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OPENSEQ.org
cI_5_6_cI_2_4_tt
Genes: A B A+B
Length: 207 182 339
Sequences: 1086 1192 538
Seq/Len: 5.25 6.55 1.59
MirrorTree (Pazo et al. 2001) 0.87
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 0.01 0.01
2 0.00 0.05 0.04
5 0.01 0.05 0.13
10 0.01 0.06 1.01
20 0.01 0.06 1.11
100 0.01 0.06 1.16
∞ 0.02 0.09 1.38
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
109_G 22_V 1.58 0.90 0.38
135_I 15_K 1.48 0.86 0.30
178_D 129_L 1.33 0.77 0.21
47_N 10_L 1.25 0.71 0.17
178_D 96_L 1.23 0.69 0.16
178_D 123_D 1.23 0.69 0.16
154_E 85_E 1.23 0.69 0.16
106_D 19_S 1.11 0.58 0.11
183_F 112_A 1.10 0.57 0.10
186_G 123_D 1.10 0.56 0.10
163_R 7_A 1.09 0.56 0.10
110_S 145_P 1.09 0.55 0.10
64_R 25_P 1.09 0.55 0.10
8_E 112_A 1.08 0.54 0.10
49_L 33_L 1.07 0.53 0.09
171_R 103_L 1.07 0.53 0.09
77_L 6_L 1.06 0.52 0.09
104_V 134_E 1.05 0.51 0.09
127_E 47_P 1.05 0.51 0.09
31_R 7_A 1.03 0.49 0.08
133_R 60_A 1.02 0.48 0.08
94_V 22_V 1.02 0.48 0.08
122_F 149_E 1.01 0.47 0.07
50_A 19_S 1.01 0.47 0.07
52_I 6_L 1.00 0.45 0.07
178_D 131_Y 0.99 0.45 0.07
99_P 71_E 0.98 0.44 0.07
168_A 48_N 0.97 0.42 0.06
92_V 17_L 0.96 0.42 0.06
147_R 64_P 0.95 0.41 0.06
85_G 116_G 0.95 0.40 0.06
178_D 130_V 0.94 0.40 0.06
154_E 96_L 0.94 0.40 0.06
93_Y 15_K 0.94 0.40 0.06
36_E 16_Y 0.94 0.39 0.06
108_W 13_T 0.94 0.39 0.06
187_G 103_L 0.93 0.39 0.06
48_F 130_V 0.93 0.38 0.05
180_G 112_A 0.93 0.38 0.05
92_V 149_E 0.93 0.38 0.05
132_L 147_R 0.92 0.38 0.05
119_Y 5_A 0.92 0.37 0.05
72_Y 131_Y 0.91 0.37 0.05
8_E 4_K 0.91 0.36 0.05
136_L 106_E 0.91 0.36 0.05
36_E 22_V 0.90 0.36 0.05
102_P 82_S 0.90 0.36 0.05
167_P 20_K 0.90 0.35 0.05
77_L 85_E 0.90 0.35 0.05
29_L 142_G 0.89 0.35 0.05
101_L 142_G 0.89 0.35 0.05
146_L 122_A 0.89 0.34 0.05
142_E 118_D 0.89 0.34 0.05
101_L 16_Y 0.88 0.34 0.04
108_W 14_L 0.88 0.34 0.04
179_P 25_P 0.88 0.34 0.04
31_R 103_L 0.88 0.34 0.04
77_L 13_T 0.88 0.34 0.04
128_G 84_G 0.88 0.33 0.04
149_D 64_P 0.88 0.33 0.04
29_L 74_E 0.88 0.33 0.04
175_T 118_D 0.87 0.33 0.04
186_G 135_D 0.87 0.33 0.04
23_G 122_A 0.87 0.33 0.04
174_L 5_A 0.86 0.32 0.04
124_I 134_E 0.86 0.32 0.04
90_V 4_K 0.86 0.32 0.04
43_A 4_K 0.85 0.31 0.04
74_L 13_T 0.85 0.31 0.04
88_F 112_A 0.85 0.31 0.04
30_P 15_K 0.84 0.30 0.04
88_F 19_S 0.84 0.30 0.04
169_E 135_D 0.84 0.30 0.04
16_P 15_K 0.84 0.30 0.04
72_Y 146_Q 0.84 0.30 0.04
21_G 71_E 0.84 0.30 0.04
43_A 24_V 0.84 0.30 0.04
8_E 17_L 0.83 0.29 0.04
119_Y 132_G 0.83 0.29 0.04
117_E 53_C 0.83 0.29 0.04
117_E 56_C 0.83 0.29 0.04
117_E 59_C 0.83 0.29 0.04
117_E 98_C 0.83 0.29 0.04
117_E 108_C 0.83 0.29 0.04
117_E 109_P 0.83 0.29 0.04
123_G 53_C 0.83 0.29 0.04
123_G 56_C 0.83 0.29 0.04
123_G 59_C 0.83 0.29 0.04
123_G 98_C 0.83 0.29 0.04
123_G 108_C 0.83 0.29 0.04
123_G 109_P 0.83 0.29 0.04
14_G 15_K 0.83 0.29 0.04
95_P 147_R 0.82 0.29 0.04
10_A 103_L 0.82 0.28 0.04
183_F 130_V 0.82 0.28 0.04
35_K 47_P 0.82 0.28 0.03
68_F 29_A 0.82 0.28 0.03
11_R 4_K 0.82 0.28 0.03
171_R 9_S 0.82 0.28 0.03
85_G 30_P 0.82 0.28 0.03
104_V 117_Y 0.81 0.28 0.03
49_L 22_V 0.81 0.28 0.03
179_P 135_D 0.81 0.28 0.03
23_G 4_K 0.81 0.28 0.03
34_F 119_F 0.81 0.27 0.03
180_G 130_V 0.81 0.27 0.03
108_W 31_V 0.81 0.27 0.03
37_E 17_L 0.81 0.27 0.03
21_G 72_P 0.81 0.27 0.03
186_G 130_V 0.81 0.27 0.03
116_R 53_C 0.81 0.27 0.03
116_R 56_C 0.81 0.27 0.03
116_R 59_C 0.81 0.27 0.03
116_R 98_C 0.81 0.27 0.03
116_R 108_C 0.81 0.27 0.03
116_R 109_P 0.81 0.27 0.03
157_T 14_L 0.81 0.27 0.03
64_R 112_A 0.80 0.27 0.03
84_D 138_V 0.80 0.27 0.03
96_E 74_E 0.80 0.26 0.03
17_I 11_G 0.80 0.26 0.03
187_G 96_L 0.80 0.26 0.03
45_G 19_S 0.80 0.26 0.03
48_F 10_L 0.80 0.26 0.03
92_V 4_K 0.79 0.26 0.03
179_P 123_D 0.79 0.26 0.03
186_G 10_L 0.79 0.26 0.03
96_E 8_Q 0.79 0.26 0.03
101_L 74_E 0.79 0.26 0.03
180_G 20_K 0.79 0.26 0.03
110_S 73_A 0.79 0.25 0.03
190_K 129_L 0.78 0.25 0.03
71_V 133_K 0.78 0.25 0.03
21_G 4_K 0.78 0.25 0.03
97_E 15_K 0.78 0.25 0.03
138_P 57_S 0.77 0.24 0.03
37_E 134_E 0.77 0.24 0.03
15_Y 7_A 0.77 0.24 0.03
163_R 89_K 0.77 0.24 0.03
15_Y 19_S 0.77 0.24 0.03
106_D 7_A 0.77 0.24 0.03
69_A 48_N 0.76 0.24 0.03
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
4911 1.52 cI_5_10_cI_9_4_tt2 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4910 1.59 cI_5_6_cI_2_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4909 1.52 cI_5_10_cI_9_4_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
4908 1.56 cI_5_6_cI_9_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4907 1.7 cI_5_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4906 1.69 cI_5_6_cI_9_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4905 1.52 cI_5_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4904 0.04 cI_5_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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