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OPENSEQ.org
Tcb2 Fen1
Genes: A B A+B
Length: 218 629 810
Sequences: 701 12135 76
Seq/Len: 3.22 19.29 0.09
MirrorTree (Pazo et al. 2001) 0.36
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 0.02 0.06 0.02
2 0.03 0.06 0.02
5 0.03 0.08 0.03
10 0.03 0.09 0.05
20 0.03 0.09 0.09
100 0.04 0.12 0.26
∞ 0.06 0.17 0.47
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
189_G 200_E 1.31 0.14 0.00
44_I 269_E 1.24 0.12 0.00
52_M 87_C 1.15 0.11 0.00
172_T 98_L 1.12 0.10 0.00
192_S 219_K 1.08 0.09 0.00
174_E 459_L 1.04 0.09 0.00
149_Q 130_C 1.02 0.09 0.00
84_G 130_C 1.02 0.08 0.00
191_V 574_L 1.00 0.08 0.00
49_C 314_E 1.00 0.08 0.00
193_L 560_L 0.99 0.08 0.00
146_G 424_L 0.99 0.08 0.00
176_V 552_V 0.99 0.08 0.00
194_E 468_Q 0.99 0.08 0.00
197_E 481_L 0.98 0.08 0.00
192_S 569_T 0.97 0.08 0.00
165_G 279_I 0.94 0.07 0.00
52_M 459_L 0.93 0.07 0.00
81_N 504_K 0.92 0.07 0.00
148_L 150_D 0.91 0.07 0.00
192_S 132_N 0.90 0.07 0.00
189_G 566_E 0.90 0.07 0.00
179_W 552_V 0.90 0.07 0.00
146_G 123_I 0.89 0.07 0.00
145_S 606_R 0.89 0.07 0.00
179_W 269_E 0.89 0.07 0.00
186_N 593_M 0.88 0.07 0.00
149_Q 234_I 0.88 0.07 0.00
189_G 560_L 0.88 0.07 0.00
146_G 278_E 0.88 0.07 0.00
187_S 589_Q 0.87 0.06 0.00
141_D 424_L 0.86 0.06 0.00
165_G 205_E 0.86 0.06 0.00
49_C 487_H 0.86 0.06 0.00
8_L 77_L 0.86 0.06 0.00
5_S 578_L 0.86 0.06 0.00
186_N 546_L 0.86 0.06 0.00
52_M 437_E 0.85 0.06 0.00
157_L 560_L 0.85 0.06 0.00
189_G 600_A 0.85 0.06 0.00
189_G 621_R 0.85 0.06 0.00
141_D 327_L 0.85 0.06 0.00
172_T 249_A 0.85 0.06 0.00
153_I 444_I 0.84 0.06 0.00
52_M 529_W 0.84 0.06 0.00
174_E 469_Q 0.83 0.06 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
2641 0.09 Tcb2 Fen1 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2640 0 Tcb2 Fen1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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