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OPENSEQ.org
cI_B_10_cIII_cyt1_4_Pdenitr
Genes: A B A+B
Length: 175 263 405
Sequences: 1491 973 295
Seq/Len: 8.52 3.7 0.73
MirrorTree (Pazo et al. 2001) 0.15
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 0.01 0.01 0.00
2 0.01 0.01 0.00
5 0.02 0.01 0.00
10 0.02 0.01 0.01
20 0.03 0.01 0.01
100 0.04 0.01 0.06
∞ 0.10 0.01 0.67
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
168_R 214_A 1.69 0.80 0.04
114_I 256_I 1.10 0.35 0.01
114_I 130_R 1.05 0.32 0.01
144_I 230_V 1.00 0.28 0.01
61_Q 257_K 0.98 0.27 0.01
29_L 235_V 0.98 0.26 0.01
36_I 64_L 0.94 0.23 0.00
157_L 235_V 0.93 0.23 0.00
85_L 83_D 0.93 0.23 0.00
131_S 176_N 0.92 0.23 0.00
29_L 243_A 0.92 0.23 0.00
33_T 245_L 0.91 0.22 0.00
157_L 87_A 0.91 0.22 0.00
114_I 136_P 0.90 0.22 0.00
32_T 239_I 0.90 0.21 0.00
19_L 91_N 0.89 0.21 0.00
31_T 47_L 0.88 0.20 0.00
29_L 195_V 0.88 0.20 0.00
144_I 44_Q 0.88 0.20 0.00
46_H 88_Y 0.88 0.20 0.00
131_S 43_D 0.87 0.20 0.00
74_T 242_A 0.86 0.19 0.00
31_T 174_Y 0.86 0.19 0.00
72_F 163_G 0.85 0.19 0.00
157_L 208_M 0.85 0.19 0.00
93_T 232_F 0.85 0.18 0.00
93_T 241_L 0.84 0.18 0.00
157_L 84_Q 0.83 0.17 0.00
165_R 60_A 0.83 0.17 0.00
38_N 48_Q 0.83 0.17 0.00
162_Q 249_N 0.82 0.17 0.00
21_R 90_A 0.81 0.17 0.00
161_L 220_A 0.81 0.17 0.00
152_T 64_L 0.81 0.17 0.00
111_R 233_V 0.80 0.16 0.00
26_K 163_G 0.80 0.16 0.00
157_L 83_D 0.79 0.16 0.00
62_T 64_L 0.79 0.16 0.00
160_I 101_E 0.79 0.16 0.00
160_I 256_I 0.79 0.16 0.00
72_F 47_L 0.79 0.16 0.00
23_L 127_A 0.78 0.15 0.00
30_L 179_F 0.77 0.15 0.00
102_K 250_K 0.77 0.15 0.00
45_L 163_G 0.77 0.15 0.00
23_L 236_I 0.77 0.15 0.00
160_I 236_I 0.77 0.15 0.00
65_P 113_T 0.77 0.15 0.00
21_R 18_E 0.77 0.15 0.00
131_S 59_S 0.76 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
2999 0.73 cI_B_10_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
2998 0.75 cI_B_6_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
2997 0.74 cI_B_4_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
2996 0.77 cI_B_4_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
2830 0.75 cI_B_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
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