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OPENSEQ.org
6Q21_D Ras GTPase GCP 1WER_ Ras GAP
Genes: A B A+B
Length: 171 334 478
Sequences: 7635 889 122
Seq/Len: 44.65 2.66 0.26
MirrorTree (Pazo et al. 2001) 0.22
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 0.11 0.02 0.02
2 0.12 0.03 0.03
5 0.14 0.03 0.06
10 0.16 0.03 0.12
20 0.18 0.04 0.24
100 0.23 0.04 0.74
∞ 0.26 0.07 1.14
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_D 154_P 1.23 0.23 0.00
55_I 294_D 1.18 0.21 0.00
142_I 187_V 1.13 0.19 0.00
125_V 228_A 1.12 0.18 0.00
89_S 223_S 1.09 0.17 0.00
112_V 72_T 1.09 0.17 0.00
48_G 247_I 1.08 0.17 0.00
6_L 193_C 1.05 0.16 0.00
15_G 154_P 1.04 0.15 0.00
109_V 83_T 1.03 0.15 0.00
8_V 149_A 1.00 0.14 0.00
125_V 194_P 0.98 0.14 0.00
16_K 217_L 0.97 0.14 0.00
91_E 82_S 0.93 0.12 0.00
125_V 195_A 0.93 0.12 0.00
6_L 183_V 0.93 0.12 0.00
44_V 165_Q 0.92 0.12 0.00
16_K 199_P 0.92 0.12 0.00
6_L 226_N 0.92 0.12 0.00
117_K 154_P 0.92 0.12 0.00
115_G 118_S 0.91 0.12 0.00
155_A 8_E 0.91 0.12 0.00
6_L 139_L 0.91 0.12 0.00
80_C 105_I 0.90 0.12 0.00
116_N 257_F 0.90 0.12 0.00
153_E 257_F 0.89 0.11 0.00
112_V 103_D 0.89 0.11 0.00
144_T 42_I 0.89 0.11 0.00
130_A 105_I 0.88 0.11 0.00
152_V 265_P 0.88 0.11 0.00
131_Q 74_L 0.88 0.11 0.00
126_E 8_E 0.88 0.11 0.00
113_L 170_H 0.88 0.11 0.00
151_G 289_C 0.88 0.11 0.00
136_S 296_L 0.87 0.11 0.00
157_Y 28_L 0.87 0.11 0.00
160_V 11_S 0.87 0.11 0.00
44_V 240_M 0.86 0.10 0.00
90_F 8_E 0.86 0.10 0.00
7_V 202_F 0.86 0.10 0.00
83_A 247_I 0.86 0.10 0.00
5_K 210_S 0.85 0.10 0.00
48_G 166_K 0.85 0.10 0.00
89_S 76_R 0.85 0.10 0.00
84_I 226_N 0.85 0.10 0.00
53_L 138_I 0.83 0.10 0.00
126_E 74_L 0.83 0.10 0.00
17_S 250_N 0.82 0.10 0.00
48_G 103_D 0.82 0.10 0.00
14_V 109_M 0.82 0.10 0.00
15_G 217_L 0.82 0.10 0.00
24_I 292_H 0.82 0.10 0.00
50_T 187_V 0.82 0.10 0.00
139_I 227_L 0.82 0.09 0.00
147_K 258_L 0.82 0.09 0.00
28_F 149_A 0.81 0.09 0.00
125_V 85_M 0.81 0.09 0.00
22_Q 234_G 0.81 0.09 0.00
15_G 199_P 0.81 0.09 0.00
89_S 260_E 0.81 0.09 0.00
132_D 133_T 0.80 0.09 0.00
64_Y 112_K 0.80 0.09 0.00
115_G 233_F 0.80 0.09 0.00
89_S 82_S 0.80 0.09 0.00
65_S 148_M 0.80 0.09 0.00
127_S 220_V 0.80 0.09 0.00
17_S 255_I 0.80 0.09 0.00
143_E 286_H 0.80 0.09 0.00
138_G 282_L 0.79 0.09 0.00
10_G 217_L 0.79 0.09 0.00
89_S 43_L 0.79 0.09 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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