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OPENSEQ.org
cIV_C_4_cI_M_40_Pdenitr
Genes: A B A+B
Length: 273 513 728
Sequences: 2888 17026 3219
Seq/Len: 10.58 33.19 4.42
MirrorTree (Pazo et al. 2001) 0.51
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 0.29
2 0.00 0.65 1.51
5 0.00 0.70 3.15
10 0.00 0.71 3.40
20 0.00 0.71 3.45
100 0.00 0.71 3.57
∞ 0.01 0.71 4.10
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 1.08 0.83 0.06
208_A 273_S 0.99 0.75 0.04
265_F 290_W 0.94 0.69 0.04
176_I 388_F 0.93 0.68 0.04
201_A 369_I 0.92 0.67 0.04
37_G 196_L 0.88 0.62 0.03
125_G 348_F 0.88 0.62 0.03
136_D 36_W 0.86 0.59 0.03
262_L 162_A 0.86 0.59 0.03
99_M 351_G 0.83 0.56 0.03
207_G 328_V 0.83 0.55 0.03
58_V 284_A 0.81 0.52 0.02
183_V 408_T 0.81 0.52 0.02
154_A 379_M 0.80 0.51 0.02
165_E 300_S 0.80 0.51 0.02
177_V 71_W 0.79 0.49 0.02
6_H 130_A 0.78 0.48 0.02
122_I 292_S 0.78 0.48 0.02
183_V 223_L 0.77 0.47 0.02
8_Y 438_Y 0.77 0.47 0.02
27_M 483_T 0.77 0.46 0.02
187_G 79_M 0.76 0.46 0.02
180_I 43_T 0.76 0.46 0.02
180_I 223_L 0.75 0.45 0.02
98_V 93_T 0.75 0.45 0.02
73_G 44_A 0.75 0.44 0.02
114_Y 84_I 0.75 0.44 0.02
55_L 119_V 0.75 0.44 0.02
59_L 467_P 0.74 0.42 0.02
221_I 168_L 0.73 0.42 0.02
237_G 335_G 0.73 0.41 0.02
237_G 448_K 0.72 0.41 0.02
30_G 266_G 0.72 0.41 0.02
10_I 382_Y 0.71 0.40 0.02
134_T 79_M 0.71 0.39 0.02
166_G 100_I 0.71 0.38 0.02
242_K 421_L 0.70 0.38 0.02
207_G 322_G 0.70 0.37 0.02
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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