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OPENSEQ.org
E coli GrpE-DnaK
Genes: A B A+B
Length: 197 638 758
Sequences: 659 3498 261
Seq/Len: 3.35 5.48 0.34
MirrorTree (Pazo et al. 2001) 0.19
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 0.06 0.14
2 0.02 0.06 0.14
5 0.02 0.06 0.15
10 0.02 0.06 0.15
20 0.02 0.07 0.16
100 0.02 0.07 0.19
∞ 0.02 0.13 0.31
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
164_D 373_I 2.06 0.79 0.11
184_T 305_L 1.81 0.66 0.06
170_V 64_N 1.34 0.35 0.01
170_V 164_E 1.29 0.31 0.01
126_T 72_L 1.25 0.29 0.01
125_L 598_L 1.19 0.26 0.01
130_M 411_L 1.18 0.25 0.01
79_D 349_V 1.18 0.25 0.01
63_L 584_I 1.17 0.25 0.01
91_F 475_T 1.17 0.24 0.01
176_K 435_A 1.16 0.24 0.01
105_A 48_T 1.15 0.23 0.01
106_L 333_D 1.14 0.23 0.01
79_D 220_A 1.13 0.23 0.01
63_L 489_K 1.12 0.22 0.01
183_R 591_L 1.12 0.22 0.01
96_L 350_Q 1.11 0.21 0.01
168_G 280_D 1.09 0.21 0.01
74_R 313_V 1.08 0.20 0.01
155_Q 114_Q 1.08 0.20 0.01
153_V 333_D 1.07 0.20 0.01
83_A 193_Y 1.07 0.20 0.01
65_V 379_G 1.06 0.20 0.01
102_L 190_I 1.06 0.19 0.01
130_M 235_R 1.06 0.19 0.01
180_L 329_L 1.05 0.19 0.01
125_L 285_Y 1.05 0.19 0.01
128_K 425_V 1.04 0.18 0.01
138_G 115_I 1.04 0.18 0.01
150_D 25_R 1.04 0.18 0.01
102_L 353_V 1.03 0.18 0.01
109_A 438_I 1.03 0.18 0.01
78_L 547_R 1.01 0.17 0.01
55_Q 224_D 1.00 0.17 0.01
87_A 525_A 1.00 0.17 0.01
184_T 338_I 1.00 0.17 0.01
185_I 528_K 1.00 0.17 0.01
106_L 538_Q 0.99 0.17 0.01
75_R 262_L 0.99 0.17 0.01
161_E 485_H 0.99 0.17 0.01
126_T 25_R 0.99 0.16 0.00
60_D 333_D 0.97 0.16 0.00
91_F 114_Q 0.97 0.16 0.00
126_T 385_D 0.97 0.16 0.00
142_I 66_L 0.96 0.16 0.00
69_M 159_R 0.96 0.15 0.00
148_P 33_D 0.96 0.15 0.00
134_V 50_V 0.95 0.15 0.00
96_L 513_Q 0.95 0.15 0.00
54_A 241_V 0.95 0.15 0.00
187_A 550_V 0.95 0.15 0.00
155_Q 544_H 0.94 0.15 0.00
79_D 518_D 0.94 0.15 0.00
134_V 559_A 0.94 0.15 0.00
59_R 338_I 0.94 0.15 0.00
134_V 2_G 0.94 0.15 0.00
160_V 438_I 0.94 0.15 0.00
119_M 17_A 0.94 0.15 0.00
90_K 149_A 0.93 0.14 0.00
57_R 561_D 0.93 0.14 0.00
127_L 414_K 0.93 0.14 0.00
136_K 94_I 0.93 0.14 0.00
66_K 329_L 0.93 0.14 0.00
136_K 398_S 0.93 0.14 0.00
139_V 425_V 0.92 0.14 0.00
94_E 301_T 0.92 0.14 0.00
193_A 346_M 0.92 0.14 0.00
180_L 529_F 0.92 0.14 0.00
73_R 271_I 0.92 0.14 0.00
174_M 550_V 0.91 0.14 0.00
143_A 550_V 0.91 0.14 0.00
185_I 321_K 0.91 0.14 0.00
72_L 335_D 0.91 0.14 0.00
182_G 411_L 0.91 0.14 0.00
171_L 440_V 0.91 0.14 0.00
65_V 543_L 0.90 0.14 0.00
170_V 69_I 0.90 0.14 0.00
121_E 220_A 0.90 0.13 0.00
92_I 202_I 0.90 0.13 0.00
104_R 52_Q 0.89 0.13 0.00
163_D 463_N 0.89 0.13 0.00
185_I 469_M 0.89 0.13 0.00
158_A 509_E 0.89 0.13 0.00
166_A 22_T 0.89 0.13 0.00
164_D 66_L 0.89 0.13 0.00
85_K 125_K 0.88 0.13 0.00
99_I 327_A 0.87 0.12 0.00
82_K 547_R 0.87 0.12 0.00
119_M 517_R 0.87 0.12 0.00
73_R 385_D 0.87 0.12 0.00
78_L 354_A 0.86 0.12 0.00
89_E 2_G 0.86 0.12 0.00
164_D 134_P 0.86 0.12 0.00
161_E 496_E 0.86 0.12 0.00
99_I 481_D 0.86 0.12 0.00
126_T 299_K 0.86 0.12 0.00
125_L 113_P 0.86 0.12 0.00
52_A 202_I 0.85 0.12 0.00
159_M 202_I 0.85 0.12 0.00
107_E 543_L 0.85 0.12 0.00
89_E 408_M 0.85 0.12 0.00
131_L 190_I 0.85 0.12 0.00
89_E 238_N 0.85 0.12 0.00
102_L 305_L 0.84 0.12 0.00
54_A 383_T 0.84 0.12 0.00
153_V 337_V 0.84 0.12 0.00
146_N 242_E 0.84 0.12 0.00
91_F 491_K 0.84 0.12 0.00
153_V 413_A 0.84 0.12 0.00
180_L 296_M 0.84 0.12 0.00
63_L 334_I 0.84 0.12 0.00
157_I 149_A 0.84 0.12 0.00
135_R 66_L 0.84 0.12 0.00
84_H 382_L 0.84 0.11 0.00
121_E 316_S 0.83 0.11 0.00
185_I 542_L 0.83 0.11 0.00
139_V 182_D 0.83 0.11 0.00
142_I 69_I 0.83 0.11 0.00
187_A 544_H 0.83 0.11 0.00
118_A 236_L 0.83 0.11 0.00
130_M 359_K 0.82 0.11 0.00
144_E 370_A 0.82 0.11 0.00
188_A 539_G 0.82 0.11 0.00
158_A 439_H 0.82 0.11 0.00
136_K 330_S 0.82 0.11 0.00
124_E 21_G 0.82 0.11 0.00
138_G 42_Y 0.82 0.11 0.00
134_V 379_G 0.82 0.11 0.00
88_L 73_I 0.82 0.11 0.00
115_D 220_A 0.81 0.11 0.00
99_I 207_I 0.81 0.11 0.00
119_M 536_R 0.81 0.11 0.00
157_I 220_A 0.81 0.11 0.00
72_L 236_L 0.81 0.11 0.00
170_V 34_R 0.81 0.11 0.00
183_R 424_Q 0.81 0.11 0.00
97_P 73_I 0.81 0.11 0.00
163_D 351_K 0.80 0.10 0.00
70_E 259_M 0.80 0.10 0.00
69_M 236_L 0.80 0.10 0.00
173_I 147_N 0.80 0.10 0.00
157_I 512_I 0.80 0.10 0.00
79_D 136_T 0.80 0.10 0.00
101_S 166_K 0.80 0.10 0.00
184_T 346_M 0.80 0.10 0.00
45_A 78_Q 0.80 0.10 0.00
191_T 441_L 0.80 0.10 0.00
87_A 264_E 0.79 0.10 0.00
168_G 364_D 0.79 0.10 0.00
129_S 149_A 0.79 0.10 0.00
126_T 296_M 0.79 0.10 0.00
101_S 364_D 0.79 0.10 0.00
146_N 554_G 0.79 0.10 0.00
86_F 404_M 0.79 0.10 0.00
49_A 379_G 0.79 0.10 0.00
126_T 3_K 0.79 0.10 0.00
43_K 190_I 0.79 0.10 0.00
163_D 181_L 0.79 0.10 0.00
192_V 319_P 0.79 0.10 0.00
142_I 448_A 0.79 0.10 0.00
93_N 17_A 0.79 0.10 0.00
146_N 320_L 0.78 0.10 0.00
53_E 358_G 0.78 0.10 0.00
148_P 354_A 0.78 0.10 0.00
157_I 190_I 0.78 0.10 0.00
144_E 39_I 0.78 0.10 0.00
60_D 353_V 0.78 0.10 0.00
119_M 69_I 0.78 0.10 0.00
168_G 125_K 0.78 0.10 0.00
173_I 286_I 0.78 0.10 0.00
180_L 538_Q 0.78 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)
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