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OPENSEQ.org
6Q21_D Ras GTPase GCP 1WER_ Ras GAP
Genes: A B A+B
Length: 171 334 485
Sequences: 54056 1029 284
Seq/Len: 316.12 3.08 0.59
MirrorTree (Pazo et al. 2001) 0.12
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 0.15 0.02 0.04
2 0.16 0.03 0.06
5 0.19 0.03 0.16
10 0.21 0.04 0.28
20 0.25 0.04 0.56
100 0.31 0.05 1.36
∞ 0.33 0.08 1.65
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
55_I 109_M 1.18 0.36 0.00
48_G 103_D 1.08 0.29 0.00
52_L 220_V 1.01 0.25 0.00
131_Q 220_V 1.01 0.25 0.00
137_Y 43_L 1.01 0.25 0.00
93_I 258_L 0.99 0.24 0.00
15_G 154_P 0.98 0.23 0.00
35_T 220_V 0.97 0.22 0.00
80_C 15_E 0.96 0.21 0.00
147_K 196_I 0.95 0.21 0.00
9_V 198_N 0.93 0.20 0.00
100_I 65_I 0.92 0.20 0.00
78_F 103_D 0.92 0.19 0.00
114_V 105_I 0.91 0.19 0.00
48_G 247_I 0.89 0.18 0.00
46_I 295_E 0.89 0.18 0.00
53_L 138_I 0.89 0.18 0.00
119_D 154_P 0.89 0.18 0.00
83_A 247_I 0.89 0.18 0.00
84_I 151_E 0.88 0.18 0.00
79_L 178_M 0.88 0.18 0.00
100_I 224_V 0.88 0.18 0.00
78_F 182_V 0.88 0.18 0.00
111_M 227_L 0.88 0.17 0.00
6_L 85_M 0.87 0.17 0.00
79_L 28_L 0.87 0.17 0.00
48_G 182_V 0.86 0.17 0.00
17_S 214_A 0.86 0.17 0.00
91_E 45_R 0.86 0.17 0.00
26_N 148_M 0.85 0.16 0.00
114_V 71_A 0.84 0.16 0.00
90_F 268_P 0.84 0.16 0.00
18_A 114_S 0.84 0.16 0.00
6_L 113_Q 0.83 0.15 0.00
6_L 6_P 0.82 0.15 0.00
53_L 261_L 0.82 0.15 0.00
46_I 213_A 0.81 0.15 0.00
132_D 68_E 0.81 0.14 0.00
122_A 61_N 0.81 0.14 0.00
17_S 295_E 0.80 0.14 0.00
154_D 108_I 0.80 0.14 0.00
124_T 101_L 0.80 0.14 0.00
78_F 220_V 0.80 0.14 0.00
44_V 165_Q 0.79 0.14 0.00
6_L 183_V 0.79 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
4129 0.26 6Q21_D Ras GTPase GCP 1WER_ Ras GAP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4084 0.59 6Q21_D Ras GTPase GCP 1WER_ Ras GAP Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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