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OPENSEQ.org
cI_D_2_cIII_cyt1_2_Pdenitr
Genes: A B A+B
Length: 412 263 645
Sequences: 3478 1022 332
Seq/Len: 8.44 3.89 0.51
MirrorTree (Pazo et al. 2001) 0.16
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 0.03 0.01 0.00
10 0.03 0.01 0.01
20 0.05 0.01 0.01
100 0.06 0.02 0.06
∞ 0.13 0.02 0.49
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
66_G 216_L 1.91 0.82 0.10
286_E 203_A 1.17 0.32 0.01
205_L 105_R 1.14 0.30 0.01
127_I 230_V 1.14 0.30 0.01
138_A 196_T 1.10 0.28 0.01
361_V 206_D 1.08 0.27 0.01
139_M 254_Q 1.05 0.24 0.01
121_Y 101_E 1.04 0.24 0.01
335_T 212_V 1.04 0.24 0.01
354_G 58_C 1.01 0.22 0.01
354_G 61_C 1.01 0.22 0.01
354_G 62_H 1.01 0.22 0.01
279_C 249_N 0.99 0.21 0.01
379_A 207_Q 0.98 0.21 0.01
400_I 83_D 0.98 0.21 0.01
307_L 126_M 0.96 0.20 0.01
25_R 240_V 0.96 0.20 0.01
226_T 234_S 0.96 0.20 0.01
410_V 63_G 0.94 0.19 0.01
296_Q 220_A 0.93 0.18 0.01
167_A 206_D 0.93 0.18 0.01
101_A 207_Q 0.92 0.18 0.01
405_I 247_L 0.92 0.18 0.01
189_D 236_I 0.92 0.18 0.01
53_V 95_T 0.92 0.18 0.01
49_D 130_R 0.91 0.17 0.01
286_E 255_P 0.91 0.17 0.01
202_V 46_Q 0.91 0.17 0.00
54_E 202_P 0.90 0.17 0.00
177_G 58_C 0.90 0.17 0.00
177_G 61_C 0.90 0.17 0.00
177_G 62_H 0.90 0.17 0.00
339_K 76_G 0.89 0.17 0.00
109_V 9_T 0.89 0.17 0.00
393_L 215_F 0.89 0.17 0.00
402_T 232_F 0.89 0.16 0.00
265_I 87_A 0.88 0.16 0.00
354_G 50_G 0.88 0.16 0.00
108_T 29_E 0.88 0.16 0.00
360_L 69_L 0.88 0.16 0.00
219_L 249_N 0.88 0.16 0.00
98_W 154_I 0.88 0.16 0.00
80_L 257_K 0.87 0.16 0.00
260_E 240_V 0.86 0.15 0.00
345_V 214_A 0.86 0.15 0.00
29_I 237_F 0.86 0.15 0.00
53_V 119_M 0.86 0.15 0.00
362_A 209_A 0.85 0.15 0.00
150_G 47_L 0.85 0.15 0.00
90_A 245_L 0.85 0.15 0.00
338_F 46_Q 0.85 0.15 0.00
48_L 163_G 0.85 0.15 0.00
286_E 164_E 0.85 0.15 0.00
383_S 230_V 0.84 0.15 0.00
313_T 230_V 0.84 0.15 0.00
350_E 215_F 0.84 0.15 0.00
389_R 156_A 0.84 0.14 0.00
264_Q 243_A 0.84 0.14 0.00
281_M 240_V 0.84 0.14 0.00
139_M 67_V 0.83 0.14 0.00
65_R 58_C 0.83 0.14 0.00
65_R 61_C 0.83 0.14 0.00
65_R 62_H 0.83 0.14 0.00
178_G 58_C 0.83 0.14 0.00
178_G 61_C 0.83 0.14 0.00
178_G 62_H 0.83 0.14 0.00
165_C 154_I 0.83 0.14 0.00
372_K 214_A 0.82 0.14 0.00
120_L 23_H 0.81 0.13 0.00
134_V 108_T 0.81 0.13 0.00
201_L 237_F 0.81 0.13 0.00
291_M 151_P 0.80 0.13 0.00
46_L 151_P 0.80 0.13 0.00
410_V 193_D 0.80 0.13 0.00
205_L 84_Q 0.80 0.13 0.00
29_I 246_Y 0.80 0.13 0.00
351_A 219_T 0.80 0.13 0.00
338_F 44_Q 0.80 0.13 0.00
80_L 167_E 0.80 0.13 0.00
232_D 96_D 0.79 0.13 0.00
286_E 166_K 0.79 0.13 0.00
267_V 101_E 0.79 0.13 0.00
129_N 257_K 0.79 0.13 0.00
242_G 228_K 0.79 0.13 0.00
232_D 242_A 0.79 0.13 0.00
393_L 125_L 0.78 0.12 0.00
56_A 234_S 0.78 0.12 0.00
112_R 213_A 0.78 0.12 0.00
176_P 107_P 0.78 0.12 0.00
129_N 143_Q 0.78 0.12 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
3012 0.51 cI_D_2_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
3010 0.5 cI_D_2_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3009 0.52 cI_D_4_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
2809 0.5 cI_D_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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