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OPENSEQ.org
HK
Genes: A B A+B
Length: 290 523 757
Sequences: 610 2127 591
Seq/Len: 2.1 4.07 0.78
MirrorTree (Pazo et al. 2001) 0.82
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 0.57 0.41
2 0.02 0.58 0.54
5 0.03 0.59 0.70
10 0.04 0.59 0.72
20 0.07 0.60 0.73
100 0.11 0.71 0.74
∞ 0.18 0.73 0.75
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
33_K 501_I 1.30 0.54 0.00
104_I 159_G 1.20 0.45 0.00
202_N 308_T 1.17 0.43 0.00
169_I 226_I 1.12 0.39 0.00
34_V 488_E 1.12 0.38 0.00
51_H 327_E 1.10 0.36 0.00
195_E 226_I 1.08 0.35 0.00
226_M 279_E 1.05 0.33 0.00
34_V 181_V 1.05 0.33 0.00
256_I 221_N 1.04 0.32 0.00
34_V 326_D 1.04 0.32 0.00
84_V 331_K 1.03 0.31 0.00
172_Y 355_M 1.03 0.31 0.00
172_Y 122_A 1.02 0.30 0.00
28_A 96_V 1.00 0.29 0.00
189_N 350_R 1.00 0.29 0.00
59_M 225_N 1.00 0.29 0.00
183_L 249_V 1.00 0.29 0.00
64_E 349_G 0.99 0.28 0.00
230_E 48_T 0.98 0.28 0.00
48_L 251_Y 0.98 0.27 0.00
166_S 507_E 0.98 0.27 0.00
75_D 181_V 0.98 0.27 0.00
34_V 514_A 0.98 0.27 0.00
76_V 359_H 0.97 0.27 0.00
256_I 464_V 0.97 0.27 0.00
23_L 465_P 0.97 0.27 0.00
140_I 91_G 0.97 0.27 0.00
206_T 204_I 0.96 0.26 0.00
235_A 360_T 0.96 0.26 0.00
51_H 168_N 0.95 0.26 0.00
83_G 25_A 0.95 0.25 0.00
20_T 463_E 0.94 0.25 0.00
74_E 50_K 0.94 0.25 0.00
26_A 218_V 0.94 0.24 0.00
159_M 369_L 0.93 0.24 0.00
59_M 239_V 0.93 0.24 0.00
84_V 467_I 0.93 0.24 0.00
260_I 360_T 0.93 0.24 0.00
172_Y 251_Y 0.93 0.24 0.00
152_C 46_W 0.92 0.24 0.00
34_V 276_T 0.92 0.24 0.00
57_T 226_I 0.92 0.23 0.00
32_K 303_K 0.91 0.23 0.00
6_C 509_T 0.91 0.23 0.00
117_E 422_Y 0.90 0.22 0.00
26_A 340_I 0.90 0.22 0.00
260_I 339_P 0.90 0.22 0.00
172_Y 184_A 0.90 0.22 0.00
33_K 410_L 0.89 0.22 0.00
84_V 388_C 0.89 0.22 0.00
81_Y 422_Y 0.89 0.22 0.00
111_E 125_F 0.89 0.22 0.00
30_M 323_D 0.89 0.21 0.00
263_D 281_M 0.88 0.21 0.00
262_M 24_L 0.88 0.21 0.00
49_I 101_S 0.88 0.21 0.00
196_L 426_D 0.88 0.21 0.00
232_D 408_A 0.88 0.21 0.00
175_S 181_V 0.88 0.21 0.00
258_N 245_S 0.88 0.21 0.00
241_Y 84_K 0.88 0.21 0.00
270_M 244_L 0.88 0.21 0.00
119_D 273_A 0.87 0.21 0.00
152_C 208_F 0.87 0.21 0.00
230_E 283_D 0.87 0.20 0.00
118_D 327_E 0.87 0.20 0.00
6_C 25_A 0.87 0.20 0.00
234_K 507_E 0.87 0.20 0.00
8_I 123_A 0.87 0.20 0.00
198_I 273_A 0.86 0.20 0.00
83_G 206_R 0.86 0.20 0.00
76_V 308_T 0.86 0.20 0.00
74_E 311_H 0.86 0.20 0.00
212_V 323_D 0.86 0.20 0.00
172_Y 508_E 0.86 0.20 0.00
57_T 243_M 0.86 0.20 0.00
75_D 220_S 0.86 0.20 0.00
33_K 118_M 0.86 0.20 0.00
206_T 332_V 0.85 0.20 0.00
117_E 282_K 0.85 0.20 0.00
217_V 223_K 0.85 0.20 0.00
119_D 36_P 0.85 0.20 0.00
236_K 121_D 0.85 0.19 0.00
179_R 155_A 0.85 0.19 0.00
112_E 511_G 0.85 0.19 0.00
114_G 330_M 0.85 0.19 0.00
57_T 151_T 0.84 0.19 0.00
158_A 120_E 0.84 0.19 0.00
74_E 224_I 0.84 0.19 0.00
197_I 46_W 0.84 0.19 0.00
252_K 435_F 0.84 0.19 0.00
26_A 30_G 0.84 0.19 0.00
5_Q 249_V 0.83 0.19 0.00
274_I 204_I 0.83 0.19 0.00
59_M 36_P 0.83 0.18 0.00
26_A 106_H 0.83 0.18 0.00
239_D 291_V 0.83 0.18 0.00
146_Q 435_F 0.83 0.18 0.00
118_D 181_V 0.83 0.18 0.00
212_V 314_P 0.83 0.18 0.00
166_S 132_K 0.83 0.18 0.00
270_M 35_Y 0.83 0.18 0.00
4_R 341_P 0.82 0.18 0.00
250_D 164_A 0.82 0.18 0.00
203_K 501_I 0.82 0.18 0.00
270_M 444_G 0.82 0.18 0.00
174_N 421_V 0.82 0.18 0.00
202_N 253_L 0.82 0.18 0.00
159_M 101_S 0.82 0.18 0.00
189_N 486_G 0.82 0.18 0.00
34_V 439_P 0.82 0.18 0.00
31_G 185_H 0.82 0.18 0.00
53_K 490_A 0.82 0.18 0.00
74_E 181_V 0.82 0.18 0.00
109_F 325_T 0.81 0.18 0.00
69_E 439_P 0.81 0.17 0.00
195_E 384_L 0.81 0.17 0.00
163_N 321_G 0.81 0.17 0.00
205_G 116_D 0.81 0.17 0.00
49_I 56_N 0.81 0.17 0.00
203_K 245_S 0.81 0.17 0.00
54_A 251_Y 0.81 0.17 0.00
200_L 334_E 0.80 0.17 0.00
156_M 324_W 0.80 0.17 0.00
171_K 120_E 0.80 0.17 0.00
51_H 452_Q 0.80 0.17 0.00
232_D 286_N 0.80 0.17 0.00
125_Y 154_M 0.80 0.17 0.00
174_N 27_K 0.80 0.17 0.00
234_K 54_E 0.80 0.17 0.00
34_V 48_T 0.80 0.17 0.00
225_R 383_L 0.80 0.17 0.00
83_G 280_E 0.80 0.17 0.00
51_H 309_W 0.80 0.17 0.00
274_I 88_Y 0.80 0.17 0.00
62_A 439_P 0.80 0.17 0.00
106_A 75_A 0.79 0.17 0.00
58_I 140_A 0.79 0.17 0.00
164_N 159_G 0.79 0.17 0.00
106_A 320_M 0.79 0.17 0.00
202_N 245_S 0.79 0.17 0.00
145_A 158_I 0.79 0.17 0.00
183_L 247_M 0.79 0.16 0.00
75_D 306_E 0.79 0.16 0.00
258_N 323_D 0.79 0.16 0.00
175_S 36_P 0.79 0.16 0.00
102_G 159_G 0.79 0.16 0.00
231_Y 49_T 0.79 0.16 0.00
34_V 462_F 0.79 0.16 0.00
248_V 395_C 0.79 0.16 0.00
28_A 350_R 0.79 0.16 0.00
202_N 337_G 0.79 0.16 0.00
260_I 334_E 0.78 0.16 0.00
116_Y 118_M 0.78 0.16 0.00
5_Q 331_K 0.78 0.16 0.00
177_S 149_V 0.78 0.16 0.00
57_T 342_A 0.78 0.16 0.00
267_E 121_D 0.78 0.16 0.00
103_V 247_M 0.78 0.16 0.00
231_Y 132_K 0.78 0.16 0.00
112_E 241_K 0.78 0.16 0.00
192_R 29_D 0.78 0.16 0.00
6_C 281_M 0.78 0.16 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 (0.60 > 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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