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OPENSEQ.org
cIp_1_40_cytb_40_human
Genes: A B A+B
Length: 455 378 803
Sequences: 3417 4493 655
Seq/Len: 7.51 11.89 0.82
MirrorTree (Pazo et al. 2001) 0.27
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 0.09
∞ 0.04 0.00 0.79
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
431_R 155_Y 1.22 0.48 0.00
169_E 292_L 1.03 0.32 0.00
207_I 66_I 0.99 0.29 0.00
335_Q 156_I 0.99 0.29 0.00
60_L 194_T 0.98 0.28 0.00
62_K 156_I 0.97 0.28 0.00
233_V 229_A 0.95 0.26 0.00
233_V 284_V 0.92 0.24 0.00
318_I 194_T 0.91 0.24 0.00
326_V 118_I 0.90 0.23 0.00
122_L 237_L 0.90 0.23 0.00
251_T 14_I 0.89 0.22 0.00
407_S 233_L 0.85 0.20 0.00
186_V 52_A 0.85 0.20 0.00
252_W 301_L 0.84 0.20 0.00
203_L 239_L 0.83 0.19 0.00
345_V 352_Q 0.83 0.19 0.00
238_T 370_S 0.81 0.18 0.00
401_D 47_T 0.81 0.18 0.00
95_K 292_L 0.80 0.17 0.00
238_T 350_I 0.79 0.17 0.00
318_I 172_S 0.79 0.17 0.00
245_I 178_F 0.79 0.17 0.00
436_E 4_M 0.78 0.16 0.00
291_I 98_I 0.78 0.16 0.00
171_G 296_L 0.77 0.16 0.00
183_D 197_L 0.77 0.16 0.00
291_I 303_M 0.77 0.16 0.00
129_L 5_R 0.77 0.16 0.00
149_I 148_N 0.77 0.16 0.00
324_E 354_A 0.76 0.16 0.00
246_C 49_L 0.76 0.16 0.00
435_P 188_I 0.76 0.15 0.00
396_R 170_V 0.76 0.15 0.00
345_V 4_M 0.76 0.15 0.00
68_L 233_L 0.76 0.15 0.00
43_R 284_V 0.76 0.15 0.00
45_K 350_I 0.76 0.15 0.00
65_D 212_T 0.76 0.15 0.00
141_G 334_I 0.76 0.15 0.00
59_I 10_L 0.75 0.15 0.00
188_V 194_T 0.75 0.15 0.00
65_D 330_A 0.75 0.15 0.00
140_M 115_I 0.75 0.15 0.00
401_D 4_M 0.74 0.15 0.00
60_L 58_D 0.74 0.15 0.00
264_T 178_F 0.74 0.14 0.00
62_K 190_A 0.74 0.14 0.00
58_E 180_T 0.74 0.14 0.00
181_G 240_M 0.73 0.14 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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