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YUMMY_BmdB_BmdC_Take2

Genes: A B A+B
Length: 325 481 792
Sequences: 721 39138 141
Seq/Len: 2.22 81.37 0.18
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 0.01 0.36 0.05
2 0.01 0.36 0.06
5 0.02 0.39 0.08
10 0.02 0.40 0.09
20 0.02 0.40 0.11
100 0.02 0.41 0.17
0.02 0.44 0.43
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
140_D 91_I 1.36 0.24 0.00
95_F 38_T 1.17 0.17 0.00
319_G 207_L 1.12 0.15 0.00
169_L 423_D 1.10 0.14 0.00
137_A 399_Y 1.10 0.14 0.00
62_K 80_A 1.09 0.14 0.00
196_V 37_L 1.05 0.13 0.00
192_V 227_G 1.04 0.13 0.00
68_L 118_Y 1.01 0.12 0.00
271_E 221_R 1.01 0.12 0.00
200_R 113_L 1.01 0.12 0.00
249_L 384_I 1.00 0.12 0.00
249_L 476_N 1.00 0.12 0.00
196_V 128_D 0.99 0.12 0.00
192_V 406_I 0.98 0.11 0.00
84_P 46_S 0.98 0.11 0.00
186_G 403_L 0.97 0.11 0.00
307_L 384_I 0.97 0.11 0.00
284_E 405_E 0.95 0.10 0.00
130_I 209_M 0.94 0.10 0.00
266_F 22_Q 0.94 0.10 0.00
271_E 216_M 0.92 0.10 0.00
194_V 39_Y 0.92 0.10 0.00
142_I 46_S 0.92 0.10 0.00
141_I 35_E 0.92 0.10 0.00
257_M 39_Y 0.91 0.10 0.00
184_A 41_E 0.91 0.10 0.00
297_N 81_V 0.91 0.10 0.00
138_L 361_I 0.89 0.09 0.00
147_S 376_G 0.89 0.09 0.00
89_S 384_I 0.88 0.09 0.00
209_Y 286_G 0.88 0.09 0.00
107_K 352_D 0.87 0.09 0.00
204_V 316_A 0.87 0.09 0.00
131_Q 144_I 0.87 0.09 0.00
157_V 475_P 0.87 0.09 0.00
221_V 113_L 0.87 0.09 0.00
151_F 284_L 0.87 0.09 0.00
151_F 91_I 0.86 0.09 0.00
147_S 130_D 0.86 0.09 0.00
118_L 205_A 0.86 0.09 0.00
291_C 268_L 0.86 0.09 0.00
319_G 290_A 0.86 0.09 0.00
71_L 71_Q 0.86 0.09 0.00
78_V 376_G 0.86 0.09 0.00
213_P 315_L 0.85 0.09 0.00
95_F 343_A 0.85 0.09 0.00
257_M 228_I 0.85 0.08 0.00
285_D 340_I 0.85 0.08 0.00
225_D 87_A 0.84 0.08 0.00
283_A 340_I 0.84 0.08 0.00
131_Q 207_L 0.84 0.08 0.00
256_S 209_M 0.84 0.08 0.00
177_I 226_R 0.83 0.08 0.00
186_G 233_T 0.83 0.08 0.00
83_P 107_S 0.83 0.08 0.00
188_Y 415_D 0.82 0.08 0.00
271_E 38_T 0.82 0.08 0.00
77_L 231_W 0.81 0.08 0.00
130_I 28_V 0.81 0.08 0.00
119_N 23_R 0.81 0.08 0.00
136_G 322_V 0.80 0.08 0.00
297_N 474_T 0.80 0.08 0.00
201_V 332_V 0.80 0.08 0.00
105_Y 361_I 0.80 0.08 0.00
162_F 339_Y 0.80 0.08 0.00
151_F 13_L 0.80 0.08 0.00
264_G 339_Y 0.80 0.08 0.00
142_I 34_Q 0.80 0.08 0.00
138_L 54_Q 0.80 0.07 0.00
147_S 62_D 0.79 0.07 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)

WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.41 > 0.4) of paralogs.

ID Seq/Len Name Options I_Prob Status
7326 0.04 BmdB_BmdC_alignment_EvalueLowered Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132) Killed
7325 0.01 BmdB_BmdC_alignment_EvalueLowered Δgene:(1, 1) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed
7324 0.18 YUMMY_BmdB_BmdC_Take2 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7323 0.05 Yummy_BmdBA2Domain_BmdC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared

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