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OPENSEQ.org
cI_3_40_cI_9_40_tt
Genes: A B A+B
Length: 783 182 903
Sequences: 1200 683 519
Seq/Len: 1.53 3.75 0.57
MirrorTree (Pazo et al. 2001) 0.78
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 0.01
2 0.00 0.00 0.42
5 0.01 0.00 0.42
10 0.01 0.00 0.42
20 0.02 0.00 0.43
100 0.03 0.00 0.43
∞ 0.10 0.01 0.54
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
123_D 86_R 1.59 0.67 0.00
269_T 107_A 1.28 0.43 0.00
241_R 86_R 1.15 0.33 0.00
270_R 130_V 1.14 0.32 0.00
662_K 76_D 1.07 0.28 0.00
620_R 131_Y 1.06 0.27 0.00
514_D 15_K 1.06 0.27 0.00
659_E 17_L 1.06 0.27 0.00
360_L 113_I 1.05 0.26 0.00
390_L 134_E 1.04 0.26 0.00
736_V 153_T 1.04 0.26 0.00
165_D 161_Y 1.03 0.25 0.00
685_P 10_L 1.02 0.25 0.00
260_P 20_K 1.02 0.25 0.00
167_H 131_Y 1.02 0.25 0.00
15_P 134_E 1.01 0.24 0.00
756_G 26_Y 1.01 0.24 0.00
648_L 164_P 1.00 0.24 0.00
123_D 72_P 1.00 0.23 0.00
105_A 100_F 0.99 0.23 0.00
274_L 14_L 0.98 0.23 0.00
720_P 166_V 0.98 0.22 0.00
30_V 15_K 0.98 0.22 0.00
751_E 7_A 0.97 0.22 0.00
746_R 20_K 0.94 0.20 0.00
418_R 125_E 0.94 0.20 0.00
324_E 26_Y 0.93 0.20 0.00
170_L 47_P 0.93 0.20 0.00
525_A 26_Y 0.92 0.19 0.00
88_A 112_A 0.92 0.19 0.00
176_L 117_Y 0.92 0.19 0.00
394_D 119_F 0.92 0.19 0.00
135_V 129_L 0.92 0.19 0.00
24_F 96_L 0.91 0.19 0.00
422_P 76_D 0.91 0.19 0.00
750_R 24_V 0.91 0.19 0.00
92_V 24_V 0.91 0.19 0.00
163_H 95_M 0.91 0.18 0.00
557_S 76_D 0.91 0.18 0.00
302_D 118_D 0.91 0.18 0.00
205_R 9_S 0.90 0.18 0.00
408_I 55_G 0.90 0.18 0.00
157_F 55_G 0.90 0.18 0.00
82_S 24_V 0.90 0.18 0.00
583_V 28_D 0.90 0.18 0.00
312_R 26_Y 0.89 0.18 0.00
221_G 151_K 0.89 0.18 0.00
320_A 85_E 0.89 0.17 0.00
513_Q 152_R 0.88 0.17 0.00
618_E 129_L 0.88 0.17 0.00
586_H 119_F 0.87 0.17 0.00
320_A 26_Y 0.87 0.17 0.00
72_E 169_E 0.86 0.17 0.00
260_P 120_E 0.86 0.16 0.00
12_E 125_E 0.86 0.16 0.00
634_A 10_L 0.86 0.16 0.00
93_V 12_I 0.85 0.16 0.00
82_S 13_T 0.85 0.16 0.00
129_E 96_L 0.85 0.16 0.00
396_A 150_A 0.85 0.16 0.00
167_H 96_L 0.84 0.16 0.00
643_L 24_V 0.84 0.16 0.00
492_K 10_L 0.84 0.15 0.00
351_L 47_P 0.84 0.15 0.00
448_M 10_L 0.84 0.15 0.00
171_S 52_K 0.83 0.15 0.00
161_R 136_M 0.83 0.15 0.00
436_Q 120_E 0.83 0.15 0.00
346_A 20_K 0.83 0.15 0.00
711_A 24_V 0.82 0.15 0.00
175_I 66_Y 0.82 0.15 0.00
618_E 19_S 0.82 0.15 0.00
459_M 72_P 0.82 0.15 0.00
551_P 161_Y 0.82 0.15 0.00
408_I 86_R 0.82 0.15 0.00
18_S 149_E 0.82 0.15 0.00
72_E 167_R 0.81 0.14 0.00
536_T 15_K 0.81 0.14 0.00
310_L 62_A 0.81 0.14 0.00
176_L 150_A 0.81 0.14 0.00
9_R 55_G 0.81 0.14 0.00
608_Y 151_K 0.81 0.14 0.00
20_M 96_L 0.81 0.14 0.00
19_V 107_A 0.80 0.14 0.00
10_I 125_E 0.80 0.14 0.00
94_D 112_A 0.80 0.14 0.00
535_M 121_M 0.80 0.14 0.00
450_L 20_K 0.80 0.14 0.00
620_R 74_E 0.80 0.14 0.00
301_A 16_Y 0.80 0.14 0.00
327_L 11_G 0.80 0.14 0.00
756_G 4_K 0.79 0.14 0.00
576_A 10_L 0.79 0.14 0.00
379_A 2_T 0.79 0.14 0.00
15_P 112_A 0.79 0.14 0.00
537_P 22_V 0.79 0.14 0.00
39_L 161_Y 0.79 0.14 0.00
327_L 12_I 0.79 0.14 0.00
472_E 142_G 0.79 0.14 0.00
499_K 26_Y 0.79 0.14 0.00
390_L 17_L 0.79 0.14 0.00
584_V 130_V 0.79 0.14 0.00
739_P 145_P 0.79 0.14 0.00
477_L 146_Q 0.79 0.13 0.00
526_E 10_L 0.79 0.13 0.00
390_L 26_Y 0.79 0.13 0.00
761_S 131_Y 0.78 0.13 0.00
204_E 112_A 0.78 0.13 0.00
718_A 4_K 0.78 0.13 0.00
653_P 142_G 0.78 0.13 0.00
18_S 131_Y 0.78 0.13 0.00
604_A 112_A 0.78 0.13 0.00
605_P 61_A 0.78 0.13 0.00
618_E 100_F 0.78 0.13 0.00
376_A 112_A 0.78 0.13 0.00
74_Q 11_G 0.78 0.13 0.00
394_D 74_E 0.78 0.13 0.00
726_E 26_Y 0.78 0.13 0.00
28_Y 6_L 0.78 0.13 0.00
35_S 37_F 0.78 0.13 0.00
754_P 77_P 0.78 0.13 0.00
270_R 72_P 0.77 0.13 0.00
389_D 8_Q 0.77 0.13 0.00
111_T 88_A 0.77 0.13 0.00
89_D 7_A 0.77 0.13 0.00
177_D 130_V 0.77 0.13 0.00
369_L 73_A 0.77 0.13 0.00
6_V 37_F 0.77 0.13 0.00
322_W 166_V 0.77 0.13 0.00
333_L 146_Q 0.77 0.13 0.00
581_R 134_E 0.77 0.13 0.00
77_P 120_E 0.76 0.13 0.00
673_M 7_A 0.76 0.13 0.00
413_L 55_G 0.76 0.13 0.00
212_G 2_T 0.76 0.13 0.00
201_D 141_V 0.76 0.13 0.00
419_D 107_A 0.76 0.12 0.00
196_G 93_I 0.76 0.12 0.00
213_T 10_L 0.76 0.12 0.00
129_E 130_V 0.76 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
4967 0.57 cI_3_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4959 0.54 cI_3_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4958 0.5 cI_3_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4957 0.63 cI_3_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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