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OPENSEQ.org
cI_2_4_cI_3_4_tt
Genes: A B A+B
Length: 181 783 902
Sequences: 2539 1268 936
Seq/Len: 14.03 1.62 1.04
MirrorTree (Pazo et al. 2001) 0.67
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 0.10
2 0.00 0.00 0.87
5 0.01 0.01 0.91
10 0.01 0.01 0.91
20 0.02 0.01 0.91
100 0.04 0.03 0.91
∞ 0.10 0.09 0.97
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
13_E 3_R 0.96 0.31 0.00
65_S 336_A 0.96 0.31 0.00
68_S 6_V 0.95 0.31 0.00
113_P 479_A 0.93 0.29 0.00
62_G 201_D 0.92 0.28 0.00
66_F 30_V 0.90 0.27 0.00
137_N 329_L 0.89 0.26 0.00
154_L 274_L 0.88 0.25 0.00
105_G 106_G 0.88 0.25 0.00
135_Q 30_V 0.86 0.24 0.00
54_G 423_P 0.86 0.24 0.00
33_R 454_Y 0.85 0.23 0.00
145_V 487_S 0.82 0.22 0.00
65_S 274_L 0.82 0.21 0.00
152_A 331_E 0.82 0.21 0.00
9_D 413_L 0.82 0.21 0.00
85_T 20_M 0.82 0.21 0.00
106_I 332_G 0.82 0.21 0.00
127_S 635_E 0.82 0.21 0.00
154_L 578_K 0.81 0.21 0.00
3_F 229_I 0.80 0.20 0.00
64_A 157_F 0.80 0.20 0.00
87_S 39_L 0.79 0.19 0.00
156_G 342_G 0.77 0.19 0.00
109_G 270_R 0.77 0.18 0.00
136_V 306_L 0.77 0.18 0.00
145_V 458_L 0.77 0.18 0.00
146_T 27_G 0.75 0.17 0.00
41_I 634_A 0.75 0.17 0.00
113_P 87_V 0.75 0.17 0.00
77_K 335_E 0.75 0.17 0.00
131_A 476_I 0.74 0.17 0.00
146_T 483_D 0.74 0.17 0.00
105_G 490_V 0.74 0.17 0.00
152_A 446_D 0.74 0.17 0.00
48_E 278_R 0.74 0.17 0.00
61_M 203_I 0.74 0.17 0.00
98_D 5_K 0.74 0.17 0.00
63_V 353_E 0.74 0.17 0.00
110_E 742_R 0.74 0.17 0.00
121_K 24_F 0.73 0.17 0.00
127_S 176_L 0.73 0.17 0.00
117_F 303_Q 0.73 0.16 0.00
118_S 13_V 0.73 0.16 0.00
150_L 709_Q 0.73 0.16 0.00
126_G 269_T 0.72 0.16 0.00
22_G 401_D 0.72 0.16 0.00
80_L 392_Q 0.72 0.16 0.00
45_R 30_V 0.71 0.15 0.00
15_F 2_V 0.71 0.15 0.00
54_G 517_A 0.71 0.15 0.00
76_G 126_G 0.71 0.15 0.00
138_D 160_T 0.71 0.15 0.00
137_N 11_V 0.71 0.15 0.00
40_W 410_H 0.71 0.15 0.00
43_P 648_L 0.71 0.15 0.00
41_I 398_V 0.71 0.15 0.00
47_E 174_V 0.71 0.15 0.00
131_A 622_L 0.71 0.15 0.00
57_P 82_S 0.71 0.15 0.00
43_P 399_L 0.70 0.15 0.00
73_V 659_E 0.70 0.15 0.00
106_I 27_G 0.70 0.15 0.00
74_P 749_H 0.70 0.15 0.00
42_R 98_D 0.70 0.15 0.00
66_F 19_V 0.70 0.15 0.00
36_Q 260_P 0.70 0.15 0.00
51_R 592_P 0.70 0.15 0.00
125_L 506_I 0.69 0.14 0.00
155_A 660_A 0.69 0.14 0.00
120_Q 177_D 0.69 0.14 0.00
34_V 24_F 0.69 0.14 0.00
96_L 202_F 0.69 0.14 0.00
63_V 309_P 0.69 0.14 0.00
69_Y 82_S 0.69 0.14 0.00
133_V 521_A 0.69 0.14 0.00
65_S 236_L 0.69 0.14 0.00
116_L 608_Y 0.69 0.14 0.00
111_V 19_V 0.69 0.14 0.00
65_S 742_R 0.69 0.14 0.00
87_S 692_F 0.69 0.14 0.00
131_A 528_K 0.68 0.14 0.00
80_L 74_Q 0.68 0.14 0.00
77_K 360_L 0.68 0.14 0.00
131_A 488_E 0.68 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
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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