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OPENSEQ.org
FliI-FliH-HHblits-SEQ
Genes: A B A+B
Length: 456 136 556
Sequences: 5188 1016 780
Seq/Len: 11.38 7.47 1.4
MirrorTree (Pazo et al. 2001) 0.72
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 0.14 0.00 1.31
2 0.43 0.00 1.32
5 0.44 0.00 1.31
10 0.45 0.00 1.32
20 0.46 0.00 1.33
100 0.47 0.00 1.35
∞ 0.51 0.04 1.40
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
150_L 39_V 1.34 0.74 0.02
445_S 61_Q 1.15 0.57 0.01
169_L 117_D 1.12 0.55 0.01
230_A 96_L 1.12 0.54 0.01
196_A 16_T 1.11 0.54 0.01
331_E 6_M 1.10 0.53 0.01
65_V 40_I 1.10 0.52 0.01
233_V 28_L 1.07 0.50 0.01
448_A 102_L 1.07 0.49 0.01
305_L 75_P 1.06 0.48 0.01
163_V 13_F 1.04 0.46 0.01
422_I 54_Q 1.03 0.45 0.01
270_I 123_R 1.02 0.44 0.01
27_R 131_A 1.00 0.42 0.01
170_L 83_E 0.98 0.41 0.01
379_L 109_V 0.97 0.39 0.01
65_V 81_V 0.97 0.39 0.01
35_T 114_G 0.97 0.39 0.01
218_D 134_G 0.96 0.38 0.01
303_A 111_A 0.96 0.38 0.01
231_R 99_D 0.95 0.38 0.01
132_P 127_L 0.95 0.37 0.01
167_N 123_R 0.94 0.37 0.01
372_I 67_G 0.93 0.35 0.01
352_V 64_L 0.92 0.35 0.01
415_D 115_D 0.92 0.34 0.01
369_E 114_G 0.91 0.34 0.01
38_V 25_A 0.90 0.33 0.01
449_L 39_V 0.90 0.33 0.01
442_W 49_S 0.90 0.33 0.01
249_G 20_L 0.90 0.32 0.01
293_A 63_P 0.89 0.32 0.01
198_Y 123_R 0.89 0.32 0.01
357_L 71_L 0.89 0.31 0.01
146_P 114_G 0.88 0.31 0.01
270_I 16_T 0.88 0.31 0.01
204_I 127_L 0.87 0.30 0.01
209_I 29_M 0.87 0.30 0.01
400_R 107_C 0.87 0.30 0.01
168_A 89_L 0.87 0.30 0.01
368_I 126_E 0.87 0.30 0.01
252_Y 25_A 0.87 0.30 0.01
130_G 74_H 0.86 0.29 0.00
363_Y 32_A 0.86 0.29 0.00
284_I 125_Q 0.86 0.29 0.00
117_L 120_V 0.86 0.29 0.00
279_M 16_T 0.86 0.29 0.00
84_E 120_V 0.85 0.29 0.00
444_D 127_L 0.85 0.29 0.00
94_V 97_R 0.85 0.29 0.00
178_M 124_W 0.85 0.28 0.00
39_L 39_V 0.85 0.28 0.00
196_A 124_W 0.85 0.28 0.00
229_R 40_I 0.84 0.28 0.00
237_A 52_I 0.84 0.27 0.00
196_A 114_G 0.84 0.27 0.00
449_L 109_V 0.83 0.27 0.00
91_G 112_D 0.83 0.27 0.00
285_A 38_Q 0.83 0.27 0.00
45_Q 58_L 0.83 0.27 0.00
26_R 126_E 0.83 0.27 0.00
293_A 74_H 0.83 0.27 0.00
354_S 72_R 0.83 0.27 0.00
117_L 99_D 0.82 0.26 0.00
156_E 55_I 0.82 0.26 0.00
440_A 71_L 0.82 0.26 0.00
220_I 131_A 0.82 0.26 0.00
163_V 8_Q 0.81 0.26 0.00
32_T 83_E 0.81 0.26 0.00
88_I 83_E 0.81 0.26 0.00
148_N 123_R 0.81 0.26 0.00
113_G 94_W 0.81 0.25 0.00
165_A 71_L 0.81 0.25 0.00
89_L 110_S 0.81 0.25 0.00
230_A 22_S 0.81 0.25 0.00
451_L 83_E 0.81 0.25 0.00
150_L 58_L 0.81 0.25 0.00
309_V 88_T 0.81 0.25 0.00
202_D 51_L 0.80 0.25 0.00
159_L 111_A 0.80 0.25 0.00
203_V 6_M 0.80 0.25 0.00
178_M 31_M 0.80 0.25 0.00
203_V 43_T 0.80 0.24 0.00
431_F 22_S 0.80 0.24 0.00
277_Y 36_A 0.80 0.24 0.00
221_E 29_M 0.80 0.24 0.00
82_L 131_A 0.80 0.24 0.00
114_P 102_L 0.80 0.24 0.00
168_A 123_R 0.79 0.24 0.00
351_I 105_G 0.79 0.24 0.00
87_G 105_G 0.79 0.24 0.00
249_G 33_L 0.79 0.23 0.00
217_K 79_Q 0.79 0.23 0.00
157_H 98_G 0.78 0.23 0.00
121_L 103_H 0.78 0.23 0.00
412_K 110_S 0.78 0.23 0.00
255_R 62_E 0.78 0.23 0.00
39_L 69_P 0.78 0.23 0.00
354_S 105_G 0.78 0.23 0.00
443_E 84_M 0.78 0.23 0.00
46_L 130_L 0.78 0.23 0.00
28_Y 115_D 0.77 0.23 0.00
390_L 59_L 0.77 0.23 0.00
35_T 73_V 0.77 0.23 0.00
161_T 63_P 0.77 0.22 0.00
121_L 44_P 0.77 0.22 0.00
63_K 74_H 0.77 0.22 0.00
396_S 116_L 0.77 0.22 0.00
370_A 48_N 0.77 0.22 0.00
409_A 127_L 0.77 0.22 0.00
209_I 38_Q 0.77 0.22 0.00
132_P 105_G 0.77 0.22 0.00
140_G 59_L 0.76 0.22 0.00
155_I 33_L 0.76 0.22 0.00
425_W 108_K 0.76 0.22 0.00
156_E 109_V 0.76 0.22 0.00
67_S 77_D 0.76 0.22 0.00
375_A 85_L 0.76 0.22 0.00
38_V 43_T 0.76 0.21 0.00
120_V 69_P 0.76 0.21 0.00
331_E 13_F 0.76 0.21 0.00
178_M 83_E 0.76 0.21 0.00
452_I 13_F 0.76 0.21 0.00
231_R 101_T 0.76 0.21 0.00
405_V 25_A 0.75 0.21 0.00
200_R 126_E 0.75 0.21 0.00
98_N 29_M 0.75 0.21 0.00
107_G 105_G 0.75 0.21 0.00
196_A 54_Q 0.75 0.21 0.00
324_A 110_S 0.75 0.21 0.00
417_M 51_L 0.74 0.21 0.00
229_R 112_D 0.74 0.20 0.00
52_C 109_V 0.74 0.20 0.00
304_K 134_G 0.74 0.20 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 (0.43 > 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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