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OPENSEQ.org
cI_D_4_cIII_cyt1_2_Pdenitr
Genes: A B A+B
Length: 412 263 645
Sequences: 3488 1022 333
Seq/Len: 8.47 3.89 0.52
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 0.04 0.01 0.01
20 0.05 0.01 0.01
100 0.06 0.02 0.07
∞ 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 1.89 0.82 0.08
127_I 230_V 1.22 0.36 0.01
286_E 203_A 1.14 0.30 0.01
361_V 206_D 1.14 0.30 0.01
360_L 69_L 1.10 0.28 0.01
121_Y 101_E 1.08 0.27 0.01
205_L 105_R 1.07 0.26 0.01
139_M 254_Q 1.04 0.25 0.01
219_L 249_N 1.04 0.24 0.01
109_V 9_T 1.02 0.23 0.01
177_G 58_C 0.99 0.21 0.01
177_G 61_C 0.99 0.21 0.01
177_G 62_H 0.99 0.21 0.01
354_G 58_C 0.99 0.21 0.01
354_G 61_C 0.99 0.21 0.01
354_G 62_H 0.99 0.21 0.01
53_V 119_M 0.98 0.21 0.01
379_A 207_Q 0.97 0.20 0.01
400_I 83_D 0.96 0.20 0.01
167_A 206_D 0.95 0.20 0.01
189_D 236_I 0.95 0.20 0.01
313_T 230_V 0.94 0.19 0.00
405_I 247_L 0.93 0.18 0.00
101_A 207_Q 0.93 0.18 0.00
53_V 95_T 0.93 0.18 0.00
345_V 214_A 0.93 0.18 0.00
232_D 96_D 0.92 0.18 0.00
410_V 63_G 0.92 0.18 0.00
335_T 212_V 0.92 0.18 0.00
203_D 256_I 0.91 0.18 0.00
25_R 240_V 0.91 0.18 0.00
48_L 163_G 0.91 0.17 0.00
281_M 240_V 0.90 0.17 0.00
139_M 67_V 0.90 0.17 0.00
29_I 237_F 0.89 0.17 0.00
260_E 240_V 0.89 0.17 0.00
177_G 50_G 0.87 0.16 0.00
354_G 50_G 0.87 0.16 0.00
362_A 209_A 0.87 0.16 0.00
393_L 215_F 0.87 0.16 0.00
202_V 46_Q 0.87 0.16 0.00
261_F 250_K 0.86 0.16 0.00
165_C 23_H 0.86 0.16 0.00
389_R 101_E 0.86 0.16 0.00
49_D 130_R 0.86 0.16 0.00
279_C 249_N 0.86 0.16 0.00
150_G 47_L 0.85 0.15 0.00
90_A 245_L 0.85 0.15 0.00
383_S 230_V 0.85 0.15 0.00
402_T 212_V 0.84 0.15 0.00
286_E 255_P 0.84 0.15 0.00
54_E 202_P 0.83 0.14 0.00
289_K 229_Q 0.83 0.14 0.00
229_D 27_H 0.83 0.14 0.00
228_A 101_E 0.83 0.14 0.00
80_L 257_K 0.83 0.14 0.00
389_R 156_A 0.83 0.14 0.00
232_D 242_A 0.83 0.14 0.00
232_D 245_L 0.83 0.14 0.00
286_E 149_G 0.83 0.14 0.00
108_T 29_E 0.83 0.14 0.00
204_D 37_G 0.82 0.14 0.00
178_G 58_C 0.82 0.14 0.00
178_G 61_C 0.82 0.14 0.00
178_G 62_H 0.82 0.14 0.00
191_I 44_Q 0.82 0.14 0.00
65_R 58_C 0.81 0.14 0.00
65_R 61_C 0.81 0.14 0.00
65_R 62_H 0.81 0.14 0.00
338_F 46_Q 0.81 0.14 0.00
350_E 215_F 0.81 0.14 0.00
29_I 246_Y 0.81 0.14 0.00
281_M 232_F 0.81 0.14 0.00
246_A 60_A 0.81 0.13 0.00
176_P 107_P 0.80 0.13 0.00
251_R 68_P 0.80 0.13 0.00
402_T 232_F 0.80 0.13 0.00
372_K 214_A 0.80 0.13 0.00
228_A 17_Q 0.80 0.13 0.00
21_E 60_A 0.80 0.13 0.00
183_L 22_S 0.80 0.13 0.00
223_G 149_G 0.80 0.13 0.00
410_V 193_D 0.80 0.13 0.00
267_V 101_E 0.79 0.13 0.00
98_W 154_I 0.79 0.13 0.00
246_A 84_Q 0.79 0.13 0.00
129_N 257_K 0.79 0.13 0.00
201_L 237_F 0.79 0.13 0.00
180_H 54_Y 0.78 0.13 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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