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OPENSEQ.org
cI_K_10_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 101 263 347
Sequences: 4172 954 352
Seq/Len: 41.31 3.63 1.01
MirrorTree (Pazo et al. 2001) 0.13
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 0.02
100 0.03 0.01 0.12
∞ 0.07 0.01 0.97
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
20_F 63_G 1.43 0.72 0.01
88_R 214_A 1.27 0.59 0.01
19_I 239_I 1.14 0.47 0.00
90_T 137_Y 1.10 0.43 0.00
30_I 88_Y 1.03 0.37 0.00
42_A 82_E 1.03 0.36 0.00
13_I 85_V 1.03 0.36 0.00
14_L 245_L 0.97 0.32 0.00
1_M 49_R 0.94 0.29 0.00
11_G 205_V 0.92 0.28 0.00
35_S 236_I 0.91 0.27 0.00
90_T 221_E 0.90 0.27 0.00
94_E 81_P 0.90 0.26 0.00
55_G 52_Q 0.90 0.26 0.00
17_T 154_I 0.89 0.26 0.00
24_V 100_E 0.88 0.25 0.00
14_L 141_L 0.87 0.24 0.00
70_A 212_V 0.85 0.23 0.00
35_S 135_G 0.85 0.23 0.00
89_G 181_G 0.85 0.23 0.00
90_T 33_F 0.84 0.22 0.00
42_A 212_V 0.82 0.21 0.00
57_L 108_T 0.81 0.20 0.00
78_L 227_R 0.80 0.20 0.00
29_V 124_S 0.79 0.19 0.00
5_T 240_V 0.79 0.19 0.00
90_T 182_N 0.79 0.19 0.00
61_V 216_L 0.79 0.19 0.00
19_I 29_E 0.79 0.19 0.00
12_A 91_N 0.78 0.19 0.00
8_L 240_V 0.78 0.18 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
2919 0 cI_K_60_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) Killed - Shared
2914 0.67 cI_K_40_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.80 Done - Shared
2913 1.01 cI_K_10_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2912 0.53 cI_K_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2911 0.82 cI_K_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
2910 0.81 cI_K_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
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