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OPENSEQ.org
cI_J_10_cIII_isp_6_Pdenitr
Genes: A B A+B
Length: 200 190 384
Sequences: 2223 1587 500
Seq/Len: 11.12 8.35 1.3
MirrorTree (Pazo et al. 2001) 0.68
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 0.01 0.00
2 0.00 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.02
100 0.02 0.01 0.09
∞ 0.03 0.04 1.28
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
102_A 31_A 1.41 0.78 0.03
53_A 12_G 1.30 0.69 0.02
80_A 28_T 1.16 0.56 0.01
107_A 124_E 1.16 0.56 0.01
193_D 131_V 1.13 0.54 0.01
20_V 73_G 1.10 0.50 0.01
128_A 28_T 1.08 0.48 0.01
58_V 78_I 1.08 0.48 0.01
127_A 189_L 1.07 0.48 0.01
12_S 105_S 1.07 0.47 0.01
185_P 24_A 1.06 0.47 0.01
108_F 29_V 1.05 0.45 0.01
52_V 38_L 1.02 0.42 0.01
135_L 159_Y 1.00 0.41 0.01
14_C 61_V 0.99 0.39 0.01
29_S 76_V 0.98 0.38 0.01
153_V 186_T 0.97 0.38 0.01
196_P 176_I 0.96 0.36 0.01
191_L 189_L 0.95 0.36 0.01
142_R 60_G 0.94 0.35 0.01
52_V 48_V 0.94 0.34 0.01
147_F 18_F 0.93 0.34 0.01
102_A 131_V 0.92 0.33 0.01
162_I 59_S 0.92 0.33 0.01
12_S 31_A 0.92 0.33 0.01
11_I 176_I 0.91 0.32 0.01
120_L 83_E 0.91 0.32 0.01
53_A 117_R 0.91 0.32 0.01
93_A 65_T 0.90 0.32 0.01
138_V 35_A 0.90 0.31 0.01
195_K 144_A 0.90 0.31 0.01
17_G 91_E 0.90 0.31 0.01
18_F 163_G 0.89 0.31 0.01
98_V 35_A 0.89 0.30 0.01
179_E 32_G 0.89 0.30 0.01
57_V 178_V 0.89 0.30 0.01
146_M 188_K 0.89 0.30 0.01
175_Q 30_A 0.89 0.30 0.01
145_L 76_V 0.88 0.29 0.01
124_P 62_E 0.88 0.29 0.01
98_V 12_G 0.87 0.29 0.01
144_V 163_G 0.87 0.29 0.01
22_I 98_I 0.87 0.29 0.01
133_L 125_W 0.87 0.29 0.01
130_E 127_V 0.87 0.28 0.01
152_L 148_G 0.86 0.28 0.01
155_L 145_G 0.86 0.28 0.01
97_G 131_V 0.86 0.28 0.01
121_R 83_E 0.86 0.28 0.01
121_R 159_Y 0.86 0.28 0.01
34_I 150_W 0.85 0.27 0.01
53_A 186_T 0.85 0.27 0.01
97_G 141_G 0.85 0.27 0.01
36_A 58_V 0.85 0.27 0.01
197_G 159_Y 0.85 0.27 0.01
83_K 55_Q 0.85 0.27 0.01
25_N 30_A 0.85 0.27 0.01
57_V 55_Q 0.85 0.27 0.01
91_P 52_A 0.84 0.26 0.01
149_L 60_G 0.84 0.26 0.01
130_E 189_L 0.84 0.26 0.01
82_L 176_I 0.83 0.26 0.01
109_S 36_W 0.83 0.26 0.01
181_M 72_L 0.83 0.26 0.01
114_S 56_V 0.83 0.26 0.01
146_M 98_I 0.82 0.25 0.01
179_E 183_D 0.82 0.25 0.01
29_S 83_E 0.82 0.25 0.01
55_L 24_A 0.82 0.24 0.01
139_L 183_D 0.82 0.24 0.01
72_V 52_A 0.81 0.24 0.01
187_K 32_G 0.81 0.24 0.01
193_D 189_L 0.81 0.24 0.01
106_I 187_I 0.81 0.24 0.01
156_V 144_A 0.81 0.24 0.01
132_T 65_T 0.81 0.24 0.01
153_V 166_R 0.80 0.23 0.01
147_F 168_G 0.80 0.23 0.01
74_M 177_P 0.80 0.23 0.01
193_D 30_A 0.80 0.23 0.00
47_Q 42_M 0.80 0.23 0.00
140_Y 111_P 0.80 0.23 0.00
152_L 185_T 0.80 0.23 0.00
41_A 22_A 0.79 0.23 0.00
195_K 96_Q 0.79 0.23 0.00
45_V 22_A 0.79 0.23 0.00
144_V 65_T 0.79 0.23 0.00
160_G 165_I 0.79 0.23 0.00
46_L 29_V 0.79 0.23 0.00
36_A 84_D 0.79 0.22 0.00
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
2989 0.8 cI_J_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2978 1.3 cI_J_20_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2977 0.84 cI_J_20_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
2968 1.26 cI_J_20_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
2949 0.84 cI_J_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
2938 1.3 cI_J_10_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
2937 1.26 cI_J_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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