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OPENSEQ.org
UMUC_SALTY - UMUD_SALTY HHBlits
Genes: A B A+B
Length: 422 139 525
Sequences: 6719 4925 1003
Seq/Len: 15.92 35.43 1.91
MirrorTree (Pazo et al. 2001) 0.71
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.04 1.37
2 0.02 0.04 1.59
5 0.02 0.04 1.64
10 0.03 0.04 1.71
20 0.03 0.05 1.79
100 0.04 0.07 2.23
∞ 0.13 0.14 4.12
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
415_Y 38_I 3.81 1.00 1.00
132_H 76_S 1.85 0.98 0.95
78_A 34_I 1.75 0.96 0.93
421_V 54_V 1.66 0.95 0.90
130_R 50_S 1.63 0.94 0.89
129_K 79_N 1.55 0.92 0.86
74_Y 33_Y 1.45 0.88 0.80
419_L 54_V 1.41 0.86 0.77
140_A 56_A 1.30 0.80 0.68
100_I 30_A 1.14 0.66 0.52
415_Y 53_F 1.13 0.65 0.50
404_R 33_Y 1.10 0.62 0.47
420_R 57_S 1.08 0.59 0.44
187_V 91_E 1.07 0.59 0.43
140_A 36_Q 1.02 0.53 0.37
131_T 52_Y 1.01 0.53 0.37
75_E 33_Y 1.01 0.52 0.36
419_L 94_F 0.97 0.48 0.32
415_Y 71_L 0.95 0.46 0.30
128_L 87_I 0.94 0.45 0.29
79_D 37_R 0.93 0.43 0.28
130_R 47_H 0.91 0.41 0.25
100_I 28_S 0.89 0.39 0.24
87_T 50_S 0.89 0.39 0.23
417_D 22_V 0.88 0.38 0.23
72_S 33_Y 0.87 0.37 0.22
182_E 127_I 0.87 0.37 0.22
422_K 127_I 0.86 0.36 0.21
281_E 84_D 0.85 0.35 0.20
84_V 119_V 0.84 0.34 0.19
320_R 98_R 0.82 0.32 0.18
277_K 31_A 0.81 0.32 0.17
288_I 131_V 0.81 0.32 0.17
75_E 35_E 0.81 0.31 0.17
418_L 94_F 0.81 0.31 0.17
129_K 78_R 0.81 0.31 0.17
343_A 119_V 0.80 0.30 0.17
97_I 59_D 0.80 0.30 0.16
418_L 59_D 0.80 0.30 0.16
418_L 53_F 0.80 0.30 0.16
256_R 64_A 0.80 0.30 0.16
105_C 45_V 0.80 0.30 0.16
345_V 63_E 0.80 0.30 0.16
131_T 71_L 0.79 0.29 0.16
74_Y 30_A 0.79 0.29 0.15
292_V 104_T 0.78 0.28 0.15
142_T 135_I 0.78 0.28 0.15
90_E 90_I 0.78 0.28 0.14
127_V 62_I 0.78 0.28 0.14
68_V 127_I 0.78 0.28 0.14
287_F 136_K 0.77 0.28 0.14
401_A 98_R 0.77 0.28 0.14
133_L 124_T 0.76 0.27 0.14
418_L 23_P 0.76 0.27 0.14
127_V 119_V 0.76 0.27 0.13
80_M 76_S 0.76 0.26 0.13
416_S 80_A 0.76 0.26 0.13
270_Y 33_Y 0.75 0.26 0.13
419_L 74_V 0.75 0.26 0.13
250_S 33_Y 0.75 0.26 0.13
321_D 121_S 0.75 0.25 0.13
236_E 122_E 0.75 0.25 0.13
97_I 112_G 0.75 0.25 0.12
132_H 128_F 0.74 0.25 0.12
257_V 54_V 0.74 0.25 0.12
342_K 39_D 0.74 0.25 0.12
407_L 56_A 0.74 0.25 0.12
420_R 56_A 0.73 0.24 0.12
393_G 136_K 0.73 0.24 0.11
118_D 45_V 0.73 0.24 0.11
402_M 123_D 0.72 0.23 0.11
385_G 69_G 0.72 0.23 0.11
64_R 85_I 0.72 0.23 0.11
233_P 87_I 0.71 0.22 0.10
100_I 29_P 0.71 0.22 0.10
194_K 56_A 0.71 0.22 0.10
380_L 54_V 0.71 0.22 0.10
407_L 72_L 0.70 0.22 0.10
123_I 118_P 0.70 0.22 0.10
74_Y 28_S 0.70 0.22 0.10
360_L 97_K 0.70 0.22 0.10
108_T 68_D 0.70 0.22 0.10
372_K 34_I 0.69 0.21 0.10
377_L 104_T 0.69 0.21 0.10
271_A 14_P 0.69 0.21 0.10
272_A 128_F 0.69 0.21 0.10
124_R 96_V 0.69 0.21 0.10
415_Y 94_F 0.69 0.21 0.09
192_S 85_I 0.69 0.20 0.09
125_A 55_K 0.68 0.20 0.09
176_L 80_A 0.68 0.20 0.09
91_M 92_G 0.68 0.20 0.09
383_K 98_R 0.67 0.20 0.09
272_A 38_I 0.67 0.20 0.09
406_M 19_S 0.67 0.20 0.08
133_L 119_V 0.67 0.19 0.08
401_A 9_L 0.67 0.19 0.08
89_E 87_I 0.67 0.19 0.08
296_P 72_L 0.67 0.19 0.08
224_R 125_L 0.66 0.19 0.08
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
7046 3.78 UMUC_SALTY - UMUD_SALTY Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done - Shared
6931 1.91 UMUC_SALTY - UMUD_SALTY HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
6890 4.97 UMUC_SALTY - UMUD_SALTY Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done - Shared
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