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OPENSEQ.org
cIV_A_40_cIII_cyt1_4_Pdenitr
Genes: A B A+B
Length: 538 263 763
Sequences: 3263 973 326
Seq/Len: 6.07 3.7 0.43
MirrorTree (Pazo et al. 2001) 0.17
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 0.01 0.00
2 0.00 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.01
100 0.02 0.01 0.06
∞ 0.06 0.01 0.41
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
405_V 77_G 1.24 0.33 0.00
486_F 200_G 1.20 0.31 0.00
273_I 237_F 1.12 0.26 0.00
435_M 63_G 1.06 0.23 0.00
155_S 129_A 1.04 0.21 0.00
277_V 130_R 1.03 0.21 0.00
477_A 52_Q 0.98 0.19 0.00
437_F 250_K 0.98 0.19 0.00
533_R 54_Y 0.97 0.18 0.00
359_W 214_A 0.97 0.18 0.00
146_V 216_L 0.97 0.18 0.00
405_V 208_M 0.96 0.18 0.00
278_I 163_G 0.95 0.17 0.00
172_V 219_T 0.94 0.17 0.00
425_P 230_V 0.94 0.17 0.00
482_A 236_I 0.92 0.16 0.00
184_I 240_V 0.92 0.16 0.00
212_A 105_R 0.90 0.15 0.00
127_A 151_P 0.90 0.15 0.00
337_I 230_V 0.90 0.15 0.00
48_Y 118_G 0.89 0.15 0.00
362_G 199_D 0.87 0.14 0.00
254_I 244_L 0.87 0.14 0.00
339_V 127_A 0.87 0.14 0.00
511_A 130_R 0.87 0.14 0.00
205_A 105_R 0.86 0.14 0.00
411_G 137_Y 0.86 0.14 0.00
198_L 83_D 0.86 0.14 0.00
377_L 241_L 0.85 0.14 0.00
502_N 244_L 0.85 0.14 0.00
313_T 243_A 0.84 0.13 0.00
236_G 193_D 0.84 0.13 0.00
277_V 95_T 0.83 0.13 0.00
362_G 209_A 0.83 0.13 0.00
442_L 93_D 0.83 0.13 0.00
483_S 82_E 0.82 0.12 0.00
131_A 254_Q 0.82 0.12 0.00
146_V 151_P 0.81 0.12 0.00
118_S 215_F 0.81 0.12 0.00
182_I 90_A 0.80 0.12 0.00
23_A 237_F 0.80 0.12 0.00
121_M 241_L 0.80 0.12 0.00
243_A 194_Q 0.80 0.12 0.00
170_V 241_L 0.80 0.12 0.00
378_S 90_A 0.79 0.12 0.00
69_H 118_G 0.79 0.12 0.00
411_G 53_V 0.78 0.11 0.00
198_L 63_G 0.78 0.11 0.00
504_P 195_V 0.78 0.11 0.00
172_V 69_L 0.78 0.11 0.00
75_I 63_G 0.78 0.11 0.00
83_M 213_A 0.78 0.11 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
3080 0.57 cIV_A_4_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3079 0.43 cIV_A_40_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3078 0.55 cIV_A_20_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3077 0.31 cIV_A_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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