.07 0.00
112_Y 41_L 0.79 0.07 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
4464 0.16 TnnC_I Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4390 0.01 troponinI_C Δgene:(1, ∞) A:(1E-80, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
4388 0 troponinI_C Δgene:(1, 20) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
4385 0.01 troponinI_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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