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OPENSEQ.org
CCMC_CCME
Genes: A B A+B
Length: 245 159 398
Sequences: 1895 225 187
Seq/Len: 7.73 1.42 0.47
MirrorTree (Pazo et al. 2001) 0.83
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 0.00 0.00 0.03
2 0.00 0.00 0.46
5 0.00 0.00 0.46
10 0.00 0.00 0.47
20 0.00 0.00 0.46
100 0.00 0.00 0.47
∞ 0.02 0.03 0.47
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
157_R 89_G 2.23 0.92 0.61
22_I 91_V 1.51 0.55 0.14
157_R 139_V 1.50 0.54 0.13
41_F 67_M 1.48 0.53 0.12
192_Q 32_S 1.47 0.52 0.12
162_L 112_Q 1.43 0.49 0.11
32_V 133_N 1.41 0.48 0.10
152_R 149_R 1.38 0.45 0.09
93_V 139_V 1.34 0.43 0.08
161_I 18_G 1.34 0.42 0.08
155_A 68_P 1.34 0.42 0.08
156_G 68_P 1.28 0.38 0.06
2_W 6_K 1.25 0.35 0.06
231_R 133_N 1.24 0.35 0.06
93_V 142_A 1.24 0.35 0.06
195_D 139_V 1.22 0.34 0.05
157_R 67_M 1.22 0.33 0.05
222_R 112_Q 1.20 0.32 0.05
231_R 144_E 1.19 0.32 0.04
10_I 144_E 1.19 0.31 0.04
162_L 18_G 1.18 0.31 0.04
221_M 48_R 1.18 0.31 0.04
161_I 26_V 1.17 0.31 0.04
29_S 26_V 1.17 0.30 0.04
157_R 87_A 1.15 0.29 0.04
41_F 109_V 1.15 0.29 0.04
21_F 77_S 1.15 0.29 0.04
57_I 135_T 1.13 0.28 0.04
42_G 32_S 1.13 0.28 0.04
203_R 135_T 1.13 0.28 0.04
40_G 137_P 1.12 0.27 0.03
202_L 137_P 1.12 0.27 0.03
113_A 84_I 1.12 0.27 0.03
9_A 5_R 1.12 0.27 0.03
196_P 60_L 1.11 0.27 0.03
163_V 135_T 1.11 0.27 0.03
147_H 42_E 1.10 0.26 0.03
150_D 43_I 1.10 0.26 0.03
156_G 15_V 1.10 0.26 0.03
187_S 32_S 1.09 0.26 0.03
189_R 88_E 1.08 0.25 0.03
226_L 44_L 1.08 0.25 0.03
211_L 96_E 1.08 0.25 0.03
90_N 62_V 1.07 0.24 0.03
225_I 118_G 1.07 0.24 0.03
235_V 53_M 1.06 0.24 0.03
161_I 25_L 1.06 0.24 0.03
190_M 109_V 1.06 0.24 0.03
136_L 142_A 1.04 0.23 0.03
165_I 3_I 1.04 0.23 0.03
91_L 112_Q 1.04 0.23 0.03
124_V 77_S 1.03 0.23 0.03
223_N 23_I 1.03 0.22 0.02
88_M 51_Q 1.02 0.22 0.02
69_G 19_L 1.02 0.22 0.02
200_S 60_L 1.02 0.22 0.02
225_I 116_E 1.02 0.22 0.02
168_V 95_Y 1.02 0.22 0.02
175_Y 149_R 1.01 0.21 0.02
212_L 13_C 1.01 0.21 0.02
8_L 3_I 1.01 0.21 0.02
63_A 79_K 1.01 0.21 0.02
146_W 112_Q 1.00 0.21 0.02
20_W 11_I 1.00 0.21 0.02
112_S 70_S 0.99 0.20 0.02
178_E 27_L 0.99 0.20 0.02
90_N 18_G 0.99 0.20 0.02
163_V 109_V 0.98 0.20 0.02
51_G 35_D 0.98 0.20 0.02
17_I 114_E 0.98 0.20 0.02
229_E 144_E 0.98 0.20 0.02
89_A 6_K 0.98 0.20 0.02
207_F 20_A 0.98 0.20 0.02
226_L 133_N 0.97 0.20 0.02
42_G 3_I 0.97 0.20 0.02
63_A 92_D 0.97 0.20 0.02
156_G 121_I 0.97 0.20 0.02
14_L 135_T 0.96 0.19 0.02
41_F 88_E 0.96 0.19 0.02
63_A 74_D 0.95 0.18 0.02
57_I 10_W 0.95 0.18 0.02
70_I 145_A 0.95 0.18 0.02
52_N 135_T 0.95 0.18 0.02
203_R 109_V 0.94 0.18 0.02
225_I 151_A 0.94 0.18 0.02
192_Q 109_V 0.94 0.18 0.02
170_L 35_D 0.94 0.18 0.02
134_V 32_S 0.94 0.18 0.02
238_L 24_G 0.94 0.18 0.02
29_S 116_E 0.94 0.18 0.02
161_I 112_Q 0.94 0.18 0.02
35_V 25_L 0.93 0.18 0.02
122_W 29_A 0.93 0.17 0.02
178_E 77_S 0.93 0.17 0.02
188_T 6_K 0.93 0.17 0.02
121_T 28_Y 0.93 0.17 0.01
211_L 119_N 0.92 0.17 0.01
43_F 125_E 0.92 0.17 0.01
25_L 96_E 0.92 0.17 0.01
158_A 25_L 0.92 0.17 0.01
132_E 124_K 0.92 0.17 0.01
204_W 11_I 0.92 0.17 0.01
203_R 32_S 0.92 0.17 0.01
237_E 74_D 0.91 0.17 0.01
158_A 18_G 0.91 0.17 0.01
87_K 12_A 0.91 0.17 0.01
99_I 6_K 0.91 0.17 0.01
96_M 143_M 0.91 0.17 0.01
94_A 142_A 0.91 0.16 0.01
195_D 11_I 0.91 0.16 0.01
175_Y 43_I 0.91 0.16 0.01
190_M 88_E 0.90 0.16 0.01
170_L 20_A 0.90 0.16 0.01
165_I 111_V 0.90 0.16 0.01
132_E 72_Q 0.90 0.16 0.01
7_Q 135_T 0.90 0.16 0.01
157_R 26_V 0.90 0.16 0.01
7_Q 32_S 0.90 0.16 0.01
41_F 89_G 0.90 0.16 0.01
150_D 139_V 0.89 0.16 0.01
189_R 141_K 0.89 0.16 0.01
174_H 144_E 0.89 0.16 0.01
217_T 44_L 0.89 0.16 0.01
118_M 72_Q 0.89 0.16 0.01
29_S 48_R 0.88 0.15 0.01
106_I 74_D 0.88 0.15 0.01
223_N 60_L 0.88 0.15 0.01
124_V 125_E 0.88 0.15 0.01
109_V 140_E 0.88 0.15 0.01
124_V 56_V 0.88 0.15 0.01
156_G 16_L 0.88 0.15 0.01
16_Q 91_V 0.88 0.15 0.01
196_P 10_W 0.87 0.15 0.01
213_S 143_M 0.87 0.15 0.01
17_I 95_Y 0.87 0.15 0.01
189_R 109_V 0.87 0.15 0.01
29_S 91_V 0.87 0.15 0.01
200_S 119_N 0.87 0.15 0.01
142_V 125_E 0.87 0.15 0.01
150_D 143_M 0.87 0.15 0.01
229_E 22_T 0.86 0.15 0.01
161_I 6_K 0.86 0.15 0.01
144_A 98_I 0.86 0.15 0.01
105_F 47_K 0.86 0.15 0.01
155_A 88_E 0.86 0.15 0.01
99_I 122_L 0.86 0.15 0.01
162_L 79_K 0.86 0.15 0.01
70_I 133_N 0.86 0.15 0.01
13_R 94_S 0.86 0.15 0.01
46_A 114_E 0.86 0.14 0.01
193_S 32_S 0.86 0.14 0.01
57_I 92_D 0.86 0.14 0.01
213_S 139_V 0.86 0.14 0.01
192_Q 67_M 0.85 0.14 0.01
204_W 145_A 0.85 0.14 0.01
212_L 156_D 0.85 0.14 0.01
215_T 52_Q 0.85 0.14 0.01
27_I 20_A 0.85 0.14 0.01
154_L 121_I 0.85 0.14 0.01
21_F 12_A 0.85 0.14 0.01
58_Y 17_A 0.85 0.14 0.01
182_T 97_G 0.84 0.14 0.01
93_V 22_T 0.84 0.14 0.01
8_L 109_V 0.84 0.14 0.01
57_I 16_L 0.84 0.14 0.01
12_P 111_V 0.84 0.14 0.01
209_F 119_N 0.84 0.14 0.01
44_A 60_L 0.84 0.14 0.01
19_G 112_Q 0.84 0.14 0.01
103_F 42_E 0.84 0.14 0.01
200_S 7_N 0.84 0.14 0.01
155_A 89_G 0.84 0.14 0.01
20_W 96_E 0.84 0.14 0.01
157_R 14_A 0.84 0.14 0.01
132_E 143_M 0.84 0.14 0.01
175_Y 50_T 0.84 0.14 0.01
11_P 43_I 0.84 0.14 0.01
79_F 14_A 0.83 0.14 0.01
238_L 19_L 0.83 0.14 0.01
90_N 26_V 0.83 0.14 0.01
5_L 36_L 0.83 0.14 0.01
99_I 119_N 0.83 0.14 0.01
158_A 43_I 0.83 0.14 0.01
154_L 22_T 0.83 0.13 0.01
99_I 150_P 0.83 0.13 0.01
12_P 3_I 0.83 0.13 0.01
73_S 79_K 0.83 0.13 0.01
208_G 28_Y 0.82 0.13 0.01
96_M 31_R 0.82 0.13 0.01
205_S 152_S 0.82 0.13 0.01
221_M 51_Q 0.82 0.13 0.01
154_L 84_I 0.82 0.13 0.01
4_T 109_V 0.82 0.13 0.01
164_L 68_P 0.82 0.13 0.01
228_M 149_R 0.82 0.13 0.01
175_Y 19_L 0.82 0.13 0.01
158_A 47_K 0.82 0.13 0.01
221_M 7_N 0.82 0.13 0.01
86_M 15_V 0.82 0.13 0.01
58_Y 118_G 0.81 0.13 0.01
118_M 70_S 0.81 0.13 0.01
195_D 22_T 0.81 0.13 0.01
93_V 145_A 0.81 0.13 0.01
197_A 48_R 0.81 0.13 0.01
209_F 6_K 0.81 0.13 0.01
190_M 67_M 0.81 0.13 0.01
99_I 20_A 0.81 0.13 0.01
38_I 6_K 0.81 0.13 0.01
112_S 12_A 0.81 0.13 0.01
7_Q 67_M 0.81 0.13 0.01
96_M 145_A 0.81 0.13 0.01
32_V 16_L 0.80 0.13 0.01
239_I 79_K 0.80 0.13 0.01
69_G 71_V 0.80 0.13 0.01
1_M 4_R 0.80 0.13 0.01
66_W 149_R 0.80 0.13 0.01
158_A 42_E 0.80 0.12 0.01
199_R 32_S 0.80 0.12 0.01
22_I 20_A 0.80 0.12 0.01
182_T 84_I 0.80 0.12 0.01
155_A 151_A 0.80 0.12 0.01
22_I 16_L 0.80 0.12 0.01
146_W 50_T 0.80 0.12 0.01
233_P 138_E 0.80 0.12 0.01
9_A 4_R 0.80 0.12 0.01
228_M 15_V 0.79 0.12 0.01
79_F 142_A 0.79 0.12 0.01
88_M 96_E 0.79 0.12 0.01
164_L 121_I 0.79 0.12 0.01
76_V 62_V 0.79 0.12 0.01
2_W 4_R 0.79 0.12 0.01
146_W 19_L 0.79 0.12 0.01
163_V 140_E 0.79 0.12 0.01
186_G 98_I 0.79 0.12 0.01
199_R 135_T 0.79 0.12 0.01
168_V 87_A 0.79 0.12 0.01
187_S 68_P 0.79 0.12 0.01
208_G 145_A 0.79 0.12 0.01
26_A 81_T 0.79 0.12 0.01
187_S 109_V 0.78 0.12 0.01
29_S 21_L 0.78 0.12 0.01
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
8059 1.57 cCmCE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.95 Done - Shared
7373 1.66 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-40, 2) msa: Jackhmmer (r132) 0.98 Done
7372 2.68 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-40, 4) msa: Jackhmmer (r132) 1.00 Done
7371 2.77 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 1.00 Done
7370 0.47 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (r132) 0.70 Done
7369 0.06 CCMC_CCME Δgene:(1, 2) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (r132) Killed
7351 3.08 CCMC_CCME Δgene:(1, 2) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 1.00 Done
7347 0.47 CCMC_CCME Δgene:(1, 2) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132) 0.61 Done
7037 4.74 CCMC_CCME Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.99 Done
7034 3.44 CCMC_CCME Δgene:(1, 2) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
6982 5.17 ccmc_ccme Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.20 Done - Shared
2431 1.73 ccme-ccmc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1105 0.93 CCMC_CCME Δgene:(1, 2) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.94 Done
1099 1.4 CCMC_CCME Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.98 Done
1097 0.15 CCMC_CCME Δgene:(1, 1) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed
1094 1.28 CCMC_CCME Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done
1049 1.51 CCMC_CCME Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done
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