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OPENSEQ.org
cIm_N_4_1_isp_2_human
Genes: A B A+B
Length: 347 274 502
Sequences: 8936 609 168
Seq/Len: 25.75 2.22 0.33
MirrorTree (Pazo et al. 2001) 0.23
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 0.03 0.00 0.00
2 0.03 0.00 0.00
5 0.03 0.00 0.00
10 0.03 0.00 0.00
20 0.04 0.00 0.00
100 0.04 0.00 0.01
∞ 0.04 0.00 0.27
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
296_L 64_L 1.46 0.42 0.00
77_N 216_V 1.42 0.39 0.00
147_P 66_A 1.31 0.32 0.00
203_L 216_V 1.20 0.26 0.00
210_I 64_L 1.19 0.25 0.00
265_A 272_I 1.13 0.22 0.00
164_A 92_R 1.11 0.21 0.00
271_T 108_E 1.11 0.21 0.00
60_F 87_D 1.09 0.20 0.00
214_T 132_A 1.07 0.19 0.00
86_M 90_E 1.06 0.19 0.00
178_I 108_E 1.04 0.18 0.00
141_I 142_A 1.03 0.18 0.00
112_H 196_R 1.03 0.18 0.00
241_T 102_S 1.02 0.17 0.00
176_R 271_V 0.99 0.16 0.00
228_L 79_S 0.97 0.15 0.00
88_N 250_R 0.96 0.15 0.00
69_I 116_L 0.95 0.15 0.00
69_I 250_R 0.95 0.15 0.00
230_L 123_V 0.94 0.14 0.00
156_T 96_V 0.91 0.13 0.00
55_A 266_T 0.91 0.13 0.00
281_I 93_R 0.90 0.13 0.00
160_L 272_I 0.89 0.13 0.00
176_R 184_I 0.89 0.13 0.00
208_Y 270_M 0.87 0.12 0.00
284_T 179_R 0.87 0.12 0.00
197_N 123_V 0.87 0.12 0.00
178_I 162_G 0.86 0.12 0.00
272_K 88_F 0.85 0.12 0.00
36_N 165_M 0.84 0.11 0.00
170_L 173_P 0.84 0.11 0.00
292_F 102_S 0.84 0.11 0.00
194_L 165_M 0.83 0.11 0.00
170_L 272_I 0.83 0.11 0.00
280_T 121_T 0.82 0.11 0.00
178_I 65_V 0.82 0.11 0.00
44_L 107_S 0.82 0.11 0.00
53_T 133_V 0.81 0.11 0.00
83_Q 66_A 0.81 0.11 0.00
36_N 176_V 0.81 0.10 0.00
157_L 64_L 0.81 0.10 0.00
145_I 176_V 0.80 0.10 0.00
101_A 170_R 0.80 0.10 0.00
23_S 90_E 0.79 0.10 0.00
160_L 204_R 0.79 0.10 0.00
156_T 176_V 0.79 0.10 0.00
161_S 118_T 0.78 0.10 0.00
29_T 204_R 0.78 0.10 0.00
29_T 123_V 0.78 0.10 0.00
141_I 86_P 0.78 0.10 0.00
72_M 124_G 0.78 0.10 0.00
258_T 272_I 0.78 0.10 0.00
193_V 270_M 0.77 0.10 0.00
162_I 123_V 0.77 0.10 0.00
264_W 212_I 0.77 0.10 0.00
69_I 71_N 0.77 0.10 0.00
265_A 66_A 0.77 0.10 0.00
200_M 188_A 0.77 0.10 0.00
178_I 89_S 0.77 0.10 0.00
103_A 199_Q 0.77 0.10 0.00
239_W 65_V 0.77 0.09 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
5739 0.33 cIm_N_4_1_isp_2_human Δgene:(1, ∞) A:(1E-04, 1) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5738 0 cIm_N_20_1_isp_2_human Δgene:(1, ∞) A:(1E-20, 1) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Killed - Shared
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