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OPENSEQ.org
cI_A_10_cIII_cyt1_6_Pdenitr
Genes: A B A+B
Length: 147 263 367
Sequences: 3938 954 289
Seq/Len: 26.79 3.63 0.79
MirrorTree (Pazo et al. 2001) 0.35
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 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.01 0.01 0.01
100 0.01 0.01 0.05
∞ 0.02 0.01 0.70
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
119_R 241_L 1.68 0.81 0.05
126_T 242_A 1.56 0.74 0.04
95_S 242_A 1.51 0.71 0.03
95_S 73_A 1.47 0.68 0.03
10_I 39_F 1.42 0.64 0.02
115_V 105_R 1.32 0.56 0.02
22_V 202_P 1.29 0.53 0.02
72_A 29_E 1.26 0.51 0.02
82_A 251_K 1.21 0.46 0.01
77_I 154_I 1.19 0.44 0.01
104_A 94_I 1.17 0.43 0.01
38_G 245_L 1.15 0.41 0.01
112_A 246_Y 1.10 0.37 0.01
114_L 96_D 1.06 0.34 0.01
36_F 141_L 1.06 0.34 0.01
102_E 91_N 1.05 0.33 0.01
71_V 224_M 1.04 0.32 0.01
16_F 104_P 1.02 0.31 0.01
32_V 214_A 1.02 0.31 0.01
95_S 59_S 1.02 0.30 0.01
124_D 82_E 1.01 0.30 0.01
30_M 124_S 1.01 0.30 0.01
112_A 93_D 1.00 0.29 0.01
117_L 96_D 0.99 0.29 0.01
112_A 20_G 0.98 0.28 0.01
36_F 193_D 0.97 0.27 0.01
21_I 209_A 0.95 0.26 0.01
94_E 82_E 0.95 0.26 0.01
109_V 245_L 0.95 0.26 0.01
124_D 236_I 0.95 0.26 0.01
99_G 44_Q 0.94 0.25 0.01
47_N 28_I 0.94 0.25 0.01
94_E 41_K 0.94 0.25 0.01
21_I 54_Y 0.92 0.24 0.01
20_L 52_Q 0.92 0.24 0.01
112_A 215_F 0.92 0.24 0.01
40_R 59_S 0.92 0.24 0.01
72_A 241_L 0.92 0.23 0.01
108_F 87_A 0.91 0.23 0.01
91_S 249_N 0.90 0.23 0.01
103_A 246_Y 0.89 0.22 0.01
77_I 73_A 0.89 0.22 0.01
98_V 249_N 0.89 0.22 0.01
92_I 88_Y 0.89 0.22 0.01
24_I 224_M 0.89 0.22 0.01
92_I 133_F 0.88 0.21 0.01
109_V 124_S 0.88 0.21 0.00
16_F 229_Q 0.88 0.21 0.00
8_E 29_E 0.87 0.21 0.00
92_I 215_F 0.87 0.21 0.00
29_L 38_P 0.87 0.21 0.00
60_A 239_I 0.87 0.21 0.00
112_A 97_P 0.87 0.21 0.00
33_G 131_A 0.87 0.21 0.00
40_R 216_L 0.86 0.20 0.00
35_W 33_F 0.86 0.20 0.00
20_L 201_T 0.86 0.20 0.00
18_I 177_A 0.86 0.20 0.00
57_V 47_L 0.85 0.20 0.00
60_A 63_G 0.85 0.20 0.00
124_D 257_K 0.85 0.20 0.00
14_W 129_A 0.85 0.20 0.00
23_A 241_L 0.85 0.20 0.00
68_F 100_E 0.85 0.19 0.00
72_A 12_P 0.84 0.19 0.00
22_V 155_H 0.84 0.19 0.00
99_G 220_A 0.84 0.19 0.00
100_F 88_Y 0.83 0.19 0.00
98_V 91_N 0.83 0.18 0.00
25_G 17_Q 0.82 0.18 0.00
95_S 232_F 0.82 0.18 0.00
8_E 17_Q 0.82 0.18 0.00
82_A 162_D 0.82 0.18 0.00
107_I 250_K 0.82 0.18 0.00
45_S 228_K 0.82 0.18 0.00
111_L 71_T 0.82 0.18 0.00
38_G 216_L 0.82 0.18 0.00
16_F 47_L 0.81 0.18 0.00
72_A 14_G 0.81 0.17 0.00
38_G 250_K 0.81 0.17 0.00
95_S 16_A 0.81 0.17 0.00
67_K 237_F 0.81 0.17 0.00
22_V 240_V 0.80 0.17 0.00
18_I 246_Y 0.80 0.17 0.00
124_D 218_W 0.80 0.17 0.00
124_D 131_A 0.80 0.17 0.00
112_A 108_T 0.79 0.17 0.00
60_A 88_Y 0.79 0.17 0.00
95_S 116_G 0.79 0.16 0.00
28_C 81_P 0.79 0.16 0.00
14_W 241_L 0.79 0.16 0.00
115_V 29_E 0.79 0.16 0.00
85_L 72_L 0.79 0.16 0.00
14_W 177_A 0.79 0.16 0.00
103_A 135_G 0.78 0.16 0.00
95_S 18_E 0.78 0.16 0.00
98_V 243_A 0.78 0.16 0.00
98_V 216_L 0.78 0.16 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
2960 0.79 cI_A_10_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2959 0.79 cI_A_10_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
2958 0.52 cI_A_10_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2957 0.79 cI_A_20_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2956 0.79 cI_A_10_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
2425 0.77 cI_E_cIII_cyt1_4 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.22 Done - Shared
2419 0.76 cI_E_cIII_cyt1_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.16 Done - Shared
2418 0.74 cI_E_cIII_cyt1_10 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.34 Done - Shared
2292 0.47 cI_E_cIII_cyt1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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