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OPENSEQ.org
cI_J_10_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 200 190 384
Sequences: 2223 1539 484
Seq/Len: 11.12 8.1 1.26
MirrorTree (Pazo et al. 2001) 0.69
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 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.08
∞ 0.03 0.04 1.24
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
14_C 61_V 1.61 0.88 0.23
53_A 12_G 1.32 0.70 0.10
102_A 31_A 1.27 0.66 0.09
153_V 186_T 1.21 0.59 0.07
107_A 124_E 1.17 0.56 0.06
193_D 131_V 1.17 0.56 0.06
12_S 31_A 1.13 0.52 0.06
185_P 24_A 1.12 0.51 0.05
179_E 183_D 1.10 0.49 0.05
97_G 131_V 1.10 0.49 0.05
106_I 187_I 1.09 0.48 0.05
162_I 59_S 1.06 0.45 0.04
58_V 78_I 1.04 0.44 0.04
160_G 165_I 1.02 0.41 0.04
105_G 53_S 1.00 0.40 0.04
196_P 176_I 0.99 0.39 0.03
103_Q 184_D 0.99 0.39 0.03
195_K 144_A 0.99 0.38 0.03
146_M 188_K 0.97 0.37 0.03
33_L 160_D 0.97 0.37 0.03
187_K 32_G 0.97 0.36 0.03
29_S 83_E 0.96 0.36 0.03
74_M 177_P 0.95 0.35 0.03
25_N 30_A 0.95 0.35 0.03
17_G 91_E 0.95 0.34 0.03
145_L 76_V 0.94 0.34 0.03
31_L 48_V 0.94 0.34 0.03
151_G 47_D 0.94 0.34 0.03
34_I 150_W 0.93 0.33 0.03
37_F 135_L 0.93 0.33 0.03
80_A 28_T 0.93 0.33 0.03
161_A 27_G 0.93 0.33 0.03
98_V 12_G 0.91 0.32 0.03
114_S 56_V 0.91 0.32 0.03
39_S 15_R 0.91 0.31 0.03
9_F 133_T 0.90 0.31 0.02
135_L 159_Y 0.90 0.30 0.02
107_A 163_G 0.89 0.30 0.02
46_L 29_V 0.89 0.30 0.02
36_A 58_V 0.89 0.30 0.02
128_A 28_T 0.89 0.30 0.02
147_F 18_F 0.89 0.29 0.02
130_E 189_L 0.89 0.29 0.02
4_F 105_S 0.88 0.29 0.02
108_F 29_V 0.87 0.28 0.02
192_K 33_A 0.87 0.28 0.02
27_V 153_P 0.87 0.28 0.02
22_I 32_G 0.87 0.28 0.02
149_L 60_G 0.86 0.28 0.02
181_M 72_L 0.86 0.27 0.02
108_F 28_T 0.86 0.27 0.02
179_E 32_G 0.86 0.27 0.02
57_V 178_V 0.86 0.27 0.02
144_V 172_Q 0.85 0.27 0.02
38_L 148_G 0.85 0.27 0.02
134_G 39_V 0.85 0.27 0.02
20_V 19_L 0.84 0.26 0.02
22_I 98_I 0.84 0.26 0.02
55_L 58_V 0.84 0.26 0.02
197_G 159_Y 0.84 0.26 0.02
53_A 186_T 0.83 0.25 0.02
113_P 60_G 0.83 0.25 0.02
156_V 144_A 0.83 0.25 0.02
53_A 117_R 0.83 0.25 0.02
47_Q 42_M 0.83 0.25 0.02
98_V 87_Q 0.83 0.25 0.02
21_V 88_A 0.83 0.25 0.02
18_F 60_G 0.83 0.25 0.02
190_E 141_G 0.82 0.25 0.02
136_G 29_V 0.82 0.25 0.02
184_D 87_Q 0.82 0.24 0.02
122_A 24_A 0.82 0.24 0.02
100_L 142_D 0.82 0.24 0.02
146_M 98_I 0.81 0.24 0.02
132_T 68_T 0.81 0.24 0.02
153_V 166_R 0.81 0.24 0.02
195_K 66_Q 0.81 0.24 0.02
107_A 28_T 0.81 0.23 0.02
58_V 63_T 0.81 0.23 0.02
121_R 51_L 0.81 0.23 0.02
39_S 43_N 0.81 0.23 0.02
90_L 124_E 0.81 0.23 0.02
90_L 26_A 0.81 0.23 0.02
138_V 35_A 0.81 0.23 0.02
97_G 140_I 0.80 0.23 0.02
190_E 28_T 0.80 0.23 0.02
142_R 60_G 0.80 0.23 0.02
138_V 118_T 0.80 0.23 0.02
155_L 145_G 0.80 0.23 0.02
153_V 115_E 0.80 0.23 0.02
159_I 91_E 0.79 0.22 0.01
191_L 39_V 0.79 0.22 0.01
91_P 52_A 0.79 0.22 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
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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