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OPENSEQ.org
cI_2_40_cI_3_40_tt
Genes: A B A+B
Length: 181 783 915
Sequences: 1903 1200 608
Seq/Len: 10.51 1.53 0.66
MirrorTree (Pazo et al. 2001) 0.72
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 0.02
2 0.00 0.00 0.47
5 0.01 0.01 0.50
10 0.01 0.01 0.50
20 0.01 0.02 0.50
100 0.02 0.03 0.52
∞ 0.04 0.10 0.63
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
68_S 6_V 1.39 0.56 0.00
49_I 98_D 1.21 0.41 0.00
77_K 601_V 1.11 0.34 0.00
69_Y 39_L 1.11 0.33 0.00
106_I 485_E 1.07 0.30 0.00
50_A 312_R 1.06 0.30 0.00
103_T 89_D 1.06 0.30 0.00
29_P 105_A 1.05 0.29 0.00
64_A 204_E 1.01 0.27 0.00
150_L 761_S 0.98 0.25 0.00
93_A 19_V 0.97 0.24 0.00
120_Q 177_D 0.97 0.24 0.00
77_K 335_E 0.96 0.24 0.00
72_F 19_V 0.94 0.22 0.00
92_G 21_D 0.94 0.22 0.00
65_S 417_V 0.93 0.21 0.00
51_R 579_G 0.93 0.21 0.00
28_M 107_M 0.92 0.21 0.00
126_G 269_T 0.91 0.21 0.00
150_L 282_V 0.91 0.21 0.00
60_V 490_V 0.91 0.20 0.00
113_P 483_D 0.90 0.20 0.00
103_T 413_L 0.90 0.20 0.00
65_S 269_T 0.89 0.20 0.00
136_V 632_G 0.88 0.19 0.00
70_Y 544_L 0.88 0.19 0.00
48_E 278_R 0.87 0.18 0.00
10_F 727_A 0.87 0.18 0.00
41_I 634_A 0.87 0.18 0.00
111_V 136_E 0.86 0.18 0.00
110_E 360_L 0.86 0.18 0.00
130_T 32_L 0.86 0.18 0.00
137_N 22_A 0.85 0.18 0.00
16_A 736_V 0.85 0.18 0.00
41_I 216_F 0.85 0.17 0.00
145_V 179_E 0.85 0.17 0.00
106_I 27_G 0.85 0.17 0.00
109_G 737_E 0.85 0.17 0.00
106_I 573_P 0.85 0.17 0.00
116_L 608_Y 0.84 0.17 0.00
154_L 102_E 0.84 0.17 0.00
111_V 105_A 0.84 0.17 0.00
18_Y 355_L 0.84 0.17 0.00
60_V 626_P 0.83 0.17 0.00
150_L 21_D 0.83 0.17 0.00
109_G 416_F 0.82 0.16 0.00
115_G 188_V 0.82 0.16 0.00
77_K 569_G 0.82 0.16 0.00
106_I 768_G 0.82 0.16 0.00
113_P 667_R 0.82 0.16 0.00
78_Y 523_L 0.81 0.16 0.00
4_F 341_V 0.81 0.16 0.00
46_I 51_R 0.81 0.16 0.00
110_E 6_V 0.81 0.16 0.00
122_V 265_I 0.81 0.16 0.00
138_D 618_E 0.81 0.15 0.00
155_A 581_R 0.80 0.15 0.00
108_P 413_L 0.80 0.15 0.00
8_Q 52_I 0.79 0.15 0.00
137_N 631_N 0.79 0.15 0.00
135_Q 391_L 0.79 0.15 0.00
137_N 500_A 0.78 0.14 0.00
18_Y 337_R 0.78 0.14 0.00
154_L 274_L 0.78 0.14 0.00
136_V 98_D 0.78 0.14 0.00
100_L 449_A 0.78 0.14 0.00
77_K 725_A 0.78 0.14 0.00
115_G 190_Y 0.78 0.14 0.00
64_A 621_V 0.78 0.14 0.00
112_T 569_G 0.77 0.14 0.00
42_R 674_G 0.77 0.14 0.00
49_I 156_R 0.77 0.14 0.00
9_D 693_Y 0.77 0.14 0.00
113_P 502_N 0.76 0.14 0.00
136_V 520_R 0.76 0.14 0.00
18_Y 607_F 0.76 0.14 0.00
34_V 140_Y 0.76 0.14 0.00
80_L 766_A 0.76 0.14 0.00
32_R 197_D 0.76 0.14 0.00
66_F 130_L 0.76 0.14 0.00
8_Q 102_E 0.76 0.14 0.00
126_G 302_D 0.76 0.14 0.00
129_H 26_A 0.76 0.14 0.00
142_V 22_A 0.76 0.14 0.00
148_A 707_K 0.76 0.14 0.00
100_L 499_K 0.76 0.13 0.00
58_T 750_R 0.76 0.13 0.00
117_F 396_A 0.75 0.13 0.00
46_I 616_N 0.75 0.13 0.00
155_A 18_S 0.75 0.13 0.00
87_S 202_F 0.75 0.13 0.00
3_F 458_L 0.75 0.13 0.00
10_F 355_L 0.74 0.13 0.00
21_E 442_P 0.74 0.13 0.00
153_L 313_K 0.74 0.13 0.00
126_G 192_E 0.74 0.13 0.00
156_G 575_E 0.74 0.13 0.00
144_C 742_R 0.74 0.13 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
4773 0.66 cI_2_40_cI_3_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4771 1.04 cI_2_4_cI_3_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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