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OPENSEQ.org
cI_A_cIII_isp_human_med6
Genes: A B A+B
Length: 115 143 254
Sequences: 4367 1087 339
Seq/Len: 37.97 7.6 1.33
MirrorTree (Pazo et al. 2001) 0.56
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.00 0.01 0.03
100 0.01 0.01 0.13
∞ 0.02 0.03 1.31
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
7_L 25_L 1.56 0.87 0.18
20_I 129_V 1.49 0.83 0.15
3_F 85_V 1.38 0.76 0.11
11_T 25_L 1.29 0.69 0.09
86_L 5_F 1.24 0.65 0.07
103_A 50_Q 1.17 0.58 0.06
88_V 45_V 1.16 0.57 0.06
3_F 9_M 1.15 0.56 0.06
16_L 12_S 1.14 0.54 0.05
105_E 109_G 1.11 0.52 0.05
96_V 15_V 1.08 0.49 0.04
4_A 78_E 1.08 0.48 0.04
16_L 14_D 1.06 0.47 0.04
15_L 2_V 1.05 0.46 0.04
5_L 9_M 1.05 0.46 0.04
25_P 121_G 1.02 0.42 0.03
77_W 65_R 1.00 0.41 0.03
59_A 73_R 0.99 0.40 0.03
10_N 92_V 0.99 0.40 0.03
34_S 125_L 0.99 0.40 0.03
20_I 85_V 0.97 0.38 0.03
8_M 58_A 0.96 0.37 0.03
11_T 142_V 0.96 0.37 0.03
59_A 20_K 0.94 0.36 0.03
21_T 99_D 0.94 0.35 0.03
59_A 6_V 0.94 0.35 0.03
64_L 71_L 0.94 0.35 0.03
9_I 15_V 0.93 0.35 0.03
22_F 8_S 0.93 0.34 0.03
43_P 129_V 0.91 0.33 0.02
78_A 121_G 0.90 0.32 0.02
77_W 112_Y 0.90 0.32 0.02
58_V 26_S 0.89 0.31 0.02
88_V 85_V 0.89 0.31 0.02
112_D 32_K 0.89 0.30 0.02
5_L 72_D 0.88 0.30 0.02
15_L 52_E 0.88 0.30 0.02
13_L 85_V 0.87 0.29 0.02
5_L 32_K 0.86 0.29 0.02
78_A 29_P 0.86 0.29 0.02
8_M 54_E 0.86 0.28 0.02
5_L 71_L 0.86 0.28 0.02
103_A 2_V 0.86 0.28 0.02
27_L 25_L 0.86 0.28 0.02
103_A 75_K 0.86 0.28 0.02
31_M 8_S 0.86 0.28 0.02
103_A 72_D 0.84 0.27 0.02
59_A 77_P 0.84 0.27 0.02
93_L 72_D 0.84 0.27 0.02
87_M 23_I 0.84 0.26 0.02
90_S 71_L 0.83 0.26 0.02
19_I 79_W 0.83 0.26 0.02
20_I 39_R 0.82 0.25 0.02
100_L 94_I 0.82 0.25 0.02
47_A 139_M 0.81 0.25 0.02
21_T 14_D 0.81 0.24 0.01
91_S 98_G 0.81 0.24 0.01
88_V 40_G 0.81 0.24 0.01
36_P 40_G 0.81 0.24 0.01
107_L 128_E 0.80 0.24 0.01
6_I 40_G 0.80 0.24 0.01
112_D 29_P 0.80 0.23 0.01
85_P 50_Q 0.80 0.23 0.01
21_T 5_F 0.79 0.23 0.01
83_N 28_I 0.79 0.23 0.01
22_F 39_R 0.78 0.23 0.01
78_A 5_F 0.78 0.22 0.01
106_W 44_F 0.78 0.22 0.01
89_M 47_H 0.78 0.22 0.01
4_A 73_R 0.78 0.22 0.01
53_M 113_D 0.78 0.22 0.01
96_V 57_A 0.78 0.22 0.01
67_L 132_Y 0.78 0.22 0.01
85_P 115_S 0.78 0.22 0.01
112_D 95_A 0.77 0.22 0.01
49_V 24_K 0.77 0.22 0.01
45_S 45_V 0.77 0.22 0.01
43_P 141_I 0.77 0.22 0.01
24_L 125_L 0.77 0.21 0.01
36_P 140_V 0.77 0.21 0.01
100_L 96_N 0.77 0.21 0.01
22_F 5_F 0.77 0.21 0.01
23_W 132_Y 0.76 0.21 0.01
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
2563 1.33 cI_A_cIII_isp_human_med6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
2497 1.43 cI_A_cIII_isp_human_med Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.39 Done - Shared
2496 0.04 cI_A_cIII_isp_human_med Δgene:(1, 20) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) Killed - Shared
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