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OPENSEQ.org
cIV_C_6_cI_M_80_Pdenitr
Genes: A B A+B
Length: 273 513 728
Sequences: 2876 12268 2876
Seq/Len: 10.53 23.91 3.95
MirrorTree (Pazo et al. 2001) 0.46
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 0.57 0.12
2 0.00 0.61 1.26
5 0.00 0.66 2.69
10 0.00 0.67 2.99
20 0.00 0.68 3.05
100 0.00 0.68 3.15
∞ 0.01 0.68 3.66
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
201_A 287_Y 1.35 0.95 0.56
208_A 273_S 1.02 0.75 0.26
8_Y 190_T 0.98 0.70 0.22
205_Y 360_I 0.93 0.65 0.19
266_V 113_Y 0.93 0.65 0.19
265_F 290_W 0.91 0.62 0.17
235_L 412_V 0.90 0.61 0.17
265_F 255_V 0.88 0.59 0.16
123_K 223_L 0.88 0.58 0.15
138_W 255_V 0.87 0.57 0.15
10_I 382_Y 0.86 0.56 0.15
114_Y 84_I 0.86 0.56 0.15
179_V 463_W 0.86 0.56 0.15
183_V 42_T 0.86 0.55 0.14
211_M 89_V 0.85 0.54 0.14
121_P 100_I 0.83 0.52 0.13
147_I 130_A 0.83 0.52 0.13
225_I 345_S 0.83 0.52 0.13
48_P 407_L 0.82 0.51 0.13
242_K 227_A 0.82 0.51 0.13
262_L 186_R 0.82 0.50 0.12
108_F 169_Y 0.82 0.50 0.12
130_E 435_L 0.81 0.49 0.12
33_A 329_F 0.81 0.49 0.12
165_E 426_G 0.81 0.49 0.12
201_A 369_I 0.81 0.49 0.12
172_I 94_F 0.81 0.48 0.12
201_A 422_V 0.80 0.48 0.12
98_V 93_T 0.80 0.48 0.12
121_P 50_L 0.80 0.48 0.12
25_F 184_M 0.80 0.47 0.11
13_P 240_T 0.79 0.46 0.11
166_G 100_I 0.79 0.46 0.11
26_V 183_A 0.78 0.46 0.11
136_D 283_V 0.78 0.46 0.11
51_F 43_T 0.78 0.46 0.11
158_A 71_W 0.78 0.45 0.11
121_P 293_A 0.78 0.45 0.10
181_L 410_M 0.78 0.45 0.10
208_A 288_V 0.78 0.45 0.10
35_M 365_H 0.78 0.45 0.10
27_M 386_F 0.77 0.43 0.10
51_F 365_H 0.76 0.43 0.10
155_V 151_I 0.76 0.42 0.10
61_V 391_M 0.76 0.42 0.10
169_K 48_I 0.76 0.42 0.10
196_A 169_Y 0.76 0.42 0.10
260_V 266_G 0.75 0.42 0.10
195_H 322_G 0.75 0.41 0.09
197_A 125_I 0.75 0.41 0.09
237_G 276_M 0.74 0.40 0.09
239_M 457_M 0.74 0.40 0.09
162_F 182_I 0.74 0.40 0.09
99_M 126_G 0.74 0.40 0.09
150_L 386_F 0.73 0.39 0.09
8_Y 438_Y 0.73 0.39 0.09
61_V 383_A 0.73 0.39 0.09
7_D 113_Y 0.73 0.38 0.08
229_V 378_R 0.73 0.38 0.08
194_S 360_I 0.73 0.38 0.08
30_G 396_L 0.72 0.38 0.08
262_L 167_F 0.72 0.38 0.08
134_T 79_M 0.72 0.38 0.08
8_Y 188_A 0.72 0.38 0.08
205_Y 179_V 0.72 0.37 0.08
8_Y 177_M 0.72 0.37 0.08
8_Y 429_L 0.72 0.37 0.08
27_M 272_F 0.72 0.37 0.08
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.68 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
4052 3.95 cIV_C_6_cI_M_80_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
3192 2.03 cIV_C_4_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3191 1.88 cIV_C_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3190 0.82 cIV_C_4_cI_M_60_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3189 3.94 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
3188 4.24 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3187 4.42 cIV_C_4_cI_M_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
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