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OPENSEQ.org
1CTQ_A Ras GTPase 1GNP 2II0_A Son of sevenless
Genes: A B A+B
Length: 166 490 610
Sequences: 7559 1381 218
Seq/Len: 45.54 2.82 0.36
MirrorTree (Pazo et al. 2001) 0.35
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 0.03 0.04
2 0.12 0.04 0.08
5 0.14 0.04 0.13
10 0.16 0.04 0.20
20 0.18 0.05 0.33
100 0.23 0.07 0.79
∞ 0.26 0.10 1.18
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
138_G 324_V 1.30 0.33 0.00
6_L 296_I 1.11 0.22 0.00
112_V 292_V 1.09 0.21 0.00
8_V 72_Y 1.09 0.21 0.00
17_S 139_E 1.06 0.20 0.00
138_G 264_K 1.05 0.20 0.00
147_K 299_I 1.03 0.19 0.00
17_S 223_I 1.02 0.18 0.00
84_I 76_C 1.02 0.18 0.00
55_I 416_Q 1.01 0.18 0.00
135_R 225_I 0.97 0.16 0.00
147_K 158_F 0.97 0.16 0.00
17_S 307_N 0.96 0.16 0.00
8_V 321_S 0.96 0.16 0.00
136_S 334_I 0.95 0.15 0.00
128_R 88_R 0.95 0.15 0.00
147_K 422_L 0.94 0.15 0.00
111_M 190_G 0.93 0.15 0.00
125_V 77_K 0.93 0.15 0.00
90_F 432_F 0.92 0.14 0.00
11_A 159_I 0.92 0.14 0.00
125_V 306_L 0.91 0.14 0.00
114_V 300_L 0.90 0.14 0.00
6_L 290_V 0.90 0.14 0.00
125_V 293_V 0.89 0.14 0.00
18_A 315_V 0.89 0.13 0.00
48_G 42_I 0.88 0.13 0.00
17_S 404_K 0.88 0.13 0.00
84_I 276_F 0.88 0.13 0.00
130_A 155_M 0.87 0.13 0.00
82_F 201_T 0.87 0.13 0.00
17_S 355_K 0.87 0.13 0.00
138_G 45_G 0.87 0.13 0.00
89_S 281_V 0.86 0.13 0.00
48_G 237_Y 0.86 0.12 0.00
79_L 323_P 0.86 0.12 0.00
15_G 315_V 0.86 0.12 0.00
19_L 332_E 0.85 0.12 0.00
19_L 55_T 0.85 0.12 0.00
7_V 159_I 0.85 0.12 0.00
154_D 99_A 0.85 0.12 0.00
95_Q 81_L 0.84 0.12 0.00
92_D 67_T 0.84 0.12 0.00
82_F 208_R 0.83 0.12 0.00
89_S 266_I 0.83 0.12 0.00
64_Y 340_K 0.83 0.12 0.00
152_V 304_Q 0.83 0.12 0.00
86_N 281_V 0.82 0.12 0.00
31_E 345_A 0.82 0.11 0.00
17_S 358_A 0.82 0.11 0.00
138_G 457_I 0.82 0.11 0.00
8_V 334_I 0.82 0.11 0.00
108_D 152_L 0.82 0.11 0.00
86_N 413_Q 0.81 0.11 0.00
82_F 80_E 0.81 0.11 0.00
100_I 349_S 0.81 0.11 0.00
146_A 42_I 0.81 0.11 0.00
64_Y 232_L 0.81 0.11 0.00
16_K 289_R 0.81 0.11 0.00
125_V 371_F 0.81 0.11 0.00
94_H 151_L 0.81 0.11 0.00
151_G 459_P 0.80 0.11 0.00
44_V 131_L 0.80 0.11 0.00
128_R 415_Y 0.80 0.11 0.00
77_G 342_L 0.80 0.11 0.00
125_V 27_I 0.79 0.11 0.00
90_F 120_K 0.79 0.10 0.00
55_I 457_I 0.79 0.10 0.00
51_C 47_V 0.79 0.10 0.00
159_L 342_L 0.79 0.10 0.00
31_E 51_I 0.78 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)
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