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OPENSEQ.org
cI_A_cIII_isp_human_med
Genes: A B A+B
Length: 115 143 255
Sequences: 4153 1210 365
Seq/Len: 36.11 8.46 1.43
MirrorTree (Pazo et al. 2001) 0.56
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.01
20 0.00 0.01 0.03
100 0.01 0.01 0.15
∞ 0.01 0.02 1.41
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
3_F 85_V 1.63 0.91 0.39
20_I 129_V 1.51 0.86 0.30
86_L 5_F 1.31 0.72 0.18
7_L 25_L 1.14 0.57 0.10
88_V 85_V 1.11 0.54 0.10
5_L 9_M 1.04 0.47 0.07
87_M 23_I 1.04 0.47 0.07
21_T 99_D 1.03 0.46 0.07
20_I 85_V 1.00 0.43 0.06
78_A 121_G 1.00 0.43 0.06
96_V 15_V 1.00 0.42 0.06
103_A 2_V 0.99 0.42 0.06
31_M 8_S 0.98 0.41 0.06
3_F 9_M 0.97 0.40 0.06
11_T 25_L 0.97 0.39 0.06
16_L 12_S 0.96 0.39 0.05
15_L 2_V 0.96 0.39 0.05
5_L 142_V 0.96 0.38 0.05
25_P 71_L 0.93 0.36 0.05
26_Q 37_K 0.92 0.35 0.05
59_A 77_P 0.91 0.34 0.04
59_A 6_V 0.91 0.34 0.04
16_L 14_D 0.91 0.34 0.04
67_L 132_Y 0.91 0.34 0.04
55_F 52_E 0.90 0.33 0.04
105_E 109_G 0.89 0.32 0.04
103_A 50_Q 0.87 0.30 0.04
96_V 62_S 0.86 0.30 0.04
15_L 25_L 0.86 0.30 0.04
83_N 28_I 0.85 0.28 0.03
100_L 94_I 0.84 0.28 0.03
104_Y 45_V 0.84 0.28 0.03
21_T 14_D 0.84 0.28 0.03
36_P 140_V 0.83 0.27 0.03
15_L 52_E 0.82 0.27 0.03
9_I 118_I 0.82 0.26 0.03
89_M 27_D 0.81 0.25 0.03
8_M 37_K 0.80 0.25 0.03
64_L 80_V 0.80 0.25 0.03
59_A 20_K 0.79 0.24 0.03
3_F 128_E 0.79 0.24 0.03
100_L 53_I 0.79 0.24 0.03
17_L 116_G 0.79 0.24 0.03
50_P 139_M 0.78 0.24 0.03
112_D 29_P 0.78 0.23 0.03
78_A 5_F 0.78 0.23 0.03
78_A 27_D 0.78 0.23 0.03
88_V 45_V 0.78 0.23 0.03
99_A 94_I 0.77 0.23 0.02
22_F 8_S 0.77 0.23 0.02
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
2563 1.33 cI_A_cIII_isp_human_med6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
2497 1.43 cI_A_cIII_isp_human_med Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.39 Done - Shared
2496 0.04 cI_A_cIII_isp_human_med Δgene:(1, 20) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) Killed - Shared
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