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OPENSEQ.org
cIp_1_4_cytb_4_human
Genes: A B A+B
Length: 455 378 800
Sequences: 3873 4516 726
Seq/Len: 8.51 11.95 0.91
MirrorTree (Pazo et al. 2001) 0.08
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.01
20 0.00 0.00 0.02
100 0.01 0.00 0.10
∞ 0.06 0.00 0.87
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
246_C 49_L 0.92 0.26 0.00
60_L 194_T 0.89 0.24 0.00
295_A 232_L 0.89 0.24 0.00
63_G 92_I 0.87 0.23 0.00
188_V 356_V 0.85 0.21 0.00
66_W 1_M 0.83 0.20 0.00
335_Q 156_I 0.83 0.20 0.00
160_L 162_Q 0.83 0.20 0.00
431_R 155_Y 0.83 0.20 0.00
318_I 172_S 0.82 0.20 0.00
407_S 233_L 0.81 0.19 0.00
435_P 188_I 0.81 0.19 0.00
318_I 213_S 0.78 0.18 0.00
302_W 318_R 0.78 0.18 0.00
66_W 307_L 0.78 0.17 0.00
169_E 292_L 0.78 0.17 0.00
435_P 52_A 0.78 0.17 0.00
287_L 103_Y 0.78 0.17 0.00
62_K 190_A 0.77 0.17 0.00
326_V 118_I 0.77 0.17 0.00
73_T 191_A 0.77 0.17 0.00
273_V 333_L 0.76 0.17 0.00
250_G 296_L 0.76 0.16 0.00
71_I 61_T 0.74 0.16 0.00
111_G 159_D 0.74 0.16 0.00
203_L 239_L 0.74 0.16 0.00
251_T 14_I 0.74 0.16 0.00
58_E 180_T 0.74 0.16 0.00
273_V 225_T 0.74 0.15 0.00
49_S 75_Y 0.73 0.15 0.00
70_E 334_I 0.73 0.15 0.00
345_V 352_Q 0.73 0.15 0.00
105_V 8_N 0.73 0.15 0.00
318_I 194_T 0.72 0.15 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
5863 0.82 cIp_1_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5862 0.91 cIp_1_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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