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OPENSEQ.org
cI_D_cIII_isp
Genes: A B A+B
Length: 485 190 660
Sequences: 1691 1442 444
Seq/Len: 3.49 7.59 0.67
MirrorTree (Pazo et al. 2001) 0.62
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.01 0.00 0.01
100 0.01 0.01 0.05
∞ 0.02 0.02 0.66
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
145_Y 31_A 1.26 0.45 0.00
221_V 59_S 1.25 0.45 0.00
176_L 15_R 1.21 0.42 0.00
210_M 35_A 1.18 0.39 0.00
386_I 98_I 1.18 0.39 0.00
320_E 32_G 1.17 0.38 0.00
429_A 187_I 1.15 0.37 0.00
123_N 28_T 1.13 0.35 0.00
289_L 42_M 1.11 0.34 0.00
86_A 35_A 1.10 0.33 0.00
202_L 183_D 1.08 0.31 0.00
277_A 174_L 1.07 0.31 0.00
363_R 53_S 1.07 0.31 0.00
243_A 76_V 1.06 0.30 0.00
377_T 35_A 1.05 0.30 0.00
427_R 73_G 1.05 0.30 0.00
353_G 174_L 1.02 0.28 0.00
459_I 183_D 1.02 0.27 0.00
99_N 54_I 1.01 0.27 0.00
202_L 15_R 1.00 0.26 0.00
454_G 39_V 1.00 0.26 0.00
96_E 59_S 0.98 0.25 0.00
308_Y 39_V 0.97 0.24 0.00
94_W 27_G 0.96 0.24 0.00
32_R 187_I 0.96 0.23 0.00
432_L 163_G 0.94 0.23 0.00
161_I 177_P 0.94 0.23 0.00
277_A 95_G 0.93 0.22 0.00
344_V 56_V 0.93 0.22 0.00
26_L 34_A 0.93 0.22 0.00
366_F 52_A 0.93 0.22 0.00
238_V 78_I 0.93 0.22 0.00
283_F 125_W 0.93 0.22 0.00
120_A 59_S 0.92 0.21 0.00
106_Y 150_W 0.91 0.21 0.00
139_L 30_A 0.91 0.21 0.00
309_L 35_A 0.91 0.21 0.00
210_M 38_L 0.91 0.21 0.00
88_C 67_L 0.91 0.20 0.00
155_A 31_A 0.91 0.20 0.00
207_F 127_V 0.91 0.20 0.00
181_S 183_D 0.90 0.20 0.00
328_V 76_V 0.90 0.20 0.00
268_A 162_S 0.90 0.20 0.00
83_A 78_I 0.89 0.20 0.00
325_A 129_I 0.89 0.20 0.00
125_L 15_R 0.88 0.19 0.00
420_I 45_S 0.88 0.19 0.00
381_L 68_T 0.88 0.19 0.00
239_S 76_V 0.88 0.19 0.00
419_A 129_I 0.88 0.19 0.00
418_S 184_D 0.88 0.19 0.00
11_L 14_T 0.87 0.19 0.00
433_Y 125_W 0.87 0.19 0.00
294_I 106_N 0.87 0.19 0.00
161_I 176_I 0.87 0.18 0.00
389_T 84_D 0.86 0.18 0.00
282_I 34_A 0.86 0.18 0.00
278_F 34_A 0.86 0.18 0.00
371_I 159_Y 0.86 0.18 0.00
226_W 169_P 0.85 0.18 0.00
466_V 90_R 0.85 0.17 0.00
127_S 28_T 0.85 0.17 0.00
250_I 19_L 0.85 0.17 0.00
429_A 129_I 0.84 0.17 0.00
135_I 181_F 0.84 0.17 0.00
305_H 168_G 0.84 0.17 0.00
248_I 174_L 0.84 0.17 0.00
411_V 181_F 0.83 0.17 0.00
219_S 36_W 0.83 0.17 0.00
165_A 42_M 0.83 0.17 0.00
210_M 60_G 0.83 0.17 0.00
164_A 148_G 0.83 0.17 0.00
190_G 168_G 0.83 0.17 0.00
315_A 33_A 0.83 0.17 0.00
112_A 95_G 0.83 0.17 0.00
69_V 58_V 0.82 0.17 0.00
276_I 92_V 0.82 0.16 0.00
409_W 174_L 0.82 0.16 0.00
411_V 159_Y 0.82 0.16 0.00
107_L 122_A 0.82 0.16 0.00
281_I 90_R 0.82 0.16 0.00
55_V 185_T 0.82 0.16 0.00
225_L 173_N 0.82 0.16 0.00
285_N 70_K 0.82 0.16 0.00
138_P 28_T 0.82 0.16 0.00
470_W 35_A 0.82 0.16 0.00
221_V 31_A 0.81 0.16 0.00
238_V 114_D 0.81 0.16 0.00
279_A 183_D 0.81 0.16 0.00
325_A 32_G 0.81 0.16 0.00
203_L 27_G 0.81 0.16 0.00
50_V 189_L 0.81 0.16 0.00
374_A 61_V 0.81 0.16 0.00
283_F 32_G 0.81 0.16 0.00
416_V 183_D 0.80 0.15 0.00
343_V 175_H 0.80 0.15 0.00
294_I 15_R 0.80 0.15 0.00
348_S 30_A 0.80 0.15 0.00
273_L 165_I 0.80 0.15 0.00
95_L 159_Y 0.80 0.15 0.00
374_A 105_S 0.80 0.15 0.00
105_F 55_Q 0.80 0.15 0.00
156_S 159_Y 0.80 0.15 0.00
176_L 166_R 0.79 0.15 0.00
189_L 143_G 0.79 0.15 0.00
149_Q 68_T 0.79 0.15 0.00
39_T 176_I 0.79 0.15 0.00
238_V 34_A 0.79 0.15 0.00
95_L 26_A 0.79 0.15 0.00
312_A 127_V 0.79 0.15 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)
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