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OPENSEQ.org
cIV_B_40_cIII_isp_40_Pdenitr
Genes: A B A+B
Length: 252 190 426
Sequences: 4089 1013 339
Seq/Len: 16.23 5.33 0.8
MirrorTree (Pazo et al. 2001) 0.35
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 0.00 0.01 0.01
10 0.00 0.01 0.02
20 0.01 0.01 0.03
100 0.01 0.01 0.12
∞ 0.03 0.02 0.77
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
47_I 140_I 1.50 0.70 0.01
118_G 176_I 1.24 0.49 0.00
225_A 168_G 1.10 0.37 0.00
53_L 49_Q 1.08 0.36 0.00
30_D 61_V 1.05 0.33 0.00
188_F 145_G 1.02 0.31 0.00
170_V 52_A 1.00 0.29 0.00
40_Y 122_A 0.98 0.28 0.00
64_A 176_I 0.97 0.27 0.00
69_A 187_I 0.95 0.26 0.00
51_L 96_Q 0.95 0.26 0.00
80_I 29_V 0.92 0.24 0.00
87_L 61_V 0.90 0.23 0.00
58_V 29_V 0.88 0.22 0.00
166_V 76_V 0.88 0.22 0.00
240_E 127_V 0.88 0.21 0.00
195_V 59_S 0.87 0.21 0.00
77_I 35_A 0.86 0.21 0.00
207_D 176_I 0.86 0.21 0.00
76_P 31_A 0.86 0.20 0.00
174_V 46_A 0.84 0.19 0.00
164_V 83_E 0.83 0.19 0.00
134_F 69_V 0.83 0.19 0.00
64_A 31_A 0.83 0.18 0.00
176_A 38_L 0.82 0.18 0.00
185_I 91_E 0.82 0.18 0.00
156_L 34_A 0.82 0.18 0.00
238_K 34_A 0.82 0.18 0.00
217_S 159_Y 0.82 0.18 0.00
164_V 43_N 0.82 0.18 0.00
12_K 183_D 0.81 0.17 0.00
195_V 88_A 0.81 0.17 0.00
117_I 162_S 0.80 0.17 0.00
164_V 31_A 0.80 0.17 0.00
131_G 95_G 0.80 0.17 0.00
239_Y 22_A 0.80 0.17 0.00
105_E 176_I 0.80 0.17 0.00
185_I 69_V 0.80 0.17 0.00
137_L 186_T 0.79 0.17 0.00
132_V 176_I 0.79 0.17 0.00
79_V 32_G 0.79 0.17 0.00
114_I 67_L 0.79 0.17 0.00
91_A 28_T 0.78 0.16 0.00
222_I 187_I 0.78 0.16 0.00
187_A 181_F 0.78 0.16 0.00
97_L 48_V 0.78 0.16 0.00
166_V 56_V 0.78 0.16 0.00
83_L 140_I 0.78 0.16 0.00
246_A 88_A 0.78 0.16 0.00
16_G 15_R 0.78 0.16 0.00
21_Q 47_D 0.77 0.16 0.00
248_E 184_D 0.77 0.16 0.00
132_V 67_L 0.77 0.16 0.00
103_S 77_F 0.77 0.16 0.00
39_L 39_V 0.77 0.16 0.00
112_L 59_S 0.77 0.15 0.00
229_I 67_L 0.76 0.15 0.00
55_I 84_D 0.76 0.15 0.00
59_R 187_I 0.76 0.15 0.00
73_H 91_E 0.76 0.15 0.00
182_A 29_V 0.76 0.15 0.00
112_L 39_V 0.76 0.15 0.00
190_V 23_T 0.75 0.15 0.00
132_V 20_Y 0.75 0.15 0.00
166_V 181_F 0.74 0.15 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
3113 0.9 cIV_B_6_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3112 0.35 cIV_B_10_cIII_isp_60_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3111 0.9 cIV_B_10_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.24 Done - Shared
3110 1.66 cIV_B_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3109 0.91 cIV_B_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
3108 1.65 cIV_B_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3107 0.8 cIV_B_40_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3106 1.7 cIV_B_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3099 0.9 cIV_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
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