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OPENSEQ.org
HK
Genes: A B A+B
Length: 290 523 753
Sequences: 13821 2129 631
Seq/Len: 47.66 4.07 0.84
MirrorTree (Pazo et al. 2001) 0.73
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 0.03 0.56 0.43
2 0.04 0.58 0.57
5 0.05 0.59 0.73
10 0.07 0.59 0.75
20 0.08 0.60 0.78
100 0.12 0.71 0.81
∞ 0.18 0.74 0.88
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 1.13 0.41 0.00
172_Y 122_A 1.07 0.36 0.00
172_Y 355_M 1.04 0.33 0.00
34_V 181_V 1.02 0.32 0.00
166_S 507_E 1.01 0.31 0.00
84_V 388_C 0.99 0.29 0.00
57_T 325_T 0.98 0.29 0.00
256_I 221_N 0.95 0.27 0.00
34_V 488_E 0.95 0.27 0.00
270_M 35_Y 0.95 0.27 0.00
118_D 327_E 0.95 0.27 0.00
34_V 326_D 0.94 0.26 0.00
48_L 251_Y 0.94 0.26 0.00
152_C 311_H 0.92 0.25 0.00
6_C 181_V 0.92 0.24 0.00
6_C 25_A 0.91 0.24 0.00
74_E 311_H 0.91 0.24 0.00
84_V 331_K 0.91 0.24 0.00
202_N 308_T 0.90 0.23 0.00
104_I 159_G 0.90 0.23 0.00
49_I 101_S 0.90 0.23 0.00
81_Y 422_Y 0.90 0.23 0.00
239_D 291_V 0.89 0.23 0.00
79_A 55_L 0.88 0.22 0.00
212_V 314_P 0.87 0.22 0.00
152_C 208_F 0.87 0.21 0.00
252_K 49_T 0.86 0.21 0.00
235_A 360_T 0.86 0.21 0.00
172_Y 508_E 0.86 0.21 0.00
140_I 91_G 0.86 0.21 0.00
220_R 169_S 0.84 0.20 0.00
75_D 220_S 0.83 0.19 0.00
64_E 349_G 0.83 0.19 0.00
83_G 206_R 0.83 0.19 0.00
34_V 276_T 0.83 0.19 0.00
57_T 338_Q 0.82 0.19 0.00
145_A 158_I 0.82 0.19 0.00
172_Y 184_A 0.82 0.19 0.00
6_C 509_T 0.82 0.19 0.00
83_G 48_T 0.82 0.19 0.00
183_L 332_V 0.82 0.19 0.00
267_E 29_D 0.82 0.19 0.00
34_V 48_T 0.82 0.18 0.00
177_S 149_V 0.82 0.18 0.00
28_A 332_V 0.81 0.18 0.00
175_S 36_P 0.81 0.18 0.00
263_D 359_H 0.81 0.18 0.00
34_V 404_K 0.81 0.18 0.00
203_K 501_I 0.80 0.18 0.00
28_A 96_V 0.80 0.18 0.00
23_L 328_F 0.80 0.17 0.00
267_E 245_S 0.80 0.17 0.00
75_D 443_I 0.80 0.17 0.00
246_R 380_V 0.80 0.17 0.00
261_T 21_K 0.80 0.17 0.00
263_D 50_K 0.79 0.17 0.00
34_V 514_A 0.79 0.17 0.00
194_D 339_P 0.79 0.17 0.00
117_E 122_A 0.79 0.17 0.00
226_M 434_V 0.79 0.17 0.00
226_M 279_E 0.79 0.17 0.00
202_N 253_L 0.79 0.17 0.00
51_H 327_E 0.79 0.17 0.00
74_E 50_K 0.79 0.17 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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