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OPENSEQ.org
FliI-FliH-PDBFILE-SEQ-JACK
Genes: A B A+B
Length: 456 136 573
Sequences: 11129 1275 832
Seq/Len: 24.41 9.38 1.45
MirrorTree (Pazo et al. 2001) 0.71
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 0.05 0.00 1.41
2 0.49 0.00 1.41
5 0.50 0.00 1.41
10 0.51 0.00 1.41
20 0.52 0.00 1.41
100 0.53 0.00 1.43
∞ 0.55 0.01 1.51
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
248_Q 124_W 1.23 0.66 0.00
158_V 43_T 1.22 0.65 0.00
196_A 16_T 1.22 0.65 0.00
196_A 124_W 1.16 0.60 0.00
279_M 124_W 1.15 0.59 0.00
78_F 69_P 1.15 0.58 0.00
279_M 16_T 1.12 0.56 0.00
168_A 59_L 1.12 0.56 0.00
277_Y 39_V 1.12 0.55 0.00
38_V 16_T 1.12 0.55 0.00
330_T 55_I 1.11 0.55 0.00
396_S 37_R 1.10 0.53 0.00
252_Y 25_A 1.08 0.52 0.00
401_N 94_W 1.08 0.51 0.00
218_D 41_G 1.05 0.48 0.00
171_T 73_V 1.04 0.48 0.00
38_V 25_A 1.04 0.47 0.00
155_I 96_L 1.04 0.47 0.00
401_N 39_V 1.02 0.46 0.00
247_M 123_R 1.02 0.45 0.00
88_I 38_Q 1.01 0.44 0.00
82_L 114_G 1.00 0.43 0.00
31_L 114_G 0.99 0.42 0.00
279_M 89_L 0.99 0.42 0.00
270_I 62_E 0.99 0.42 0.00
239_A 94_W 0.99 0.42 0.00
360_A 103_H 0.98 0.41 0.00
35_T 16_T 0.98 0.41 0.00
443_E 100_P 0.97 0.41 0.00
218_D 39_V 0.97 0.40 0.00
54_I 102_L 0.96 0.40 0.00
398_F 55_I 0.96 0.39 0.00
203_V 100_P 0.96 0.39 0.00
279_M 114_G 0.96 0.39 0.00
39_L 69_P 0.96 0.39 0.00
196_A 114_G 0.94 0.37 0.00
218_D 43_T 0.94 0.37 0.00
248_Q 126_E 0.93 0.36 0.00
202_D 26_S 0.93 0.36 0.00
35_T 28_L 0.93 0.36 0.00
147_F 27_R 0.93 0.36 0.00
164_R 107_C 0.92 0.36 0.00
181_F 71_L 0.92 0.35 0.00
156_E 109_V 0.92 0.35 0.00
218_D 58_L 0.91 0.35 0.00
125_G 117_D 0.91 0.35 0.00
422_I 104_H 0.91 0.35 0.00
48_L 81_V 0.91 0.35 0.00
390_L 59_L 0.91 0.34 0.00
128_L 108_K 0.91 0.34 0.00
250_A 85_L 0.91 0.34 0.00
16_E 34_E 0.91 0.34 0.00
134_P 120_V 0.90 0.34 0.00
312_A 102_L 0.90 0.33 0.00
277_Y 51_L 0.90 0.33 0.00
409_A 127_L 0.89 0.32 0.00
249_G 20_L 0.88 0.32 0.00
223_I 21_D 0.88 0.32 0.00
384_H 27_R 0.88 0.32 0.00
252_Y 124_W 0.88 0.32 0.00
285_A 38_Q 0.88 0.32 0.00
232_S 102_L 0.88 0.32 0.00
339_I 21_D 0.88 0.31 0.00
65_V 111_A 0.87 0.31 0.00
200_R 59_L 0.87 0.31 0.00
149_P 63_P 0.87 0.31 0.00
412_K 11_S 0.87 0.31 0.00
375_A 36_A 0.87 0.30 0.00
196_A 62_E 0.86 0.30 0.00
57_Q 104_H 0.86 0.30 0.00
442_W 83_E 0.86 0.30 0.00
155_I 114_G 0.86 0.30 0.00
363_Y 28_L 0.86 0.30 0.00
131_L 101_T 0.86 0.30 0.00
279_M 20_L 0.86 0.30 0.00
51_T 43_T 0.85 0.29 0.00
35_T 25_A 0.85 0.29 0.00
265_Q 11_S 0.85 0.29 0.00
147_F 71_L 0.85 0.29 0.00
402_R 99_D 0.84 0.28 0.00
266_H 12_E 0.84 0.28 0.00
200_R 39_V 0.84 0.28 0.00
171_T 36_A 0.84 0.28 0.00
270_I 16_T 0.83 0.28 0.00
32_T 29_M 0.83 0.28 0.00
164_R 36_A 0.83 0.28 0.00
96_A 123_R 0.83 0.28 0.00
339_I 29_M 0.83 0.28 0.00
39_L 61_Q 0.83 0.28 0.00
196_A 33_L 0.82 0.27 0.00
172_V 17_L 0.82 0.27 0.00
411_A 101_T 0.82 0.27 0.00
184_S 81_V 0.82 0.27 0.00
203_V 57_Q 0.82 0.27 0.00
171_T 66_S 0.82 0.27 0.00
363_Y 102_L 0.82 0.26 0.00
138_E 76_D 0.82 0.26 0.00
76_R 71_L 0.81 0.26 0.00
396_S 14_Q 0.81 0.26 0.00
379_L 28_L 0.81 0.26 0.00
351_I 5_R 0.81 0.26 0.00
198_Y 128_C 0.81 0.26 0.00
235_I 45_A 0.81 0.25 0.00
237_A 48_N 0.81 0.25 0.00
368_I 94_W 0.81 0.25 0.00
271_M 121_A 0.80 0.25 0.00
93_R 37_R 0.80 0.25 0.00
209_I 48_N 0.80 0.25 0.00
417_M 102_L 0.80 0.25 0.00
266_H 121_A 0.80 0.25 0.00
270_I 123_R 0.80 0.25 0.00
128_L 99_D 0.80 0.25 0.00
121_L 32_A 0.79 0.24 0.00
253_A 127_L 0.79 0.24 0.00
380_I 59_L 0.79 0.24 0.00
203_V 86_G 0.79 0.24 0.00
248_Q 89_L 0.79 0.24 0.00
249_G 27_R 0.79 0.24 0.00
93_R 80_R 0.79 0.24 0.00
203_V 24_I 0.78 0.24 0.00
27_R 55_I 0.78 0.24 0.00
405_V 63_P 0.78 0.23 0.00
431_F 84_M 0.78 0.23 0.00
431_F 107_C 0.78 0.23 0.00
58_D 51_L 0.78 0.23 0.00
388_V 107_C 0.78 0.23 0.00
28_Y 71_L 0.78 0.23 0.00
226_P 71_L 0.78 0.23 0.00
107_G 73_V 0.78 0.23 0.00
238_P 21_D 0.78 0.23 0.00
322_I 75_P 0.77 0.23 0.00
375_A 106_G 0.77 0.23 0.00
88_I 7_Q 0.77 0.23 0.00
400_R 40_I 0.77 0.23 0.00
449_L 51_L 0.77 0.23 0.00
270_I 115_D 0.77 0.23 0.00
158_V 46_V 0.77 0.23 0.00
67_S 40_I 0.77 0.23 0.00
386_A 102_L 0.77 0.23 0.00
141_A 29_M 0.76 0.22 0.00
91_G 89_L 0.76 0.22 0.00
232_S 79_Q 0.76 0.22 0.00
132_P 127_L 0.76 0.22 0.00
168_A 10_V 0.76 0.22 0.00
218_D 40_I 0.76 0.22 0.00
378_A 32_A 0.76 0.22 0.00
431_F 55_I 0.76 0.22 0.00
279_M 34_E 0.76 0.22 0.00
265_Q 36_A 0.76 0.22 0.00
35_T 114_G 0.76 0.22 0.00
39_L 38_Q 0.76 0.22 0.00
180_L 94_W 0.75 0.22 0.00
150_L 38_Q 0.75 0.21 0.00
305_L 75_P 0.75 0.21 0.00
429_E 124_W 0.75 0.21 0.00
443_E 4_A 0.75 0.21 0.00
439_R 26_S 0.75 0.21 0.00
196_A 63_P 0.74 0.21 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 A, there is a high ratio (0.52 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
10708 1.42 flih-fliI Δgene:(1, 20) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done
8140 1.39 FliI-FliH-HHblits-SEQ Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done
8139 0.28 FliI-FliH-HHblits-SEQ Δgene:(0, 1) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done
8138 1.39 FliI-FliH-HHblits-SEQ Δgene:(0, 1) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done
8137 0.28 FliI-FliH-HHblits-SEQ Δgene:(0, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done
8136 1.39 FliI-FliH-HHblits-SEQ Δgene:(1, 2) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
8125 1.4 FliI-FliH-HHblits-SEQ Δgene:(1, 2) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
8124 1.4 FliI-FliH-HHblits-SEQ Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
8123 1.4 FliI-FliH-HHblits-SEQ Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8090 1.42 FliI-FliH-HHblits-SEQ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
8089 1.45 FliI-FliH-PDBFILE-SEQ-JACK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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