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OPENSEQ.org
cI_A_cIII_isp_ecoli_4
Genes: A B A+B
Length: 147 183 296
Sequences: 3696 2199 578
Seq/Len: 25.14 12.02 1.95
MirrorTree (Pazo et al. 2001) 0.49
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 0.02
10 0.00 0.01 0.02
20 0.00 0.01 0.04
100 0.01 0.01 0.16
∞ 0.01 0.04 1.75
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
16_F 121_Y 1.50 0.91 0.40
29_L 35_V 1.17 0.69 0.17
108_F 32_A 1.12 0.64 0.15
120_I 176_V 1.11 0.64 0.15
16_F 28_A 1.06 0.58 0.12
92_I 28_A 1.01 0.53 0.10
34_G 40_S 1.01 0.52 0.10
37_L 102_Q 0.99 0.50 0.09
41_A 162_L 0.98 0.50 0.09
18_I 94_D 0.98 0.49 0.09
40_R 19_L 0.94 0.45 0.08
94_E 149_T 0.94 0.45 0.08
37_L 163_A 0.93 0.44 0.08
83_L 121_Y 0.93 0.44 0.07
34_G 47_K 0.92 0.43 0.07
83_L 154_T 0.92 0.43 0.07
18_I 42_L 0.91 0.41 0.07
105_I 102_Q 0.88 0.38 0.06
90_T 147_F 0.88 0.38 0.06
33_G 164_I 0.88 0.38 0.06
85_L 32_A 0.88 0.38 0.06
97_W 103_S 0.88 0.38 0.06
67_K 145_S 0.86 0.37 0.06
13_H 37_P 0.86 0.36 0.06
112_A 87_I 0.85 0.36 0.06
49_P 175_I 0.85 0.35 0.05
23_A 23_T 0.84 0.34 0.05
40_R 136_L 0.83 0.34 0.05
100_F 161_N 0.83 0.33 0.05
33_G 68_I 0.83 0.33 0.05
99_G 113_P 0.82 0.33 0.05
21_I 71_I 0.82 0.33 0.05
20_L 10_E 0.82 0.33 0.05
122_A 158_A 0.82 0.33 0.05
100_F 61_G 0.82 0.32 0.05
23_A 115_W 0.82 0.32 0.05
71_V 60_A 0.81 0.32 0.05
82_A 176_V 0.81 0.32 0.05
88_W 72_W 0.81 0.31 0.04
67_K 158_A 0.81 0.31 0.04
77_I 66_Q 0.80 0.31 0.04
77_I 80_H 0.80 0.31 0.04
29_L 134_G 0.80 0.31 0.04
15_A 145_S 0.80 0.30 0.04
18_I 180_T 0.80 0.30 0.04
68_F 166_D 0.79 0.29 0.04
27_C 147_F 0.79 0.29 0.04
94_E 22_L 0.79 0.29 0.04
86_F 72_W 0.78 0.29 0.04
107_I 70_R 0.78 0.29 0.04
44_R 9_G 0.78 0.28 0.04
32_V 102_Q 0.78 0.28 0.04
26_L 12_Q 0.77 0.28 0.04
11_A 168_A 0.77 0.28 0.04
98_V 174_Q 0.77 0.28 0.04
121_G 148_D 0.77 0.27 0.04
28_C 85_E 0.77 0.27 0.04
16_F 42_L 0.77 0.27 0.04
40_R 134_G 0.77 0.27 0.04
101_V 136_L 0.76 0.27 0.04
24_I 23_T 0.76 0.27 0.04
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
2468 0.95 cI_A_cIII_isp_ecoli Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 1) msa: Jackhmmer (2015_03) 0.29 Done - Shared
2467 1.18 cI_A_cIII_isp_ecoli_2hhblits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2013_03) 0.07 Done - Shared
2466 1.94 cI_A_cIII_isp_ecoli_2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.75 Done - Shared
2457 1.95 cI_A_cIII_isp_ecoli_4 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.40 Done - Shared
2454 1.94 cI_A_cIII_isp_ecoli_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.03 Done - Shared
2453 2.01 cI_A_cIII_isp_ecoli Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.22 Done - Shared
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