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OPENSEQ.org
cIV_C_4_cI_M_60_Pdenitr
Genes: A B A+B
Length: 273 513 728
Sequences: 2888 16159 3084
Seq/Len: 10.58 31.5 4.24
MirrorTree (Pazo et al. 2001) 0.50
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 0.60 0.22
2 0.00 0.65 1.40
5 0.00 0.69 2.97
10 0.00 0.70 3.25
20 0.00 0.70 3.28
100 0.00 0.70 3.39
∞ 0.01 0.71 3.92
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
265_F 255_V 1.00 0.75 0.02
208_A 273_S 0.94 0.68 0.02
183_V 408_T 0.91 0.65 0.01
125_G 348_F 0.90 0.63 0.01
98_V 93_T 0.89 0.62 0.01
10_I 382_Y 0.87 0.60 0.01
147_I 344_L 0.85 0.57 0.01
260_V 266_G 0.84 0.56 0.01
266_V 113_Y 0.84 0.56 0.01
108_F 392_A 0.84 0.56 0.01
27_M 483_T 0.83 0.55 0.01
265_F 290_W 0.82 0.53 0.01
8_Y 177_M 0.82 0.52 0.01
201_A 287_Y 0.82 0.52 0.01
37_G 196_L 0.82 0.52 0.01
77_E 335_G 0.81 0.52 0.01
8_Y 438_Y 0.81 0.51 0.01
114_Y 84_I 0.80 0.50 0.01
51_F 365_H 0.80 0.50 0.01
251_A 117_F 0.80 0.50 0.01
207_G 328_V 0.80 0.49 0.01
23_G 300_S 0.79 0.49 0.01
211_M 125_I 0.79 0.48 0.01
84_I 425_S 0.79 0.48 0.01
165_E 300_S 0.78 0.47 0.01
8_Y 190_T 0.78 0.46 0.01
180_I 43_T 0.77 0.46 0.01
52_L 421_L 0.77 0.46 0.01
8_Y 483_T 0.77 0.45 0.01
201_A 369_I 0.77 0.45 0.01
8_Y 129_T 0.76 0.45 0.01
55_L 119_V 0.76 0.44 0.01
54_G 59_A 0.75 0.43 0.01
108_F 169_Y 0.75 0.43 0.01
57_G 269_F 0.75 0.43 0.01
176_I 388_F 0.75 0.42 0.01
98_V 60_N 0.74 0.42 0.01
203_T 113_Y 0.74 0.41 0.01
10_I 181_M 0.74 0.41 0.01
196_A 169_Y 0.74 0.41 0.01
262_L 167_F 0.73 0.40 0.01
114_Y 128_F 0.73 0.40 0.01
63_F 164_F 0.72 0.39 0.01
114_Y 49_S 0.71 0.38 0.01
153_V 328_V 0.71 0.38 0.01
180_I 223_L 0.71 0.38 0.01
183_V 90_L 0.71 0.37 0.01
122_I 292_S 0.71 0.37 0.01
27_M 386_F 0.70 0.37 0.01
13_P 447_I 0.70 0.37 0.01
225_I 345_S 0.70 0.37 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.71 > 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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