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OPENSEQ.org
ProBA
Genes: A B A+B
Length: 417 367 780
Sequences: 17595 1893 1106
Seq/Len: 42.19 5.16 1.42
MirrorTree (Pazo et al. 2001) 0.48
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 0.03 0.07 1.12
2 0.04 0.07 1.22
5 0.04 0.07 1.30
10 0.06 0.07 1.35
20 0.08 0.07 1.41
100 0.14 0.07 1.64
∞ 0.21 0.08 2.22
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
112_L 24_N 1.26 0.68 0.01
155_T 264_N 1.02 0.45 0.00
321_K 358_A 1.01 0.44 0.00
50_V 366_T 1.00 0.43 0.00
330_I 315_I 0.96 0.39 0.00
265_I 324_A 0.96 0.39 0.00
115_I 324_A 0.93 0.36 0.00
240_K 323_I 0.89 0.32 0.00
365_Y 105_R 0.88 0.31 0.00
145_G 34_Q 0.87 0.30 0.00
198_I 46_V 0.85 0.29 0.00
255_T 269_I 0.85 0.29 0.00
15_K 323_I 0.83 0.27 0.00
45_A 39_H 0.83 0.27 0.00
341_S 105_R 0.83 0.27 0.00
140_V 293_S 0.83 0.27 0.00
115_I 311_E 0.82 0.27 0.00
11_Q 9_V 0.82 0.26 0.00
176_I 157_A 0.82 0.26 0.00
257_E 74_L 0.81 0.26 0.00
245_A 233_I 0.81 0.25 0.00
272_A 47_I 0.79 0.24 0.00
380_L 32_V 0.79 0.24 0.00
210_R 14_S 0.79 0.24 0.00
8_A 280_V 0.78 0.23 0.00
212_Q 263_E 0.78 0.23 0.00
320_V 139_V 0.77 0.23 0.00
306_A 175_Y 0.77 0.23 0.00
155_T 112_E 0.77 0.23 0.00
415_I 304_T 0.77 0.22 0.00
79_D 31_L 0.77 0.22 0.00
273_L 7_L 0.77 0.22 0.00
213_S 257_A 0.76 0.22 0.00
415_I 110_D 0.76 0.22 0.00
400_E 115_L 0.76 0.22 0.00
245_A 87_W 0.75 0.21 0.00
251_S 114_F 0.75 0.21 0.00
220_G 15_V 0.75 0.21 0.00
251_S 72_K 0.75 0.21 0.00
44_N 3_D 0.75 0.21 0.00
155_T 49_T 0.75 0.21 0.00
213_S 39_H 0.75 0.21 0.00
39_S 188_I 0.75 0.21 0.00
234_E 362_D 0.74 0.21 0.00
327_D 191_V 0.74 0.20 0.00
380_L 21_R 0.74 0.20 0.00
83_V 32_V 0.74 0.20 0.00
345_L 87_W 0.73 0.20 0.00
75_G 341_H 0.73 0.20 0.00
363_A 117_A 0.73 0.20 0.00
135_K 125_L 0.73 0.20 0.00
136_T 362_D 0.73 0.20 0.00
146_K 86_L 0.73 0.20 0.00
279_E 303_V 0.73 0.20 0.00
115_I 328_S 0.73 0.20 0.00
209_C 49_T 0.73 0.20 0.00
159_I 166_L 0.72 0.19 0.00
13_S 323_I 0.72 0.19 0.00
409_G 141_T 0.72 0.19 0.00
251_S 221_A 0.71 0.19 0.00
389_Q 14_S 0.71 0.19 0.00
251_S 27_H 0.71 0.18 0.00
378_F 288_I 0.71 0.18 0.00
198_I 254_L 0.71 0.18 0.00
52_D 9_V 0.71 0.18 0.00
274_S 91_F 0.70 0.18 0.00
151_T 222_D 0.70 0.18 0.00
38_Q 300_I 0.70 0.18 0.00
267_D 192_Y 0.70 0.18 0.00
322_I 280_V 0.70 0.18 0.00
352_A 357_V 0.70 0.18 0.00
290_A 311_E 0.70 0.18 0.00
133_C 123_A 0.70 0.18 0.00
110_V 207_S 0.70 0.18 0.00
12_A 300_I 0.70 0.18 0.00
321_K 332_S 0.69 0.18 0.00
281_G 315_I 0.69 0.17 0.00
225_C 262_L 0.69 0.17 0.00
24_K 255_F 0.69 0.17 0.00
197_L 82_R 0.69 0.17 0.00
160_Q 132_V 0.69 0.17 0.00
87_A 343_S 0.69 0.17 0.00
310_D 332_S 0.69 0.17 0.00
251_S 169_T 0.69 0.17 0.00
391_L 209_L 0.69 0.17 0.00
37_A 130_V 0.68 0.17 0.00
219_T 15_V 0.68 0.17 0.00
8_A 359_V 0.68 0.17 0.00
225_C 358_A 0.68 0.17 0.00
75_G 89_Q 0.68 0.17 0.00
198_I 72_K 0.68 0.17 0.00
95_D 292_G 0.67 0.16 0.00
330_I 86_L 0.67 0.16 0.00
270_L 218_L 0.67 0.16 0.00
187_M 349_I 0.67 0.16 0.00
348_D 189_K 0.67 0.16 0.00
213_S 122_R 0.67 0.16 0.00
321_K 32_V 0.67 0.16 0.00
324_S 282_E 0.66 0.16 0.00
171_G 280_V 0.66 0.16 0.00
121_A 71_S 0.66 0.16 0.00
371_R 252_G 0.66 0.16 0.00
182_A 167_L 0.66 0.16 0.00
235_I 280_V 0.66 0.15 0.00
93_V 349_I 0.66 0.15 0.00
335_E 302_S 0.65 0.15 0.00
221_G 15_V 0.65 0.15 0.00
354_R 96_I 0.65 0.15 0.00
341_S 21_R 0.65 0.15 0.00
265_I 357_V 0.65 0.15 0.00
219_T 14_S 0.65 0.15 0.00
137_G 54_A 0.65 0.15 0.00
241_V 7_L 0.65 0.15 0.00
343_A 160_A 0.65 0.15 0.00
29_E 300_I 0.65 0.15 0.00
63_L 218_L 0.65 0.15 0.00
50_V 365_I 0.65 0.15 0.00
17_A 359_V 0.65 0.15 0.00
51_A 110_D 0.65 0.15 0.00
133_C 232_I 0.65 0.15 0.00
170_A 288_I 0.64 0.15 0.00
187_M 132_V 0.64 0.15 0.00
361_S 359_V 0.64 0.15 0.00
228_Y 110_D 0.64 0.15 0.00
52_D 46_V 0.64 0.15 0.00
158_V 240_G 0.64 0.15 0.00
255_T 181_S 0.64 0.15 0.00
302_V 303_V 0.64 0.14 0.00
129_V 108_M 0.64 0.14 0.00
35_L 103_L 0.64 0.14 0.00
338_T 366_T 0.64 0.14 0.00
100_D 357_V 0.64 0.14 0.00
97_G 123_A 0.63 0.14 0.00
73_L 119_D 0.63 0.14 0.00
131_S 288_I 0.63 0.14 0.00
184_V 224_A 0.63 0.14 0.00
285_H 99_G 0.63 0.14 0.00
275_K 338_I 0.63 0.14 0.00
17_A 242_I 0.63 0.14 0.00
136_T 272_A 0.63 0.14 0.00
152_N 91_F 0.63 0.14 0.00
404_T 308_S 0.63 0.14 0.00
26_R 301_K 0.63 0.14 0.00
45_A 246_M 0.63 0.14 0.00
393_A 335_L 0.63 0.14 0.00
277_M 45_I 0.62 0.14 0.00
43_L 216_T 0.62 0.14 0.00
306_A 344_Q 0.62 0.14 0.00
118_I 271_G 0.62 0.14 0.00
158_V 297_P 0.62 0.14 0.00
174_Q 11_L 0.62 0.14 0.00
107_R 55_A 0.62 0.14 0.00
361_S 334_A 0.62 0.14 0.00
44_N 318_L 0.62 0.14 0.00
232_S 317_N 0.62 0.14 0.00
376_G 153_S 0.62 0.14 0.00
327_D 253_T 0.62 0.14 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
10653 2.21 ProBA_GREMLIN Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8607 1.42 ProBA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
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