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OPENSEQ.org
Fj_PorV_vs_2389CTD
Genes: A B A+B
Length: 402 77 445
Sequences: 1221 6550 574
Seq/Len: 3.04 85.06 1.29
MirrorTree (Pazo et al. 2001) 0.11
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 0.14 0.13
2 0.00 0.17 0.16
5 0.00 0.20 0.25
10 0.01 0.24 0.34
20 0.01 0.28 0.48
100 0.04 0.37 1.00
∞ 0.11 0.39 1.20
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
235_G 7_V 1.27 0.66 0.00
368_V 49_L 1.17 0.56 0.00
117_G 29_I 1.05 0.45 0.00
152_F 64_D 1.04 0.44 0.00
91_L 63_F 1.01 0.41 0.00
152_F 16_I 1.01 0.41 0.00
395_F 14_S 1.00 0.40 0.00
376_A 63_F 1.00 0.40 0.00
140_L 21_D 0.99 0.39 0.00
124_G 8_Y 0.99 0.39 0.00
231_L 75_I 0.98 0.38 0.00
140_L 8_Y 0.97 0.38 0.00
324_Y 31_S 0.97 0.38 0.00
359_A 29_I 0.97 0.37 0.00
156_V 38_I 0.96 0.36 0.00
249_V 58_L 0.95 0.35 0.00
227_L 54_L 0.94 0.35 0.00
356_S 49_L 0.94 0.34 0.00
95_T 7_V 0.93 0.34 0.00
76_I 26_S 0.92 0.33 0.00
11_L 18_F 0.92 0.33 0.00
369_D 18_F 0.91 0.31 0.00
110_F 35_Q 0.89 0.30 0.00
215_I 29_I 0.89 0.30 0.00
231_L 42_I 0.88 0.30 0.00
153_S 61_Y 0.87 0.29 0.00
302_S 29_I 0.86 0.28 0.00
182_V 18_F 0.86 0.28 0.00
152_F 40_K 0.86 0.28 0.00
123_T 8_Y 0.85 0.27 0.00
368_V 60_F 0.85 0.27 0.00
132_E 74_I 0.85 0.27 0.00
132_E 69_H 0.84 0.26 0.00
90_S 36_K 0.84 0.26 0.00
218_D 31_S 0.84 0.26 0.00
309_G 73_K 0.84 0.26 0.00
188_Y 44_N 0.84 0.26 0.00
142_G 3_S 0.83 0.26 0.00
108_G 68_L 0.83 0.26 0.00
390_S 73_K 0.83 0.26 0.00
226_F 56_N 0.83 0.26 0.00
233_V 18_F 0.83 0.25 0.00
230_N 27_V 0.83 0.25 0.00
262_P 54_L 0.83 0.25 0.00
236_G 22_N 0.82 0.25 0.00
205_G 29_I 0.82 0.25 0.00
74_L 29_I 0.82 0.24 0.00
204_A 27_V 0.82 0.24 0.00
169_T 37_L 0.82 0.24 0.00
89_I 55_T 0.81 0.24 0.00
325_S 76_K 0.81 0.24 0.00
91_L 5_F 0.81 0.24 0.00
215_I 48_V 0.81 0.24 0.00
160_Y 31_S 0.81 0.24 0.00
229_A 75_I 0.81 0.24 0.00
44_L 5_F 0.81 0.24 0.00
152_F 35_Q 0.80 0.23 0.00
392_T 73_K 0.80 0.23 0.00
192_E 29_I 0.80 0.23 0.00
387_L 18_F 0.79 0.22 0.00
249_V 20_F 0.79 0.22 0.00
44_L 7_V 0.79 0.22 0.00
262_P 47_P 0.78 0.22 0.00
299_G 16_I 0.78 0.22 0.00
129_P 14_S 0.78 0.22 0.00
130_T 25_A 0.78 0.22 0.00
180_F 18_F 0.78 0.22 0.00
357_L 71_T 0.77 0.21 0.00
107_A 63_F 0.77 0.21 0.00
209_Q 49_L 0.77 0.21 0.00
380_K 7_V 0.77 0.21 0.00
43_G 61_Y 0.77 0.21 0.00
106_F 35_Q 0.77 0.21 0.00
152_F 31_S 0.77 0.21 0.00
235_G 20_F 0.77 0.21 0.00
255_K 31_S 0.77 0.21 0.00
391_L 75_I 0.76 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)
ID Seq/Len Name Options I_Prob Status
11394 1.29 Fj_PorV_vs_2389CTD Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done
11393 0 Fj_PorV_vs_2389CTD Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11392 0 Fj_PorV_vs_2389CTD Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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