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OPENSEQ.org
cI_B_4_cIII_cyt1_2_Pdenitr
Genes: A B A+B
Length: 175 263 409
Sequences: 1610 1022 315
Seq/Len: 9.2 3.89 0.77
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 0.02 0.07
∞ 0.10 0.02 0.72
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 1.67 0.81 0.04
85_L 83_D 1.51 0.70 0.03
144_I 26_A 1.15 0.40 0.01
114_I 256_I 1.11 0.37 0.01
144_I 230_V 1.07 0.34 0.01
157_L 87_A 1.07 0.34 0.01
160_I 256_I 1.07 0.34 0.01
111_R 105_R 1.06 0.33 0.01
39_W 241_L 1.02 0.30 0.01
22_E 237_F 0.97 0.27 0.01
160_I 86_R 0.97 0.26 0.01
93_T 241_L 0.95 0.25 0.01
29_L 235_V 0.94 0.25 0.01
60_M 250_K 0.94 0.25 0.01
144_I 229_Q 0.94 0.24 0.01
61_Q 257_K 0.93 0.24 0.01
114_I 130_R 0.92 0.23 0.00
65_P 109_D 0.92 0.23 0.00
33_T 245_L 0.92 0.23 0.00
29_L 243_A 0.91 0.23 0.00
162_Q 249_N 0.90 0.22 0.00
46_H 88_Y 0.90 0.22 0.00
109_E 105_R 0.89 0.21 0.00
131_S 43_D 0.88 0.21 0.00
93_T 228_K 0.87 0.20 0.00
93_T 232_F 0.87 0.20 0.00
31_T 174_Y 0.87 0.20 0.00
131_S 176_N 0.87 0.20 0.00
45_L 163_G 0.86 0.20 0.00
75_A 240_V 0.85 0.19 0.00
157_L 235_V 0.84 0.19 0.00
65_P 112_P 0.83 0.18 0.00
35_D 51_L 0.82 0.18 0.00
157_L 208_M 0.80 0.17 0.00
25_D 249_N 0.80 0.17 0.00
157_L 84_Q 0.80 0.17 0.00
62_T 248_T 0.79 0.16 0.00
45_L 162_D 0.79 0.16 0.00
33_T 241_L 0.79 0.16 0.00
35_D 54_Y 0.79 0.16 0.00
37_I 166_K 0.79 0.16 0.00
23_L 127_A 0.79 0.16 0.00
111_R 233_V 0.78 0.16 0.00
72_F 47_L 0.78 0.16 0.00
45_L 118_G 0.78 0.16 0.00
114_I 136_P 0.78 0.16 0.00
29_L 82_E 0.78 0.16 0.00
76_P 223_K 0.77 0.15 0.00
139_I 144_L 0.76 0.15 0.00
72_F 163_G 0.76 0.15 0.00
65_P 113_T 0.76 0.15 0.00
64_M 47_L 0.76 0.15 0.00
71_R 255_P 0.75 0.15 0.00
38_N 48_Q 0.75 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
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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