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OPENSEQ.org
cI_J_20_cIII_cytb_6_Pdenitr
Genes: A B A+B
Length: 200 190 383
Sequences: 2148 1587 496
Seq/Len: 10.74 8.35 1.3
MirrorTree (Pazo et al. 2001) 0.70
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 0.01
100 0.02 0.01 0.09
∞ 0.03 0.04 1.27
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
53_A 12_G 1.28 0.68 0.01
80_A 28_T 1.19 0.59 0.00
58_V 78_I 1.14 0.54 0.00
193_D 131_V 1.12 0.52 0.00
185_P 24_A 1.09 0.49 0.00
20_V 73_G 1.06 0.46 0.00
152_L 159_Y 1.06 0.46 0.00
14_C 61_V 1.04 0.44 0.00
104_L 31_A 1.01 0.41 0.00
149_L 60_G 1.01 0.41 0.00
135_L 159_Y 1.00 0.40 0.00
145_L 76_V 0.99 0.39 0.00
147_F 18_F 0.99 0.39 0.00
105_G 131_V 0.98 0.38 0.00
3_T 31_A 0.98 0.38 0.00
146_M 188_K 0.98 0.38 0.00
12_S 105_S 0.98 0.38 0.00
22_I 98_I 0.97 0.37 0.00
171_D 127_V 0.96 0.36 0.00
147_F 168_G 0.96 0.36 0.00
52_V 38_L 0.95 0.36 0.00
153_V 186_T 0.95 0.36 0.00
126_D 84_D 0.94 0.35 0.00
191_L 189_L 0.94 0.35 0.00
127_A 189_L 0.94 0.35 0.00
162_I 59_S 0.94 0.34 0.00
17_G 91_E 0.94 0.34 0.00
53_A 117_R 0.93 0.34 0.00
53_A 186_T 0.93 0.34 0.00
105_G 80_R 0.93 0.34 0.00
29_S 76_V 0.93 0.34 0.00
128_A 28_T 0.93 0.33 0.00
179_E 183_D 0.92 0.33 0.00
102_A 31_A 0.91 0.32 0.00
29_S 63_T 0.90 0.31 0.00
106_I 22_A 0.90 0.31 0.00
130_E 189_L 0.90 0.31 0.00
133_L 125_W 0.90 0.31 0.00
36_A 58_V 0.89 0.31 0.00
103_Q 184_D 0.89 0.30 0.00
124_P 91_E 0.88 0.30 0.00
74_M 177_P 0.88 0.29 0.00
138_V 35_A 0.88 0.29 0.00
160_G 12_G 0.88 0.29 0.00
12_S 31_A 0.88 0.29 0.00
195_K 144_A 0.87 0.29 0.00
11_I 176_I 0.87 0.28 0.00
196_P 176_I 0.86 0.28 0.00
187_K 32_G 0.86 0.28 0.00
58_V 146_D 0.86 0.28 0.00
153_V 166_R 0.86 0.28 0.00
153_V 115_E 0.86 0.28 0.00
25_N 30_A 0.86 0.28 0.00
156_V 144_A 0.86 0.28 0.00
130_E 127_V 0.85 0.28 0.00
65_A 17_D 0.85 0.27 0.00
197_G 159_Y 0.85 0.27 0.00
148_Q 114_D 0.85 0.27 0.00
99_V 31_A 0.85 0.27 0.00
193_D 189_L 0.85 0.27 0.00
34_I 150_W 0.85 0.27 0.00
27_V 18_F 0.84 0.27 0.00
47_Q 42_M 0.84 0.26 0.00
140_Y 139_P 0.84 0.26 0.00
14_C 145_G 0.84 0.26 0.00
58_V 63_T 0.84 0.26 0.00
29_S 83_E 0.83 0.26 0.00
107_A 124_E 0.83 0.26 0.00
181_M 72_L 0.83 0.26 0.00
175_Q 30_A 0.83 0.26 0.00
193_D 30_A 0.83 0.26 0.00
99_V 12_G 0.82 0.25 0.00
32_W 52_A 0.82 0.25 0.00
18_F 60_G 0.82 0.25 0.00
134_G 145_G 0.81 0.24 0.00
108_F 131_V 0.81 0.24 0.00
57_V 178_V 0.81 0.24 0.00
105_G 53_S 0.81 0.24 0.00
190_E 28_T 0.81 0.24 0.00
107_A 28_T 0.81 0.24 0.00
184_D 87_Q 0.81 0.24 0.00
72_V 52_A 0.81 0.24 0.00
146_M 53_S 0.80 0.23 0.00
136_G 29_V 0.80 0.23 0.00
126_D 59_S 0.80 0.23 0.00
140_Y 111_P 0.80 0.23 0.00
90_L 26_A 0.80 0.23 0.00
18_F 163_G 0.80 0.23 0.00
41_A 22_A 0.79 0.23 0.00
180_Q 41_Q 0.79 0.23 0.00
15_V 78_I 0.79 0.23 0.00
146_M 98_I 0.79 0.23 0.00
135_L 171_P 0.79 0.23 0.00
192_K 48_V 0.79 0.23 0.00
67_L 160_D 0.79 0.23 0.00
97_G 141_G 0.79 0.23 0.00
15_V 30_A 0.79 0.23 0.00
11_I 121_E 0.79 0.23 0.00
91_P 52_A 0.79 0.23 0.00
52_V 19_L 0.79 0.23 0.00
191_L 39_V 0.79 0.23 0.00
195_K 189_L 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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