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OPENSEQ.org
cI_A_cIII_isp_ecoli_6
Genes: A B A+B
Length: 147 183 295
Sequences: 3696 2084 573
Seq/Len: 25.14 11.39 1.94
MirrorTree (Pazo et al. 2001) 0.53
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 0.03
100 0.01 0.01 0.16
∞ 0.01 0.04 1.74
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
108_F 32_A 1.25 0.76 0.03
92_I 28_A 1.23 0.75 0.03
21_I 39_V 1.23 0.74 0.03
16_F 121_Y 1.18 0.70 0.03
90_T 147_F 1.18 0.70 0.03
41_A 162_L 1.16 0.68 0.02
94_E 22_L 1.13 0.65 0.02
112_A 70_R 1.11 0.63 0.02
18_I 42_L 1.07 0.59 0.02
16_F 42_L 1.07 0.59 0.02
115_V 35_V 1.05 0.57 0.02
34_G 47_K 1.04 0.56 0.02
29_L 92_N 1.00 0.51 0.01
49_P 175_I 0.98 0.50 0.01
37_L 102_Q 0.97 0.48 0.01
16_F 28_A 0.96 0.47 0.01
83_L 154_T 0.96 0.47 0.01
33_G 121_Y 0.95 0.46 0.01
72_A 106_E 0.94 0.45 0.01
112_A 94_D 0.94 0.45 0.01
20_L 10_E 0.94 0.45 0.01
29_L 31_V 0.93 0.43 0.01
119_R 163_A 0.91 0.41 0.01
23_A 47_K 0.89 0.40 0.01
29_L 35_V 0.89 0.40 0.01
98_V 174_Q 0.89 0.39 0.01
80_V 167_Y 0.88 0.38 0.01
18_I 94_D 0.87 0.38 0.01
24_I 117_V 0.86 0.36 0.01
16_F 155_R 0.85 0.36 0.01
36_F 22_L 0.85 0.35 0.01
66_A 28_A 0.85 0.35 0.01
37_L 74_G 0.83 0.33 0.01
18_I 66_Q 0.83 0.33 0.01
45_S 145_S 0.82 0.32 0.01
33_G 164_I 0.82 0.32 0.01
37_L 71_I 0.81 0.32 0.01
82_A 22_L 0.81 0.31 0.01
60_A 174_Q 0.81 0.31 0.01
23_A 18_C 0.81 0.31 0.01
23_A 23_T 0.81 0.31 0.01
26_L 171_S 0.81 0.31 0.01
11_A 168_A 0.80 0.30 0.01
68_F 60_A 0.80 0.30 0.01
18_I 53_E 0.80 0.30 0.01
37_L 163_A 0.79 0.30 0.01
67_K 145_S 0.79 0.29 0.01
85_L 32_A 0.79 0.29 0.01
110_L 58_S 0.78 0.29 0.01
40_R 19_L 0.78 0.29 0.01
27_C 22_L 0.78 0.29 0.01
117_L 144_G 0.78 0.28 0.01
24_I 171_S 0.78 0.28 0.01
95_S 64_A 0.77 0.28 0.01
16_F 14_Q 0.77 0.28 0.01
32_V 30_G 0.77 0.28 0.01
105_I 62_V 0.77 0.28 0.01
102_E 91_R 0.77 0.27 0.01
96_G 179_G 0.76 0.27 0.01
82_A 70_R 0.76 0.27 0.01
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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