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OPENSEQ.org
cI_D_cIII_isp_Pdenitr
Genes: A B A+B
Length: 412 190 583
Sequences: 3488 1692 597
Seq/Len: 8.47 8.91 1.02
MirrorTree (Pazo et al. 2001) 0.21
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 0.03 0.01 0.00
10 0.04 0.01 0.02
20 0.05 0.01 0.03
100 0.06 0.01 0.14
∞ 0.13 0.05 0.99
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
205_L 19_L 1.25 0.57 0.00
66_G 168_G 1.19 0.52 0.00
176_P 68_T 1.05 0.39 0.00
29_I 185_T 1.01 0.35 0.00
56_A 9_G 1.00 0.34 0.00
97_A 168_G 0.98 0.33 0.00
109_V 33_A 0.97 0.32 0.00
267_V 127_V 0.97 0.32 0.00
74_R 179_A 0.95 0.31 0.00
53_V 66_Q 0.94 0.30 0.00
98_W 45_S 0.94 0.29 0.00
29_I 40_N 0.92 0.28 0.00
286_E 34_A 0.90 0.26 0.00
112_R 88_A 0.88 0.25 0.00
226_T 15_R 0.87 0.25 0.00
56_A 187_I 0.87 0.24 0.00
53_V 143_G 0.85 0.23 0.00
221_D 28_T 0.84 0.23 0.00
279_C 58_V 0.83 0.22 0.00
23_S 34_A 0.83 0.22 0.00
158_M 166_R 0.81 0.21 0.00
279_C 45_S 0.81 0.20 0.00
240_V 32_G 0.81 0.20 0.00
189_D 148_G 0.81 0.20 0.00
196_E 187_I 0.81 0.20 0.00
354_G 152_C 0.80 0.20 0.00
202_V 93_D 0.80 0.20 0.00
347_A 50_A 0.80 0.20 0.00
354_G 134_H 0.80 0.20 0.00
53_V 91_E 0.79 0.20 0.00
239_M 131_V 0.79 0.20 0.00
104_R 34_A 0.79 0.19 0.00
227_E 178_V 0.79 0.19 0.00
354_G 155_H 0.78 0.19 0.00
338_F 39_V 0.78 0.19 0.00
29_I 12_G 0.78 0.19 0.00
278_L 22_A 0.77 0.18 0.00
354_G 132_C 0.77 0.18 0.00
97_A 159_Y 0.77 0.18 0.00
107_G 52_A 0.77 0.18 0.00
245_L 31_A 0.77 0.18 0.00
298_L 48_V 0.77 0.18 0.00
296_Q 87_Q 0.77 0.18 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
3013 1 cI_D_2_cIII_isp_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2807 1.02 cI_D_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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