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OPENSEQ.org
nifH-nifKbeta_lower E value for B
Genes: A B A+B
Length: 290 523 752
Sequences: 610 1892 486
Seq/Len: 2.1 3.62 0.65
MirrorTree (Pazo et al. 2001) 0.80
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 0.02 0.52 0.26
2 0.02 0.53 0.40
5 0.03 0.53 0.56
10 0.04 0.53 0.59
20 0.07 0.53 0.60
100 0.11 0.53 0.66
∞ 0.18 0.53 0.69
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
169_I 226_I 1.30 0.49 0.00
241_Y 84_K 1.18 0.38 0.00
114_G 330_M 1.15 0.36 0.00
202_N 416_G 1.14 0.36 0.00
34_V 488_E 1.13 0.35 0.00
226_M 279_E 1.13 0.34 0.00
76_V 162_L 1.09 0.32 0.00
205_G 116_D 1.08 0.31 0.00
59_M 225_N 1.08 0.31 0.00
26_A 218_V 1.07 0.30 0.00
48_L 251_Y 1.07 0.30 0.00
34_V 181_V 1.06 0.30 0.00
234_K 507_E 1.06 0.29 0.00
254_L 434_V 1.04 0.28 0.00
195_E 226_I 1.03 0.27 0.00
202_N 308_T 1.03 0.27 0.00
166_S 507_E 1.02 0.27 0.00
202_N 337_G 1.02 0.27 0.00
140_I 91_G 1.01 0.26 0.00
256_I 221_N 1.01 0.26 0.00
117_E 422_Y 1.01 0.26 0.00
271_E 204_I 1.01 0.26 0.00
172_Y 355_M 1.00 0.26 0.00
117_E 122_A 1.00 0.26 0.00
103_V 247_M 1.00 0.26 0.00
34_V 404_K 0.99 0.25 0.00
189_N 350_R 0.99 0.25 0.00
183_L 249_V 0.98 0.24 0.00
59_M 239_V 0.97 0.24 0.00
6_C 181_V 0.97 0.24 0.00
117_E 282_K 0.97 0.24 0.00
274_I 334_E 0.97 0.23 0.00
212_V 164_A 0.96 0.23 0.00
83_G 206_R 0.95 0.23 0.00
104_I 159_G 0.95 0.22 0.00
263_D 251_Y 0.95 0.22 0.00
28_A 96_V 0.94 0.22 0.00
250_D 291_V 0.94 0.22 0.00
225_R 46_W 0.94 0.22 0.00
172_Y 122_A 0.93 0.21 0.00
81_Y 151_T 0.93 0.21 0.00
260_I 280_E 0.93 0.21 0.00
152_C 311_H 0.93 0.21 0.00
123_V 283_D 0.92 0.21 0.00
76_V 359_H 0.92 0.21 0.00
34_V 514_A 0.92 0.21 0.00
262_M 24_L 0.92 0.21 0.00
185_C 93_Q 0.92 0.21 0.00
54_A 251_Y 0.92 0.21 0.00
26_A 340_I 0.92 0.21 0.00
268_L 333_S 0.91 0.20 0.00
74_E 290_T 0.91 0.20 0.00
31_G 185_H 0.91 0.20 0.00
57_T 149_V 0.90 0.20 0.00
152_C 46_W 0.90 0.20 0.00
103_V 225_N 0.90 0.20 0.00
159_M 282_K 0.90 0.20 0.00
34_V 326_D 0.90 0.20 0.00
172_Y 184_A 0.89 0.19 0.00
28_A 49_T 0.89 0.19 0.00
58_I 180_P 0.89 0.19 0.00
171_K 120_E 0.89 0.19 0.00
169_I 119_T 0.89 0.19 0.00
244_L 196_G 0.89 0.19 0.00
166_S 132_K 0.89 0.19 0.00
59_M 36_P 0.89 0.19 0.00
74_E 50_K 0.88 0.19 0.00
263_D 49_T 0.88 0.19 0.00
20_T 422_Y 0.88 0.19 0.00
32_K 303_K 0.88 0.19 0.00
107_I 90_H 0.88 0.19 0.00
26_A 49_T 0.87 0.18 0.00
178_V 251_Y 0.87 0.18 0.00
37_V 157_V 0.87 0.18 0.00
196_L 426_D 0.87 0.18 0.00
274_I 204_I 0.87 0.18 0.00
51_H 327_E 0.87 0.18 0.00
119_D 273_A 0.86 0.18 0.00
106_A 75_A 0.86 0.18 0.00
235_A 360_T 0.86 0.18 0.00
200_L 353_D 0.86 0.18 0.00
23_L 472_P 0.86 0.18 0.00
57_T 110_P 0.86 0.18 0.00
152_C 208_F 0.86 0.18 0.00
6_C 25_A 0.86 0.18 0.00
172_Y 508_E 0.85 0.18 0.00
26_A 30_G 0.85 0.17 0.00
230_E 416_G 0.85 0.17 0.00
198_I 204_I 0.85 0.17 0.00
206_T 332_V 0.85 0.17 0.00
83_G 25_A 0.84 0.17 0.00
202_N 245_S 0.84 0.17 0.00
8_I 227_V 0.84 0.17 0.00
172_Y 358_S 0.84 0.17 0.00
166_S 401_R 0.84 0.17 0.00
28_A 82_F 0.83 0.17 0.00
256_I 367_F 0.83 0.17 0.00
230_E 51_E 0.83 0.17 0.00
267_E 369_L 0.83 0.16 0.00
118_D 181_V 0.83 0.16 0.00
33_K 283_D 0.83 0.16 0.00
81_Y 326_D 0.83 0.16 0.00
57_T 226_I 0.83 0.16 0.00
170_V 349_G 0.82 0.16 0.00
270_M 244_L 0.82 0.16 0.00
261_T 251_Y 0.82 0.16 0.00
212_V 335_I 0.82 0.16 0.00
33_K 501_I 0.82 0.16 0.00
109_F 96_V 0.82 0.16 0.00
24_V 472_P 0.82 0.16 0.00
117_E 51_E 0.82 0.16 0.00
232_D 311_H 0.82 0.16 0.00
118_D 327_E 0.82 0.16 0.00
57_T 243_M 0.82 0.16 0.00
230_E 283_D 0.82 0.16 0.00
33_K 404_K 0.81 0.16 0.00
103_V 143_K 0.81 0.16 0.00
61_M 135_L 0.81 0.16 0.00
247_K 428_W 0.81 0.15 0.00
195_E 384_L 0.81 0.15 0.00
274_I 88_Y 0.81 0.15 0.00
258_N 245_S 0.81 0.15 0.00
94_P 95_C 0.81 0.15 0.00
164_N 95_C 0.81 0.15 0.00
222_E 95_C 0.81 0.15 0.00
225_R 383_L 0.81 0.15 0.00
172_Y 251_Y 0.81 0.15 0.00
57_T 204_I 0.81 0.15 0.00
212_V 182_P 0.81 0.15 0.00
84_V 388_C 0.80 0.15 0.00
212_V 323_D 0.80 0.15 0.00
26_A 280_E 0.80 0.15 0.00
119_D 240_I 0.80 0.15 0.00
175_S 36_P 0.80 0.15 0.00
27_L 308_T 0.80 0.15 0.00
220_R 129_Q 0.79 0.15 0.00
194_D 204_I 0.79 0.15 0.00
232_D 30_G 0.79 0.15 0.00
60_E 241_K 0.79 0.15 0.00
189_N 281_M 0.79 0.15 0.00
84_V 324_W 0.79 0.15 0.00
34_V 439_P 0.79 0.15 0.00
196_L 167_N 0.79 0.15 0.00
119_D 280_E 0.79 0.15 0.00
248_V 402_W 0.79 0.15 0.00
260_I 116_D 0.79 0.15 0.00
166_S 441_F 0.79 0.14 0.00
112_E 224_I 0.79 0.14 0.00
243_A 432_S 0.79 0.14 0.00
256_I 219_G 0.78 0.14 0.00
53_K 189_F 0.78 0.14 0.00
76_V 183_F 0.78 0.14 0.00
217_V 245_S 0.78 0.14 0.00
169_I 149_V 0.78 0.14 0.00
52_S 422_Y 0.78 0.14 0.00
159_M 369_L 0.78 0.14 0.00
34_V 276_T 0.78 0.14 0.00
71_L 273_A 0.78 0.14 0.00
175_S 44_F 0.78 0.14 0.00
57_T 338_Q 0.78 0.14 0.00
226_M 309_W 0.78 0.14 0.00
84_V 331_K 0.78 0.14 0.00
102_G 95_C 0.78 0.14 0.00
30_M 323_D 0.78 0.14 0.00
32_K 510_R 0.78 0.14 0.00
239_D 162_L 0.78 0.14 0.00
21_Q 179_F 0.77 0.14 0.00
194_D 501_I 0.77 0.14 0.00
115_A 88_Y 0.77 0.14 0.00
140_I 235_G 0.77 0.14 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.53 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
4428 0.78 HK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3952 0.84 HK Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done
3521 0.65 nifH-nifKbeta_lower E value for B Δgene:(1, 20) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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