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OPENSEQ.org
cIm_K_4_cyt1_2_human
Genes: A B A+B
Length: 98 325 351
Sequences: 6983 747 163
Seq/Len: 71.26 2.3 0.46
MirrorTree (Pazo et al. 2001) 0.06
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.01
100 0.01 0.02 0.04
∞ 0.04 0.02 0.39
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
44_G 224_G 1.34 0.42 0.00
28_S 310_K 1.14 0.28 0.00
93_L 308_R 1.04 0.23 0.00
93_L 282_H 1.04 0.23 0.00
58_I 115_Q 1.02 0.21 0.00
8_I 138_V 1.01 0.21 0.00
61_I 233_F 0.97 0.19 0.00
17_L 126_S 0.97 0.19 0.00
33_L 253_L 0.97 0.19 0.00
39_S 146_K 0.94 0.17 0.00
33_L 246_P 0.94 0.17 0.00
82_S 311_W 0.93 0.17 0.00
52_H 179_Y 0.93 0.17 0.00
8_I 245_A 0.92 0.17 0.00
62_A 300_V 0.91 0.17 0.00
91_H 158_P 0.91 0.17 0.00
82_S 188_A 0.91 0.16 0.00
39_S 160_E 0.91 0.16 0.00
94_N 237_F 0.91 0.16 0.00
26_L 77_A 0.87 0.15 0.00
42_I 247_P 0.87 0.15 0.00
87_L 74_L 0.87 0.15 0.00
87_L 278_S 0.87 0.15 0.00
62_A 186_R 0.86 0.15 0.00
87_L 75_A 0.85 0.14 0.00
80_S 158_P 0.85 0.14 0.00
16_L 127_M 0.85 0.14 0.00
14_I 307_K 0.84 0.14 0.00
39_S 142_E 0.84 0.14 0.00
93_L 310_K 0.84 0.14 0.00
26_L 313_V 0.84 0.14 0.00
33_L 179_Y 0.83 0.14 0.00
26_L 80_S 0.83 0.14 0.00
6_M 177_K 0.83 0.13 0.00
80_S 159_N 0.83 0.13 0.00
17_L 211_V 0.83 0.13 0.00
50_N 174_Y 0.82 0.13 0.00
44_G 311_W 0.82 0.13 0.00
81_I 186_R 0.82 0.13 0.00
8_I 242_I 0.81 0.13 0.00
36_M 143_D 0.81 0.13 0.00
8_I 235_P 0.81 0.13 0.00
14_I 123_S 0.81 0.13 0.00
40_L 203_A 0.80 0.12 0.00
61_I 96_W 0.80 0.12 0.00
40_L 204_R 0.79 0.12 0.00
39_S 128_D 0.78 0.12 0.00
4_I 258_G 0.78 0.12 0.00
8_I 137_G 0.77 0.11 0.00
16_L 287_R 0.77 0.11 0.00
54_L 127_M 0.77 0.11 0.00
16_L 78_L 0.77 0.11 0.00
69_C 159_N 0.77 0.11 0.00
77_L 95_P 0.76 0.11 0.00
54_L 126_S 0.76 0.11 0.00
72_A 97_S 0.76 0.11 0.00
10_L 73_G 0.76 0.11 0.00
39_S 180_P 0.75 0.11 0.00
44_G 235_P 0.75 0.11 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
5744 0 cIm_K_40_cyt1_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5742 0.46 cIm_K_4_cyt1_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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