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cI_A_cIII_isp_ecoli_2hhblits
Genes: A B A+B
Length: 147 183 292
Sequences: 1071 962 344
Seq/Len: 7.29 5.26 1.18
MirrorTree (Pazo et al. 2001) 0.64
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits 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 0.01
100 0.01 0.00 0.09
∞ 0.04 0.04 1.04
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
18_I 42_L 1.53 0.82 0.07
90_T 147_F 1.43 0.76 0.05
36_F 22_L 1.42 0.76 0.05
40_R 32_A 1.38 0.73 0.05
108_F 32_A 1.38 0.72 0.05
16_F 121_Y 1.32 0.68 0.04
47_N 56_D 1.32 0.68 0.04
36_F 46_E 1.31 0.67 0.04
115_V 84_Q 1.29 0.65 0.04
99_G 57_V 1.24 0.61 0.03
90_T 176_V 1.24 0.60 0.03
112_A 149_T 1.22 0.58 0.03
112_A 135_G 1.14 0.51 0.02
20_L 59_L 1.13 0.51 0.02
94_E 22_L 1.11 0.48 0.02
16_F 42_L 1.09 0.47 0.02
32_V 121_Y 1.09 0.46 0.02
56_S 164_I 1.09 0.46 0.02
71_V 60_A 1.08 0.46 0.02
80_V 150_S 1.08 0.46 0.02
41_A 162_L 1.07 0.44 0.02
95_S 38_L 0.99 0.37 0.01
98_V 38_L 0.99 0.37 0.01
112_A 94_D 0.98 0.36 0.01
115_V 99_I 0.98 0.36 0.01
36_F 35_V 0.96 0.35 0.01
29_L 47_K 0.96 0.34 0.01
24_I 29_A 0.96 0.34 0.01
24_I 166_D 0.94 0.33 0.01
90_T 13_E 0.94 0.33 0.01
124_D 133_P 0.93 0.32 0.01
68_F 92_N 0.92 0.31 0.01
24_I 59_L 0.92 0.31 0.01
99_G 30_G 0.92 0.31 0.01
85_L 158_A 0.91 0.30 0.01
122_A 74_G 0.91 0.30 0.01
67_K 158_A 0.90 0.29 0.01
29_L 162_L 0.90 0.29 0.01
33_G 68_I 0.89 0.29 0.01
67_K 145_S 0.89 0.28 0.01
109_V 25_F 0.88 0.28 0.01
72_A 12_Q 0.87 0.27 0.01
90_T 99_I 0.86 0.27 0.01
68_F 90_A 0.86 0.26 0.01
119_R 163_A 0.86 0.26 0.01
107_I 77_I 0.85 0.26 0.01
33_G 164_I 0.85 0.26 0.01
72_A 26_V 0.85 0.25 0.01
32_V 61_G 0.84 0.25 0.01
80_V 167_Y 0.84 0.25 0.01
23_A 60_A 0.84 0.25 0.01
82_A 174_Q 0.84 0.25 0.01
60_A 39_V 0.84 0.24 0.01
18_I 14_Q 0.84 0.24 0.01
63_R 24_K 0.83 0.24 0.01
22_V 162_L 0.83 0.24 0.01
22_V 112_H 0.83 0.24 0.01
124_D 34_A 0.83 0.24 0.01
89_S 160_A 0.82 0.23 0.01
114_L 139_I 0.82 0.23 0.01
34_G 67_T 0.82 0.23 0.01
77_I 145_S 0.81 0.23 0.01
88_W 72_W 0.81 0.23 0.01
77_I 158_A 0.81 0.23 0.01
27_C 99_I 0.81 0.23 0.01
102_E 102_Q 0.81 0.23 0.01
97_W 168_A 0.81 0.22 0.01
95_S 64_A 0.81 0.22 0.01
38_G 28_A 0.80 0.22 0.01
18_I 134_G 0.80 0.22 0.01
38_G 133_P 0.80 0.22 0.01
31_L 31_V 0.80 0.22 0.01
74_F 121_Y 0.79 0.21 0.01
110_L 74_G 0.79 0.21 0.01
23_A 62_V 0.79 0.21 0.01
109_V 42_L 0.79 0.21 0.01
119_R 66_Q 0.79 0.21 0.01
109_V 97_T 0.79 0.21 0.01
33_G 77_I 0.79 0.21 0.01
22_V 168_A 0.78 0.21 0.01
36_F 63_A 0.78 0.21 0.01
92_I 166_D 0.78 0.21 0.01
37_L 130_N 0.77 0.20 0.01
20_L 118_V 0.77 0.20 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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