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OPENSEQ.org
3HEC_A MAP kinase 14 3FYK_X MAP kinase-activated protein kinase 2
Genes: A B A+B
Length: 348 327 565
Sequences: 32976 52931 306
Seq/Len: 94.76 161.87 0.54
MirrorTree (Pazo et al. 2001) 0.44
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 0.17 0.18 0.09
2 0.18 0.20 0.15
5 0.21 0.23 0.23
10 0.23 0.25 0.33
20 0.26 0.28 0.45
100 0.31 0.32 0.71
∞ 0.33 0.34 0.77
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
203_W 203_W 2.73 0.99 0.97
149_P 145_P 2.66 0.98 0.96
104_L 96_C 2.45 0.96 0.93
280_L 257_L 1.89 0.83 0.69
46_V 46_F 1.88 0.82 0.68
101_V 93_V 1.85 0.81 0.66
212_L 212_L 1.81 0.79 0.63
186_A 187_A 1.66 0.70 0.50
152_L 148_L 1.53 0.61 0.38
26_V 26_L 1.52 0.60 0.36
167_L 166_F 1.44 0.54 0.30
72_K 66_R 1.44 0.54 0.29
130_I 126_I 1.42 0.52 0.28
113_V 106_I 1.40 0.51 0.26
105_M 97_L 1.38 0.49 0.25
181_T 182_T 1.37 0.48 0.24
198_Q 198_K 1.34 0.46 0.22
147_L 143_V 1.33 0.45 0.21
163_L 162_T 1.29 0.42 0.19
85_V 79_V 1.23 0.37 0.15
202_I 275_F 1.22 0.37 0.14
51_L 51_L 1.20 0.35 0.13
124_Q 120_S 1.19 0.35 0.13
122_H 26_L 1.19 0.35 0.13
197_N 143_V 1.15 0.32 0.11
143_I 216_Y 1.14 0.31 0.11
294_T 271_T 1.12 0.30 0.10
69_R 62_E 1.12 0.30 0.10
26_V 194_E 1.11 0.29 0.09
142_I 138_I 1.11 0.29 0.09
295_A 272_I 1.08 0.28 0.08
169_R 168_K 1.08 0.27 0.08
290_D 267_T 1.06 0.26 0.08
46_V 48_L 1.06 0.26 0.08
205_V 205_L 1.05 0.26 0.07
185_R 186_V 1.05 0.26 0.07
36_A 36_Q 1.05 0.25 0.07
215_G 214_C 1.03 0.24 0.07
214_T 207_V 1.02 0.24 0.06
121_D 26_L 1.02 0.24 0.06
281_L 258_I 1.01 0.23 0.06
71_L 64_H 1.00 0.23 0.06
142_I 156_N 1.00 0.23 0.06
289_S 266_P 1.00 0.23 0.06
137_I 133_L 1.00 0.23 0.06
284_M 190_V 1.00 0.23 0.06
78_N 126_I 0.99 0.22 0.06
298_A 275_F 0.99 0.22 0.06
147_L 139_A 0.97 0.21 0.05
297_Q 274_E 0.97 0.21 0.05
212_L 275_F 0.96 0.20 0.05
209_M 209_M 0.96 0.20 0.05
134_L 238_G 0.96 0.20 0.05
103_H 185_Y 0.95 0.20 0.05
64_T 57_A 0.95 0.20 0.05
143_I 26_L 0.94 0.20 0.04
65_Y 98_D 0.94 0.20 0.04
139_S 135_S 0.93 0.19 0.04
36_A 76_I 0.93 0.19 0.04
108_D 101_E 0.92 0.19 0.04
102_T 166_F 0.92 0.19 0.04
134_L 130_I 0.92 0.18 0.04
108_D 210_Y 0.92 0.18 0.04
153_A 149_L 0.92 0.18 0.04
189_I 190_V 0.92 0.18 0.04
162_I 161_L 0.92 0.18 0.04
62_K 124_K 0.91 0.18 0.04
38_F 38_F 0.90 0.18 0.04
82_L 143_V 0.90 0.18 0.04
143_I 149_L 0.90 0.17 0.04
158_C 157_A 0.89 0.17 0.04
147_L 23_S 0.88 0.17 0.03
294_T 115_T 0.88 0.17 0.03
299_L 276_M 0.88 0.17 0.03
119_T 115_T 0.88 0.17 0.03
107_A 100_G 0.87 0.16 0.03
199_T 204_S 0.87 0.16 0.03
150_S 146_E 0.87 0.16 0.03
186_A 271_T 0.86 0.16 0.03
192_N 193_P 0.86 0.16 0.03
148_K 144_K 0.86 0.16 0.03
208_I 208_I 0.85 0.16 0.03
40_T 204_S 0.85 0.16 0.03
134_L 134_H 0.85 0.16 0.03
224_H 95_E 0.85 0.15 0.03
188_E 27_G 0.84 0.15 0.03
51_L 63_L 0.84 0.15 0.03
279_D 167_A 0.84 0.15 0.03
194_M 194_E 0.84 0.15 0.03
231_I 226_A 0.84 0.15 0.03
74_M 31_N 0.83 0.15 0.03
184_Y 145_P 0.83 0.15 0.03
152_L 80_Y 0.83 0.15 0.03
120_D 116_E 0.83 0.15 0.03
45_R 212_L 0.83 0.15 0.03
142_I 186_V 0.82 0.14 0.03
79_V 168_K 0.82 0.14 0.03
212_L 261_L 0.82 0.14 0.03
27_G 61_V 0.82 0.14 0.03
68_L 161_L 0.82 0.14 0.02
31_Y 31_N 0.82 0.14 0.02
134_L 76_I 0.82 0.14 0.02
111_N 265_E 0.81 0.14 0.02
87_T 81_E 0.81 0.14 0.02
213_L 162_T 0.81 0.14 0.02
130_I 207_V 0.81 0.14 0.02
23_L 209_M 0.81 0.14 0.02
26_V 156_N 0.81 0.14 0.02
204_S 276_M 0.80 0.14 0.02
132_R 167_A 0.80 0.14 0.02
101_V 64_H 0.80 0.14 0.02
152_L 92_I 0.80 0.14 0.02
44_L 44_E 0.80 0.13 0.02
181_T 96_C 0.80 0.13 0.02
37_A 71_P 0.80 0.13 0.02
65_Y 58_R 0.79 0.13 0.02
186_A 122_I 0.79 0.13 0.02
38_F 137_N 0.79 0.13 0.02
293_I 78_D 0.79 0.13 0.02
150_S 37_I 0.79 0.13 0.02
196_Y 196_Y 0.79 0.13 0.02
235_V 130_I 0.79 0.13 0.02
33_S 53_D 0.78 0.13 0.02
143_I 139_A 0.78 0.13 0.02
147_L 207_V 0.78 0.13 0.02
204_S 123_M 0.78 0.13 0.02
199_T 151_T 0.77 0.12 0.02
277_A 275_F 0.77 0.12 0.02
263_K 213_L 0.77 0.12 0.02
275_P 244_N 0.77 0.12 0.02
134_L 48_L 0.77 0.12 0.02
152_L 110_G 0.77 0.12 0.02
288_D 271_T 0.77 0.12 0.02
241_E 271_T 0.77 0.12 0.02
192_N 208_I 0.77 0.12 0.02
201_D 269_R 0.76 0.12 0.02
191_L 192_G 0.76 0.12 0.02
96_N 26_L 0.76 0.12 0.02
268_N 143_V 0.76 0.12 0.02
147_L 277_N 0.76 0.12 0.02
36_A 151_T 0.76 0.12 0.02
153_A 211_I 0.76 0.12 0.02
280_L 97_L 0.76 0.12 0.02
206_G 114_F 0.76 0.12 0.02
288_D 79_V 0.75 0.12 0.02
170_H 169_E 0.75 0.12 0.02
159_E 133_L 0.75 0.12 0.02
46_V 64_H 0.75 0.12 0.02
44_L 168_K 0.75 0.12 0.02
254_Y 143_V 0.75 0.12 0.02
154_V 188_P 0.75 0.12 0.02
184_Y 185_Y 0.75 0.12 0.02
205_V 56_K 0.75 0.12 0.02
294_T 170_T 0.75 0.12 0.02
48_V 35_L 0.75 0.12 0.02
292_R 140_H 0.75 0.12 0.02
212_L 208_I 0.74 0.12 0.02
113_V 77_V 0.74 0.12 0.02
22_N 21_V 0.74 0.12 0.02
134_L 239_Q 0.74 0.12 0.02
26_V 88_K 0.74 0.12 0.02
283_K 260_N 0.74 0.12 0.02
78_N 78_D 0.74 0.12 0.02
152_L 43_Q 0.74 0.11 0.02
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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.283), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
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