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OPENSEQ.org
FliI-FliH-HHblits-SEQ
Genes: A B A+B
Length: 456 136 555
Sequences: 5039 198 154
Seq/Len: 11.05 1.46 0.28
MirrorTree (Pazo et al. 2001) 0.81
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 0.26
2 0.43 0.00 0.26
5 0.44 0.00 0.26
10 0.45 0.00 0.26
20 0.46 0.00 0.26
100 0.47 0.01 0.26
∞ 0.51 0.01 0.27
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
218_D 58_L 1.77 0.57 0.00
232_S 102_L 1.66 0.50 0.00
232_S 36_A 1.52 0.41 0.00
196_A 124_W 1.51 0.41 0.00
47_P 67_G 1.47 0.38 0.00
270_I 43_T 1.46 0.37 0.00
401_N 94_W 1.45 0.37 0.00
418_L 89_L 1.44 0.36 0.00
168_A 59_L 1.41 0.34 0.00
38_V 124_W 1.39 0.33 0.00
279_M 124_W 1.37 0.32 0.00
241_V 43_T 1.34 0.30 0.00
270_I 16_T 1.33 0.29 0.00
252_Y 25_A 1.29 0.28 0.00
252_Y 124_W 1.28 0.27 0.00
84_E 120_V 1.26 0.26 0.00
425_W 108_K 1.26 0.26 0.00
279_M 25_A 1.22 0.24 0.00
384_H 55_I 1.22 0.24 0.00
266_H 36_A 1.21 0.24 0.00
39_L 69_P 1.21 0.23 0.00
54_I 95_R 1.20 0.23 0.00
330_T 125_Q 1.20 0.23 0.00
42_T 29_M 1.17 0.22 0.00
304_K 134_G 1.16 0.21 0.00
252_Y 16_T 1.16 0.21 0.00
196_A 16_T 1.15 0.21 0.00
39_L 39_V 1.14 0.20 0.00
360_A 103_H 1.14 0.20 0.00
218_D 62_E 1.12 0.20 0.00
242_S 58_L 1.11 0.19 0.00
168_A 120_V 1.11 0.19 0.00
50_A 83_E 1.11 0.19 0.00
345_A 17_L 1.11 0.19 0.00
184_S 17_L 1.10 0.19 0.00
422_I 51_L 1.10 0.19 0.00
424_L 69_P 1.10 0.18 0.00
218_D 67_G 1.09 0.18 0.00
158_V 58_L 1.08 0.18 0.00
221_E 51_L 1.08 0.18 0.00
88_I 48_N 1.08 0.18 0.00
248_Q 124_W 1.08 0.18 0.00
178_M 17_L 1.08 0.18 0.00
295_K 111_A 1.07 0.17 0.00
198_Y 118_A 1.06 0.17 0.00
132_P 30_Q 1.06 0.17 0.00
96_A 35_A 1.06 0.17 0.00
251_A 25_A 1.04 0.16 0.00
204_I 124_W 1.04 0.16 0.00
88_I 41_G 1.04 0.16 0.00
288_I 118_A 1.03 0.16 0.00
39_L 66_S 1.03 0.16 0.00
390_L 26_S 1.03 0.16 0.00
132_P 88_T 1.03 0.16 0.00
445_S 61_Q 1.03 0.16 0.00
402_R 51_L 1.03 0.16 0.00
295_K 94_W 1.03 0.16 0.00
133_A 119_S 1.02 0.16 0.00
110_L 42_Q 1.02 0.16 0.00
295_K 34_E 1.02 0.16 0.00
278_A 77_D 1.02 0.16 0.00
163_V 34_E 1.01 0.15 0.00
196_A 89_L 1.01 0.15 0.00
356_R 86_G 1.01 0.15 0.00
431_F 63_P 1.01 0.15 0.00
389_R 41_G 1.01 0.15 0.00
134_P 71_L 1.00 0.15 0.00
375_A 115_D 1.00 0.15 0.00
196_A 13_F 1.00 0.15 0.00
38_V 89_L 1.00 0.15 0.00
270_I 25_A 1.00 0.15 0.00
85_V 51_L 1.00 0.15 0.00
38_V 25_A 0.99 0.15 0.00
79_L 94_W 0.99 0.15 0.00
196_A 132_A 0.99 0.15 0.00
241_V 73_V 0.99 0.15 0.00
111_P 93_G 0.98 0.14 0.00
92_A 114_G 0.98 0.14 0.00
256_I 121_A 0.98 0.14 0.00
263_R 73_V 0.98 0.14 0.00
351_I 26_S 0.98 0.14 0.00
122_D 38_Q 0.98 0.14 0.00
218_D 35_A 0.97 0.14 0.00
395_L 62_E 0.97 0.14 0.00
242_S 67_G 0.97 0.14 0.00
75_Q 128_C 0.96 0.14 0.00
163_V 120_V 0.96 0.14 0.00
263_R 40_I 0.96 0.14 0.00
436_I 4_A 0.96 0.14 0.00
144_T 21_D 0.96 0.14 0.00
58_D 113_E 0.96 0.14 0.00
54_I 42_Q 0.96 0.14 0.00
388_V 34_E 0.95 0.14 0.00
145_P 110_S 0.95 0.13 0.00
163_V 40_I 0.95 0.13 0.00
451_L 68_K 0.94 0.13 0.00
359_E 114_G 0.94 0.13 0.00
67_S 44_P 0.94 0.13 0.00
255_R 35_A 0.94 0.13 0.00
424_L 74_H 0.94 0.13 0.00
35_T 42_Q 0.94 0.13 0.00
121_L 71_L 0.94 0.13 0.00
418_L 124_W 0.94 0.13 0.00
112_L 126_E 0.93 0.13 0.00
398_F 51_L 0.93 0.13 0.00
400_R 124_W 0.93 0.13 0.00
422_I 94_W 0.93 0.13 0.00
145_P 58_L 0.93 0.13 0.00
34_A 67_G 0.93 0.13 0.00
221_E 122_T 0.93 0.13 0.00
279_M 114_G 0.93 0.13 0.00
452_I 97_R 0.92 0.12 0.00
307_A 54_Q 0.92 0.12 0.00
255_R 41_G 0.92 0.12 0.00
369_E 117_D 0.92 0.12 0.00
382_E 109_V 0.92 0.12 0.00
82_L 114_G 0.91 0.12 0.00
277_Y 39_V 0.91 0.12 0.00
270_I 124_W 0.91 0.12 0.00
198_Y 122_T 0.91 0.12 0.00
92_A 59_L 0.91 0.12 0.00
106_S 58_L 0.91 0.12 0.00
295_K 129_R 0.91 0.12 0.00
42_T 72_R 0.91 0.12 0.00
109_Q 58_L 0.91 0.12 0.00
406_S 59_L 0.90 0.12 0.00
342_S 5_R 0.90 0.12 0.00
98_N 126_E 0.90 0.12 0.00
30_R 70_Q 0.90 0.12 0.00
202_D 127_L 0.90 0.12 0.00
453_F 93_G 0.90 0.12 0.00
204_I 40_I 0.90 0.12 0.00
428_L 104_H 0.90 0.12 0.00
351_I 133_P 0.90 0.12 0.00
196_A 25_A 0.90 0.12 0.00
207_G 123_R 0.90 0.12 0.00
368_I 86_G 0.89 0.12 0.00
359_E 33_L 0.89 0.12 0.00
78_F 69_P 0.89 0.12 0.00
137_L 44_P 0.89 0.12 0.00
159_L 134_G 0.89 0.12 0.00
420_K 17_L 0.89 0.12 0.00
96_A 19_A 0.89 0.12 0.00
418_L 115_D 0.89 0.12 0.00
46_L 24_I 0.89 0.12 0.00
50_A 95_R 0.88 0.12 0.00
223_I 13_F 0.88 0.12 0.00
134_P 30_Q 0.88 0.12 0.00
159_L 5_R 0.88 0.11 0.00
359_E 5_R 0.88 0.11 0.00
168_A 109_V 0.88 0.11 0.00
379_L 115_D 0.88 0.11 0.00
35_T 13_F 0.88 0.11 0.00
203_V 100_P 0.88 0.11 0.00
110_L 5_R 0.88 0.11 0.00
28_Y 49_S 0.88 0.11 0.00
46_L 43_T 0.88 0.11 0.00
252_Y 132_A 0.87 0.11 0.00
34_A 58_L 0.87 0.11 0.00
380_I 121_A 0.87 0.11 0.00
38_V 100_P 0.87 0.11 0.00
407_V 82_E 0.87 0.11 0.00
263_R 41_G 0.87 0.11 0.00
368_I 47_D 0.87 0.11 0.00
88_I 92_H 0.87 0.11 0.00
99_G 81_V 0.87 0.11 0.00
395_L 111_A 0.87 0.11 0.00
169_L 74_H 0.86 0.11 0.00
288_I 24_I 0.86 0.11 0.00
112_L 116_L 0.86 0.11 0.00
82_L 41_G 0.86 0.11 0.00
266_H 102_L 0.86 0.11 0.00
304_K 71_L 0.86 0.11 0.00
345_A 28_L 0.86 0.11 0.00
67_S 113_E 0.86 0.11 0.00
46_L 25_A 0.86 0.11 0.00
326_Y 118_A 0.85 0.11 0.00
249_G 20_L 0.85 0.11 0.00
396_S 119_S 0.85 0.11 0.00
84_E 131_A 0.85 0.11 0.00
156_E 80_R 0.85 0.11 0.00
174_R 81_V 0.85 0.11 0.00
304_K 122_T 0.85 0.11 0.00
427_Q 96_L 0.85 0.11 0.00
221_E 30_Q 0.85 0.11 0.00
360_A 102_L 0.85 0.10 0.00
48_L 96_L 0.84 0.10 0.00
412_K 76_D 0.84 0.10 0.00
266_H 72_R 0.84 0.10 0.00
405_V 44_P 0.84 0.10 0.00
407_V 85_L 0.84 0.10 0.00
243_P 86_G 0.84 0.10 0.00
254_T 118_A 0.84 0.10 0.00
123_G 78_L 0.84 0.10 0.00
248_Q 25_A 0.84 0.10 0.00
266_H 18_D 0.84 0.10 0.00
60_P 87_A 0.84 0.10 0.00
248_Q 16_T 0.84 0.10 0.00
229_R 40_I 0.84 0.10 0.00
351_I 127_L 0.83 0.10 0.00
394_L 24_I 0.83 0.10 0.00
279_M 13_F 0.83 0.10 0.00
396_S 65_F 0.83 0.10 0.00
384_H 115_D 0.83 0.10 0.00
116_L 12_E 0.83 0.10 0.00
149_P 94_W 0.83 0.10 0.00
35_T 25_A 0.82 0.10 0.00
430_A 109_V 0.82 0.10 0.00
217_K 124_W 0.82 0.10 0.00
251_A 89_L 0.82 0.10 0.00
143_I 83_E 0.82 0.10 0.00
79_L 123_R 0.82 0.10 0.00
159_L 40_I 0.82 0.10 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)
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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