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OPENSEQ.org
rasgap_ph_2
Genes: A B A+B
Length: 195 102 291
Sequences: 1081 11118 101
Seq/Len: 5.54 109 0.35
MirrorTree (Pazo et al. 2001) 0.35
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 0.03 0.06 0.04
2 0.04 0.07 0.05
5 0.04 0.08 0.10
10 0.04 0.09 0.22
20 0.04 0.10 0.34
100 0.05 0.17 0.95
∞ 0.08 0.22 1.46
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
74_I 80_L 1.61 0.53 0.00
71_I 73_V 1.23 0.28 0.00
87_K 85_N 1.20 0.27 0.00
162_I 87_C 1.20 0.27 0.00
114_E 51_I 1.19 0.26 0.00
183_L 82_I 1.17 0.25 0.00
22_F 23_F 1.15 0.24 0.00
181_R 80_L 1.14 0.23 0.00
160_P 93_W 1.14 0.23 0.00
179_T 86_N 1.14 0.23 0.00
114_E 11_R 1.12 0.22 0.00
48_S 41_K 1.10 0.22 0.00
187_S 29_R 1.10 0.21 0.00
74_I 33_H 1.09 0.21 0.00
123_M 94_I 1.08 0.20 0.00
151_S 49_I 1.07 0.20 0.00
78_H 27_W 1.07 0.20 0.00
93_N 60_L 1.07 0.20 0.00
52_D 23_F 1.06 0.20 0.00
31_V 70_M 1.06 0.20 0.00
54_T 83_Q 1.05 0.20 0.00
120_P 93_W 1.05 0.19 0.00
187_S 6_G 1.04 0.19 0.00
94_L 39_K 1.01 0.18 0.00
30_E 35_F 1.01 0.17 0.00
164_S 89_E 1.00 0.17 0.00
4_E 80_L 0.99 0.17 0.00
42_R 93_W 0.99 0.17 0.00
109_F 4_K 0.97 0.16 0.00
15_H 8_M 0.96 0.16 0.00
39_T 49_I 0.96 0.16 0.00
63_L 30_L 0.96 0.15 0.00
74_I 73_V 0.95 0.15 0.00
169_Q 11_R 0.95 0.15 0.00
42_R 45_P 0.92 0.14 0.00
162_I 32_N 0.91 0.14 0.00
98_M 28_F 0.91 0.14 0.00
70_A 49_I 0.90 0.14 0.00
66_T 80_L 0.90 0.14 0.00
95_E 29_R 0.89 0.13 0.00
147_T 82_I 0.89 0.13 0.00
30_E 77_E 0.88 0.13 0.00
113_T 24_K 0.88 0.13 0.00
170_L 73_V 0.88 0.13 0.00
34_T 78_R 0.86 0.12 0.00
77_S 71_F 0.86 0.12 0.00
65_V 79_A 0.86 0.12 0.00
127_F 86_N 0.85 0.12 0.00
147_T 47_Y 0.85 0.12 0.00
180_S 56_A 0.85 0.12 0.00
48_S 11_R 0.85 0.12 0.00
195_S 95_D 0.84 0.12 0.00
24_S 25_K 0.83 0.12 0.00
45_S 93_W 0.83 0.12 0.00
41_F 57_V 0.83 0.12 0.00
5_A 84_A 0.83 0.11 0.00
110_H 58_E 0.83 0.11 0.00
114_E 79_A 0.83 0.11 0.00
34_T 10_K 0.83 0.11 0.00
67_L 76_P 0.83 0.11 0.00
146_Y 26_R 0.82 0.11 0.00
78_H 49_I 0.82 0.11 0.00
60_M 5_E 0.82 0.11 0.00
194_G 42_G 0.82 0.11 0.00
158_F 5_E 0.82 0.11 0.00
111_A 51_I 0.82 0.11 0.00
139_Q 69_N 0.81 0.11 0.00
72_E 97_L 0.81 0.11 0.00
56_K 75_Q 0.81 0.11 0.00
116_G 51_I 0.81 0.11 0.00
182_T 63_E 0.81 0.11 0.00
34_T 91_K 0.80 0.11 0.00
140_D 82_I 0.80 0.11 0.00
97_N 26_R 0.80 0.11 0.00
136_K 86_N 0.80 0.11 0.00
102_R 59_K 0.80 0.11 0.00
97_N 99_K 0.80 0.11 0.00
54_T 23_F 0.80 0.11 0.00
66_T 99_K 0.80 0.11 0.00
19_V 70_M 0.80 0.11 0.00
10_V 99_K 0.80 0.11 0.00
79_K 23_F 0.79 0.10 0.00
70_A 28_F 0.79 0.10 0.00
28_S 89_E 0.79 0.10 0.00
163_L 11_R 0.79 0.10 0.00
137_R 84_A 0.79 0.10 0.00
26_I 94_I 0.79 0.10 0.00
124_C 76_P 0.79 0.10 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
8599 0.35 rasgap_ph_2 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8589 0.01 rasgap_ph_2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8579 0.05 rasgap_ph Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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