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OPENSEQ.org
LpoP_UB2Haligned_complex
Genes: A B A+B
Length: 259 92 327
Sequences: 71 428 60
Seq/Len: 0.27 4.65 0.18
MirrorTree (Pazo et al. 2001) 0.84
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 0.00 0.00 0.18
2 0.00 0.00 0.17
5 0.00 0.00 0.17
10 0.00 0.00 0.17
20 0.00 0.00 0.17
100 0.00 0.00 0.17
∞ 0.00 0.00 0.17
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
253_Q 48_N 1.99 0.58 0.01
170_S 64_V 1.67 0.39 0.00
57_G 58_A 1.67 0.39 0.00
22_P 10_L 1.66 0.38 0.00
46_I 41_A 1.62 0.36 0.00
186_I 59_E 1.59 0.35 0.00
254_K 48_N 1.54 0.32 0.00
226_A 59_E 1.42 0.26 0.00
39_Q 38_V 1.41 0.26 0.00
196_R 89_L 1.38 0.24 0.00
214_A 72_Y 1.37 0.24 0.00
208_A 60_P 1.36 0.23 0.00
149_A 14_R 1.29 0.21 0.00
222_N 48_N 1.27 0.20 0.00
62_G 10_L 1.26 0.20 0.00
22_P 43_S 1.26 0.20 0.00
72_V 47_L 1.26 0.20 0.00
35_P 39_S 1.25 0.19 0.00
35_P 75_G 1.25 0.19 0.00
186_I 63_R 1.22 0.18 0.00
83_P 72_Y 1.22 0.18 0.00
62_G 33_S 1.22 0.18 0.00
186_I 31_S 1.21 0.18 0.00
44_F 30_P 1.20 0.17 0.00
84_I 30_P 1.19 0.17 0.00
24_H 89_L 1.19 0.17 0.00
92_G 41_A 1.19 0.17 0.00
219_S 13_S 1.18 0.17 0.00
130_A 85_A 1.18 0.17 0.00
226_A 87_A 1.17 0.16 0.00
214_A 92_L 1.17 0.16 0.00
241_K 41_A 1.16 0.16 0.00
92_G 83_E 1.16 0.16 0.00
40_E 61_A 1.14 0.15 0.00
95_P 79_A 1.13 0.15 0.00
91_S 14_R 1.11 0.14 0.00
36_V 57_G 1.09 0.14 0.00
78_G 78_Q 1.09 0.14 0.00
177_A 46_E 1.09 0.14 0.00
66_G 32_V 1.08 0.14 0.00
241_K 48_N 1.08 0.14 0.00
85_Q 37_T 1.07 0.14 0.00
226_A 63_R 1.06 0.13 0.00
63_I 38_V 1.06 0.13 0.00
46_I 13_S 1.05 0.13 0.00
60_T 46_E 1.04 0.13 0.00
40_E 48_N 1.04 0.13 0.00
86_T 41_A 1.04 0.13 0.00
61_Q 79_A 1.04 0.12 0.00
141_S 78_Q 1.03 0.12 0.00
104_G 59_E 1.02 0.12 0.00
45_R 89_L 1.02 0.12 0.00
47_T 87_A 1.02 0.12 0.00
58_A 58_A 1.02 0.12 0.00
38_N 13_S 1.02 0.12 0.00
88_P 19_R 1.02 0.12 0.00
88_P 37_T 1.02 0.12 0.00
148_A 10_L 1.01 0.12 0.00
59_A 81_G 1.01 0.12 0.00
95_P 62_Q 1.01 0.12 0.00
39_Q 83_E 1.00 0.12 0.00
100_P 45_V 1.00 0.12 0.00
57_G 33_S 1.00 0.12 0.00
111_P 19_R 1.00 0.12 0.00
92_G 13_S 1.00 0.12 0.00
84_I 72_Y 0.99 0.11 0.00
72_V 64_V 0.99 0.11 0.00
245_S 78_Q 0.98 0.11 0.00
44_F 37_T 0.98 0.11 0.00
152_Q 47_L 0.98 0.11 0.00
84_I 41_A 0.97 0.11 0.00
34_T 59_E 0.97 0.11 0.00
140_A 78_Q 0.97 0.11 0.00
91_S 75_G 0.97 0.11 0.00
169_G 75_G 0.97 0.11 0.00
48_R 31_S 0.97 0.11 0.00
99_A 72_Y 0.97 0.11 0.00
233_E 58_A 0.96 0.11 0.00
225_P 59_E 0.96 0.11 0.00
87_F 46_E 0.96 0.11 0.00
90_Q 89_L 0.96 0.11 0.00
43_G 62_Q 0.96 0.11 0.00
93_A 41_A 0.96 0.11 0.00
138_I 32_V 0.95 0.10 0.00
62_G 8_N 0.95 0.10 0.00
85_Q 30_P 0.94 0.10 0.00
145_G 72_Y 0.94 0.10 0.00
78_G 19_R 0.94 0.10 0.00
47_T 63_R 0.94 0.10 0.00
97_S 45_V 0.93 0.10 0.00
61_Q 78_Q 0.93 0.10 0.00
186_I 75_G 0.93 0.10 0.00
60_T 41_A 0.93 0.10 0.00
177_A 58_A 0.93 0.10 0.00
250_L 48_N 0.93 0.10 0.00
222_N 61_A 0.93 0.10 0.00
131_S 13_S 0.93 0.10 0.00
207_A 76_L 0.93 0.10 0.00
35_P 41_A 0.93 0.10 0.00
129_G 30_P 0.93 0.10 0.00
43_G 75_G 0.93 0.10 0.00
97_S 60_P 0.92 0.10 0.00
87_F 72_Y 0.92 0.10 0.00
44_F 33_S 0.92 0.10 0.00
49_T 14_R 0.92 0.10 0.00
35_P 32_V 0.91 0.10 0.00
66_G 78_Q 0.91 0.10 0.00
26_A 45_V 0.91 0.10 0.00
64_P 37_T 0.91 0.10 0.00
47_T 59_E 0.91 0.10 0.00
97_S 30_P 0.91 0.10 0.00
32_S 48_N 0.90 0.10 0.00
97_S 64_V 0.90 0.10 0.00
63_I 44_A 0.90 0.10 0.00
46_I 14_R 0.90 0.10 0.00
20_A 33_S 0.90 0.09 0.00
45_R 32_V 0.90 0.09 0.00
43_G 72_Y 0.90 0.09 0.00
140_A 85_A 0.90 0.09 0.00
237_Q 10_L 0.89 0.09 0.00
258_S 78_Q 0.89 0.09 0.00
106_Q 38_V 0.89 0.09 0.00
217_G 33_S 0.89 0.09 0.00
83_P 30_P 0.88 0.09 0.00
88_P 72_Y 0.88 0.09 0.00
134_A 78_Q 0.88 0.09 0.00
37_S 67_R 0.88 0.09 0.00
258_S 19_R 0.88 0.09 0.00
64_P 41_A 0.88 0.09 0.00
96_I 30_P 0.88 0.09 0.00
254_K 41_A 0.88 0.09 0.00
137_G 64_V 0.88 0.09 0.00
87_F 30_P 0.88 0.09 0.00
41_S 83_E 0.88 0.09 0.00
51_V 75_G 0.88 0.09 0.00
82_A 37_T 0.87 0.09 0.00
94_A 41_A 0.87 0.09 0.00
56_Q 77_S 0.87 0.09 0.00
132_R 37_T 0.87 0.09 0.00
111_P 58_A 0.86 0.09 0.00
132_R 77_S 0.86 0.09 0.00
88_P 30_P 0.86 0.09 0.00
25_G 77_S 0.86 0.09 0.00
41_S 48_N 0.86 0.09 0.00
34_T 63_R 0.86 0.09 0.00
62_G 62_Q 0.86 0.09 0.00
257_V 75_G 0.85 0.09 0.00
86_T 72_Y 0.85 0.09 0.00
43_G 30_P 0.85 0.09 0.00
222_N 10_L 0.85 0.09 0.00
65_Q 19_R 0.85 0.09 0.00
94_A 63_R 0.85 0.09 0.00
26_A 43_S 0.85 0.08 0.00
233_E 46_E 0.85 0.08 0.00
58_A 30_P 0.85 0.08 0.00
175_S 8_N 0.84 0.08 0.00
108_Q 79_A 0.84 0.08 0.00
103_T 85_A 0.84 0.08 0.00
26_A 39_S 0.84 0.08 0.00
63_I 83_E 0.84 0.08 0.00
132_R 32_V 0.83 0.08 0.00
116_T 10_L 0.83 0.08 0.00
222_N 45_V 0.83 0.08 0.00
48_R 64_V 0.83 0.08 0.00
74_M 22_D 0.83 0.08 0.00
34_T 85_A 0.83 0.08 0.00
43_G 58_A 0.83 0.08 0.00
253_Q 45_V 0.82 0.08 0.00
96_I 44_A 0.82 0.08 0.00
69_S 64_V 0.82 0.08 0.00
154_D 7_F 0.82 0.08 0.00
168_Q 7_F 0.82 0.08 0.00
47_T 14_R 0.82 0.08 0.00
39_Q 79_A 0.82 0.08 0.00
146_S 53_Q 0.82 0.08 0.00
170_S 33_S 0.82 0.08 0.00
233_E 72_Y 0.82 0.08 0.00
65_Q 32_V 0.82 0.08 0.00
45_R 33_S 0.81 0.08 0.00
57_G 63_R 0.81 0.08 0.00
250_L 74_S 0.81 0.08 0.00
58_A 33_S 0.81 0.08 0.00
138_I 78_Q 0.81 0.08 0.00
110_P 33_S 0.81 0.08 0.00
84_I 37_T 0.81 0.08 0.00
124_N 44_A 0.81 0.08 0.00
98_S 60_P 0.81 0.08 0.00
88_P 87_A 0.81 0.08 0.00
154_D 18_L 0.80 0.08 0.00
154_D 55_Y 0.80 0.08 0.00
154_D 86_V 0.80 0.08 0.00
168_Q 18_L 0.80 0.08 0.00
168_Q 55_Y 0.80 0.08 0.00
168_Q 86_V 0.80 0.08 0.00
47_T 31_S 0.80 0.08 0.00
47_T 41_A 0.80 0.08 0.00
85_Q 72_Y 0.80 0.08 0.00
56_Q 43_S 0.80 0.08 0.00
49_T 30_P 0.80 0.08 0.00
249_A 29_E 0.80 0.08 0.00
72_V 60_P 0.80 0.08 0.00
82_A 39_S 0.80 0.08 0.00
258_S 30_P 0.80 0.08 0.00
36_V 78_Q 0.80 0.08 0.00
258_S 82_K 0.80 0.08 0.00
142_G 78_Q 0.80 0.08 0.00
170_S 15_E 0.80 0.08 0.00
48_R 14_R 0.80 0.07 0.00
131_S 63_R 0.80 0.07 0.00
238_A 85_A 0.80 0.07 0.00
213_V 57_G 0.79 0.07 0.00
178_A 71_N 0.79 0.07 0.00
82_A 19_R 0.79 0.07 0.00
141_S 60_P 0.79 0.07 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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