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OPENSEQ.org
cI_A_cIII_isp_ecoli
Genes: A B A+B
Length: 147 183 289
Sequences: 3696 894 275
Seq/Len: 25.14 4.89 0.95
MirrorTree (Pazo et al. 2001) 0.34
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 0.00 0.02
100 0.01 0.00 0.08
∞ 0.01 0.02 0.83
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 1.77 0.89 0.29
16_F 42_L 1.51 0.76 0.15
33_G 164_I 1.40 0.68 0.11
47_N 56_D 1.39 0.67 0.11
98_V 38_L 1.37 0.66 0.10
108_F 32_A 1.36 0.65 0.10
90_T 147_F 1.28 0.58 0.08
44_R 22_L 1.27 0.57 0.07
24_I 59_L 1.24 0.54 0.07
68_F 138_W 1.19 0.50 0.06
18_I 42_L 1.17 0.47 0.05
20_L 59_L 1.15 0.46 0.05
124_D 63_A 1.12 0.43 0.04
35_W 41_A 1.11 0.42 0.04
40_R 135_G 1.09 0.40 0.04
115_V 14_Q 1.09 0.40 0.04
105_I 102_Q 1.09 0.40 0.04
38_G 30_G 1.07 0.39 0.04
91_S 38_L 1.07 0.39 0.04
72_A 164_I 1.06 0.38 0.04
23_A 115_W 1.06 0.38 0.04
29_L 63_A 1.05 0.37 0.03
44_R 41_A 1.05 0.37 0.03
117_L 144_G 1.04 0.36 0.03
24_I 29_A 1.03 0.36 0.03
100_F 79_I 1.03 0.35 0.03
92_I 155_R 1.03 0.35 0.03
91_S 61_G 1.01 0.34 0.03
14_W 32_A 1.01 0.34 0.03
56_S 173_G 1.01 0.34 0.03
124_D 66_Q 1.01 0.34 0.03
72_A 54_P 0.99 0.32 0.03
38_G 156_G 0.98 0.32 0.03
34_G 45_D 0.98 0.32 0.03
96_G 167_Y 0.98 0.31 0.03
27_C 106_E 0.98 0.31 0.03
119_R 89_A 0.97 0.31 0.03
20_L 132_Q 0.97 0.31 0.03
50_F 154_T 0.95 0.29 0.02
35_W 73_Q 0.95 0.29 0.02
68_F 102_Q 0.94 0.28 0.02
71_V 60_A 0.94 0.28 0.02
115_V 35_V 0.94 0.28 0.02
34_G 47_K 0.94 0.28 0.02
108_F 94_D 0.94 0.28 0.02
68_F 166_D 0.93 0.27 0.02
115_V 111_V 0.92 0.27 0.02
38_G 28_A 0.92 0.27 0.02
21_I 39_V 0.92 0.27 0.02
68_F 116_L 0.92 0.27 0.02
26_L 21_K 0.92 0.27 0.02
26_L 132_Q 0.92 0.27 0.02
58_G 79_I 0.90 0.26 0.02
60_A 173_G 0.89 0.25 0.02
47_N 160_A 0.89 0.24 0.02
97_W 24_K 0.88 0.24 0.02
14_W 67_T 0.88 0.24 0.02
33_G 121_Y 0.88 0.24 0.02
38_G 133_P 0.88 0.24 0.02
124_D 19_L 0.87 0.24 0.02
32_V 113_P 0.87 0.23 0.02
100_F 75_K 0.87 0.23 0.02
23_A 147_F 0.87 0.23 0.02
23_A 43_S 0.86 0.23 0.02
105_I 104_D 0.86 0.23 0.02
95_S 64_A 0.85 0.22 0.01
49_P 154_T 0.85 0.22 0.01
12_H 170_H 0.85 0.22 0.01
104_A 176_V 0.85 0.22 0.01
24_I 107_R 0.84 0.21 0.01
108_F 30_G 0.84 0.21 0.01
92_I 106_E 0.84 0.21 0.01
16_F 139_I 0.84 0.21 0.01
25_G 75_K 0.84 0.21 0.01
37_L 130_N 0.84 0.21 0.01
98_V 118_V 0.84 0.21 0.01
96_G 30_G 0.83 0.21 0.01
27_C 99_I 0.83 0.21 0.01
112_A 20_C 0.83 0.21 0.01
77_I 116_L 0.82 0.20 0.01
97_W 150_S 0.82 0.20 0.01
12_H 163_A 0.82 0.20 0.01
88_W 72_W 0.82 0.20 0.01
21_I 14_Q 0.82 0.20 0.01
11_A 85_E 0.81 0.20 0.01
24_I 114_Q 0.81 0.19 0.01
30_M 167_Y 0.80 0.19 0.01
112_A 149_T 0.80 0.19 0.01
18_I 66_Q 0.80 0.19 0.01
105_I 85_E 0.80 0.19 0.01
10_I 33_A 0.80 0.19 0.01
103_A 135_G 0.80 0.19 0.01
37_L 22_L 0.80 0.19 0.01
85_L 88_V 0.80 0.19 0.01
18_I 119_Q 0.79 0.19 0.01
28_C 35_V 0.79 0.19 0.01
26_L 169_F 0.79 0.19 0.01
26_L 116_L 0.79 0.19 0.01
101_V 43_S 0.79 0.18 0.01
11_A 45_D 0.79 0.18 0.01
14_W 50_G 0.79 0.18 0.01
20_L 118_V 0.78 0.18 0.01
82_A 23_T 0.78 0.18 0.01
23_A 128_V 0.78 0.18 0.01
115_V 84_Q 0.78 0.18 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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