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OPENSEQ.org
rpc 19 rpc40 (A, 3-335) (B, 35-142)
Genes: A B A+B
Length: 333 108 390
Sequences: 669 798 112
Seq/Len: 2.01 7.39 0.29
MirrorTree (Pazo et al. 2001) 0.58
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 0.03 0.00
2 0.02 0.03 0.00
5 0.02 0.03 0.00
10 0.02 0.03 0.01
20 0.02 0.03 0.01
100 0.02 0.05 0.03
∞ 0.04 0.07 0.25
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
134_L 34_E 2.00 0.72 0.03
83_F 90_L 1.66 0.51 0.01
209_G 61_H 1.65 0.51 0.01
294_N 83_L 1.41 0.35 0.01
219_P 60_P 1.31 0.29 0.01
312_F 71_I 1.25 0.26 0.00
209_G 62_P 1.24 0.25 0.00
137_K 33_E 1.22 0.24 0.00
191_L 31_I 1.22 0.24 0.00
186_D 31_I 1.21 0.24 0.00
159_H 102_T 1.19 0.23 0.00
88_S 73_T 1.19 0.23 0.00
86_N 34_E 1.19 0.23 0.00
72_E 43_R 1.17 0.22 0.00
294_N 71_I 1.15 0.21 0.00
302_S 82_A 1.13 0.20 0.00
302_S 75_G 1.12 0.20 0.00
160_V 14_K 1.11 0.20 0.00
322_K 62_P 1.10 0.19 0.00
100_G 43_R 1.10 0.19 0.00
103_P 73_T 1.09 0.19 0.00
182_V 28_S 1.08 0.18 0.00
132_L 74_Y 1.07 0.18 0.00
73_V 86_G 1.07 0.18 0.00
300_V 82_A 1.06 0.17 0.00
164_D 33_E 1.05 0.17 0.00
289_L 78_T 1.05 0.17 0.00
162_A 47_M 1.04 0.17 0.00
194_L 52_V 1.04 0.17 0.00
85_N 27_A 1.04 0.17 0.00
231_I 31_I 1.03 0.17 0.00
165_L 102_T 1.03 0.17 0.00
72_E 70_R 1.03 0.16 0.00
89_V 82_A 1.03 0.16 0.00
193_K 97_V 1.03 0.16 0.00
293_R 27_A 1.02 0.16 0.00
290_G 47_M 1.02 0.16 0.00
294_N 53_E 1.02 0.16 0.00
312_F 90_L 1.02 0.16 0.00
163_R 99_S 1.01 0.16 0.00
82_Y 62_P 1.01 0.16 0.00
306_M 101_F 1.01 0.16 0.00
161_Y 83_L 1.01 0.16 0.00
83_F 42_L 1.00 0.15 0.00
86_N 36_H 0.99 0.15 0.00
331_I 71_I 0.99 0.15 0.00
193_K 71_I 0.99 0.15 0.00
219_P 62_P 0.98 0.15 0.00
203_K 20_T 0.98 0.15 0.00
278_L 78_T 0.97 0.14 0.00
183_V 79_A 0.97 0.14 0.00
191_L 11_E 0.97 0.14 0.00
164_D 55_C 0.97 0.14 0.00
216_K 52_V 0.97 0.14 0.00
231_I 53_E 0.97 0.14 0.00
91_Q 56_G 0.97 0.14 0.00
102_V 59_I 0.96 0.14 0.00
303_A 67_L 0.96 0.14 0.00
322_K 61_H 0.96 0.14 0.00
287_V 79_A 0.95 0.14 0.00
145_P 11_E 0.95 0.14 0.00
51_N 47_M 0.94 0.14 0.00
195_R 101_F 0.94 0.14 0.00
129_T 58_S 0.94 0.13 0.00
161_Y 69_I 0.94 0.13 0.00
192_A 74_Y 0.93 0.13 0.00
104_L 35_D 0.93 0.13 0.00
289_L 87_L 0.92 0.13 0.00
302_S 94_C 0.92 0.13 0.00
170_Q 10_R 0.92 0.13 0.00
221_S 43_R 0.92 0.13 0.00
312_F 44_Y 0.91 0.12 0.00
91_Q 33_E 0.91 0.12 0.00
214_H 61_H 0.91 0.12 0.00
83_F 69_I 0.90 0.12 0.00
289_L 75_G 0.90 0.12 0.00
86_N 40_N 0.90 0.12 0.00
107_D 90_L 0.90 0.12 0.00
322_K 34_E 0.90 0.12 0.00
221_S 58_S 0.90 0.12 0.00
315_S 34_E 0.89 0.12 0.00
179_D 97_V 0.89 0.12 0.00
221_S 35_D 0.89 0.12 0.00
221_S 62_P 0.89 0.12 0.00
187_P 90_L 0.89 0.12 0.00
40_V 84_Q 0.89 0.12 0.00
71_S 50_P 0.88 0.12 0.00
213_D 29_F 0.88 0.12 0.00
52_F 42_L 0.88 0.12 0.00
40_V 23_D 0.87 0.11 0.00
218_S 60_P 0.87 0.11 0.00
61_I 89_D 0.87 0.11 0.00
64_A 62_P 0.87 0.11 0.00
87_T 101_F 0.87 0.11 0.00
285_D 100_K 0.86 0.11 0.00
165_L 45_V 0.86 0.11 0.00
57_I 79_A 0.86 0.11 0.00
176_T 20_T 0.86 0.11 0.00
220_V 104_K 0.85 0.11 0.00
307_T 66_L 0.85 0.11 0.00
42_I 64_E 0.85 0.11 0.00
69_M 55_C 0.85 0.11 0.00
68_I 47_M 0.84 0.11 0.00
190_L 33_E 0.84 0.11 0.00
138_C 72_Q 0.84 0.11 0.00
76_V 50_P 0.84 0.11 0.00
56_N 31_I 0.84 0.11 0.00
214_H 62_P 0.84 0.10 0.00
189_I 73_T 0.84 0.10 0.00
218_S 67_L 0.84 0.10 0.00
170_Q 8_P 0.83 0.10 0.00
308_P 38_L 0.83 0.10 0.00
300_V 62_P 0.83 0.10 0.00
164_D 67_L 0.83 0.10 0.00
200_I 35_D 0.83 0.10 0.00
188_D 13_I 0.83 0.10 0.00
184_P 107_S 0.83 0.10 0.00
163_R 71_I 0.83 0.10 0.00
198_Q 35_D 0.83 0.10 0.00
40_V 93_L 0.83 0.10 0.00
271_D 101_F 0.83 0.10 0.00
65_F 71_I 0.83 0.10 0.00
183_V 93_L 0.82 0.10 0.00
57_I 67_L 0.82 0.10 0.00
326_L 37_T 0.82 0.10 0.00
327_K 66_L 0.82 0.10 0.00
330_P 84_Q 0.82 0.10 0.00
199_E 43_R 0.82 0.10 0.00
69_M 69_I 0.82 0.10 0.00
74_P 34_E 0.81 0.10 0.00
228_L 86_G 0.81 0.10 0.00
174_S 11_E 0.81 0.10 0.00
295_H 46_I 0.81 0.10 0.00
209_G 90_L 0.81 0.10 0.00
92_D 37_T 0.81 0.10 0.00
72_E 72_Q 0.81 0.10 0.00
140_R 10_R 0.81 0.10 0.00
61_I 33_E 0.81 0.10 0.00
106_V 63_S 0.81 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
9564 0.01 rpc 19 rpc40 (A, 3-335) (B, 35-142) Δgene:(0, 0) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
9563 0.29 rpc 19 rpc40 (A, 3-335) (B, 35-142) Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.03 Done - Shared
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