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OPENSEQ.org
cIV_A_20_cIII_isp_20_Pdenitr
Genes: A B A+B
Length: 538 190 697
Sequences: 4187 1043 458
Seq/Len: 7.78 5.49 0.66
MirrorTree (Pazo et al. 2001) 0.07
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 0.00
2 0.01 0.01 0.00
5 0.02 0.01 0.00
10 0.02 0.01 0.02
20 0.03 0.01 0.02
100 0.04 0.01 0.13
∞ 0.08 0.02 0.63
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
21_F 90_R 1.21 0.41 0.00
188_F 61_V 1.17 0.38 0.00
226_I 176_I 1.13 0.35 0.00
236_G 31_A 1.11 0.33 0.00
213_W 129_I 1.09 0.32 0.00
169_A 183_D 1.06 0.30 0.00
185_I 14_T 1.03 0.28 0.00
67_N 187_I 1.02 0.27 0.00
414_Y 187_I 1.01 0.27 0.00
485_L 39_V 0.98 0.25 0.00
130_V 23_T 0.98 0.25 0.00
114_L 41_Q 0.97 0.24 0.00
175_A 101_S 0.97 0.24 0.00
472_I 56_V 0.96 0.23 0.00
420_S 181_F 0.95 0.23 0.00
127_A 80_R 0.95 0.23 0.00
224_G 187_I 0.95 0.23 0.00
29_I 78_I 0.94 0.22 0.00
302_L 151_F 0.94 0.22 0.00
175_A 90_R 0.93 0.21 0.00
273_I 127_V 0.92 0.21 0.00
301_I 32_G 0.91 0.20 0.00
438_I 56_V 0.90 0.20 0.00
83_M 128_M 0.89 0.19 0.00
438_I 129_I 0.89 0.19 0.00
469_W 129_I 0.87 0.18 0.00
431_L 59_S 0.86 0.18 0.00
32_C 31_A 0.86 0.18 0.00
225_A 161_T 0.85 0.18 0.00
76_T 55_Q 0.85 0.17 0.00
393_V 58_V 0.85 0.17 0.00
278_I 69_V 0.84 0.17 0.00
410_A 51_L 0.83 0.17 0.00
188_F 183_D 0.83 0.17 0.00
218_S 186_T 0.83 0.17 0.00
188_F 187_I 0.83 0.17 0.00
488_I 22_A 0.83 0.16 0.00
86_V 165_I 0.82 0.16 0.00
127_A 87_Q 0.82 0.16 0.00
217_L 127_V 0.81 0.16 0.00
298_A 34_A 0.81 0.15 0.00
438_I 54_I 0.81 0.15 0.00
282_A 181_F 0.80 0.15 0.00
361_F 167_R 0.80 0.15 0.00
427_W 78_I 0.80 0.15 0.00
297_A 78_I 0.79 0.15 0.00
282_A 121_E 0.79 0.15 0.00
43_H 187_I 0.79 0.15 0.00
40_E 82_T 0.78 0.14 0.00
362_G 39_V 0.78 0.14 0.00
278_I 65_T 0.77 0.14 0.00
477_A 27_G 0.77 0.14 0.00
478_Y 150_W 0.77 0.14 0.00
21_F 39_V 0.77 0.14 0.00
485_L 35_A 0.76 0.14 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
3095 0.66 cIV_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3094 1.12 cIV_A_10_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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