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OPENSEQ.org
FtsA - FtsL
Genes: A B A+B
Length: 440 117 483
Sequences: 1721 423 200
Seq/Len: 3.91 3.62 0.41
MirrorTree (Pazo et al. 2001) 0.69
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 0.00 0.01 0.00
2 0.00 0.01 0.01
5 0.00 0.01 0.03
10 0.00 0.01 0.25
20 0.00 0.01 0.36
100 0.00 0.01 0.38
∞ 0.03 0.02 0.43
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
211_G 89_D 2.04 0.83 0.16
216_I 84_E 1.81 0.71 0.09
166_L 31_T 1.63 0.60 0.06
18_K 105_L 1.44 0.46 0.03
14_T 53_V 1.44 0.46 0.03
90_N 112_V 1.39 0.42 0.03
209_I 40_L 1.34 0.39 0.02
185_L 63_N 1.34 0.39 0.02
297_A 105_L 1.32 0.37 0.02
19_V 91_S 1.31 0.37 0.02
314_G 87_V 1.26 0.33 0.02
336_S 6_Y 1.24 0.32 0.02
359_P 100_A 1.20 0.29 0.01
174_E 34_E 1.19 0.29 0.01
292_A 73_I 1.19 0.29 0.01
239_K 105_L 1.16 0.28 0.01
319_P 42_A 1.16 0.27 0.01
18_K 56_A 1.15 0.26 0.01
284_Q 36_V 1.14 0.26 0.01
172_C 96_I 1.13 0.25 0.01
154_V 59_A 1.11 0.25 0.01
7_Y 115_I 1.11 0.24 0.01
371_A 107_L 1.11 0.24 0.01
175_R 102_K 1.09 0.23 0.01
303_L 6_Y 1.09 0.23 0.01
297_A 56_A 1.08 0.23 0.01
104_V 47_S 1.08 0.23 0.01
169_L 58_A 1.08 0.23 0.01
215_T 57_Y 1.07 0.22 0.01
200_K 109_D 1.06 0.22 0.01
99_N 105_L 1.05 0.21 0.01
78_G 34_E 1.05 0.21 0.01
232_L 14_H 1.05 0.21 0.01
51_D 68_K 1.04 0.21 0.01
6_L 77_N 1.04 0.21 0.01
154_V 108_K 1.03 0.21 0.01
156_G 107_L 1.03 0.21 0.01
204_V 55_K 1.03 0.20 0.01
139_D 18_P 1.03 0.20 0.01
156_G 34_E 1.03 0.20 0.01
76_I 27_R 1.03 0.20 0.01
29_L 105_L 1.02 0.20 0.01
292_A 41_F 1.02 0.20 0.01
292_A 49_S 1.02 0.20 0.01
364_G 109_D 1.02 0.20 0.01
341_V 31_T 1.02 0.20 0.01
373_R 86_S 1.01 0.20 0.01
61_F 71_E 1.01 0.19 0.01
175_R 44_A 1.00 0.19 0.01
84_I 63_N 1.00 0.19 0.01
237_I 14_H 1.00 0.19 0.01
288_Q 113_K 1.00 0.19 0.01
217_A 82_D 0.99 0.19 0.01
224_L 80_I 0.99 0.18 0.01
21_V 33_G 0.99 0.18 0.01
69_G 35_K 0.98 0.18 0.01
247_T 34_E 0.97 0.18 0.01
145_K 34_E 0.97 0.18 0.01
264_Y 52_I 0.97 0.18 0.01
250_E 89_D 0.97 0.18 0.01
84_I 93_P 0.97 0.18 0.01
180_I 27_R 0.96 0.17 0.01
103_Q 40_L 0.96 0.17 0.01
119_V 96_I 0.96 0.17 0.01
292_A 10_K 0.96 0.17 0.01
174_E 35_K 0.96 0.17 0.01
9_S 96_I 0.95 0.17 0.01
37_V 41_F 0.95 0.17 0.01
255_V 12_Q 0.95 0.17 0.01
352_N 35_K 0.95 0.17 0.01
132_Q 114_N 0.95 0.17 0.01
22_G 38_L 0.94 0.17 0.01
48_V 37_L 0.94 0.17 0.01
292_A 65_E 0.94 0.16 0.01
296_E 54_S 0.94 0.16 0.01
346_V 35_K 0.94 0.16 0.01
84_I 31_T 0.93 0.16 0.01
17_T 68_K 0.93 0.16 0.01
293_N 76_E 0.93 0.16 0.01
58_R 69_L 0.93 0.16 0.01
222_G 114_N 0.92 0.16 0.01
318_L 105_L 0.92 0.16 0.01
238_T 31_T 0.92 0.16 0.01
230_I 70_E 0.92 0.15 0.01
202_L 85_K 0.92 0.15 0.01
255_V 87_V 0.92 0.15 0.01
84_I 29_S 0.92 0.15 0.01
273_F 53_V 0.91 0.15 0.01
158_L 15_A 0.91 0.15 0.01
323_V 42_A 0.91 0.15 0.01
173_V 35_K 0.90 0.15 0.01
228_R 102_K 0.90 0.15 0.01
219_F 63_N 0.90 0.15 0.01
133_F 72_Q 0.90 0.15 0.01
345_N 6_Y 0.90 0.15 0.01
217_A 78_K 0.89 0.15 0.01
156_G 112_V 0.89 0.14 0.01
235_E 69_L 0.88 0.14 0.00
250_E 50_L 0.88 0.14 0.00
93_V 33_G 0.88 0.14 0.00
154_V 7_Q 0.88 0.14 0.00
83_Y 2_S 0.88 0.14 0.00
109_R 55_K 0.88 0.14 0.00
47_I 50_L 0.88 0.14 0.00
348_V 67_Q 0.88 0.14 0.00
211_G 55_K 0.88 0.14 0.00
17_T 110_K 0.87 0.14 0.00
352_N 30_I 0.87 0.14 0.00
337_L 91_S 0.87 0.14 0.00
280_T 38_L 0.86 0.14 0.00
301_E 113_K 0.86 0.14 0.00
246_R 115_I 0.86 0.14 0.00
287_T 36_V 0.86 0.14 0.00
9_S 93_P 0.86 0.13 0.00
225_T 79_Q 0.86 0.13 0.00
224_L 112_V 0.86 0.13 0.00
335_M 48_V 0.86 0.13 0.00
47_I 68_K 0.86 0.13 0.00
105_E 68_K 0.86 0.13 0.00
24_M 108_K 0.85 0.13 0.00
42_L 57_Y 0.85 0.13 0.00
61_F 81_G 0.85 0.13 0.00
287_T 38_L 0.84 0.13 0.00
189_A 95_R 0.84 0.13 0.00
241_I 109_D 0.84 0.13 0.00
227_T 59_A 0.84 0.13 0.00
51_D 37_L 0.84 0.13 0.00
134_I 59_A 0.84 0.13 0.00
322_F 86_S 0.84 0.13 0.00
318_L 82_D 0.83 0.13 0.00
368_I 95_R 0.83 0.13 0.00
99_N 106_N 0.83 0.13 0.00
342_L 82_D 0.83 0.12 0.00
294_I 107_L 0.83 0.12 0.00
12_I 81_G 0.83 0.12 0.00
328_Q 108_K 0.82 0.12 0.00
122_E 94_Q 0.82 0.12 0.00
17_T 55_K 0.82 0.12 0.00
255_V 81_G 0.82 0.12 0.00
22_G 96_I 0.82 0.12 0.00
364_G 88_A 0.82 0.12 0.00
20_I 101_K 0.82 0.12 0.00
56_S 64_I 0.82 0.12 0.00
107_V 22_V 0.82 0.12 0.00
246_R 72_Q 0.82 0.12 0.00
209_I 91_S 0.82 0.12 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
8115 0.41 FtsA - FtsL Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.15 Done - Shared
8110 0.41 FtsA - FtsL Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.16 Done - Shared
8101 0.41 FtsA - FtsL Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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