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OPENSEQ.org
cIp_5_4_cIV_B_10
Genes: A B A+B
Length: 207 298 464
Sequences: 1036 2938 468
Seq/Len: 5 9.86 1.01
MirrorTree (Pazo et al. 2001) 0.31
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 0.00
2 0.00 0.00 0.02
5 0.00 0.01 0.04
10 0.00 0.01 0.07
20 0.00 0.02 0.12
100 0.00 0.03 0.20
∞ 0.01 0.08 0.93
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
110_F 205_A 1.88 0.93 0.57
91_I 145_A 1.33 0.64 0.17
124_F 273_A 1.23 0.55 0.13
53_D 118_L 1.18 0.50 0.10
124_F 99_R 1.16 0.48 0.10
137_I 241_Y 1.10 0.43 0.08
105_S 44_N 1.08 0.41 0.07
109_V 191_V 1.05 0.38 0.07
129_S 116_L 1.02 0.36 0.06
123_L 109_I 0.99 0.34 0.05
46_L 146_I 0.98 0.32 0.05
170_V 74_V 0.97 0.32 0.05
97_V 238_E 0.95 0.30 0.04
124_F 88_R 0.93 0.29 0.04
106_L 272_L 0.92 0.28 0.04
36_V 104_T 0.91 0.27 0.04
124_F 171_E 0.91 0.27 0.04
35_T 172_A 0.91 0.27 0.04
112_G 67_V 0.89 0.26 0.03
17_I 170_K 0.89 0.26 0.03
63_D 218_A 0.88 0.25 0.03
114_N 108_V 0.88 0.25 0.03
48_E 195_V 0.87 0.24 0.03
109_V 108_V 0.86 0.24 0.03
111_P 201_V 0.86 0.24 0.03
105_S 264_S 0.86 0.23 0.03
116_Y 218_A 0.86 0.23 0.03
74_A 141_L 0.86 0.23 0.03
126_I 274_G 0.85 0.23 0.03
85_M 145_A 0.85 0.23 0.03
82_L 141_L 0.84 0.22 0.03
111_P 158_N 0.84 0.22 0.03
105_S 63_L 0.83 0.22 0.03
43_V 171_E 0.82 0.21 0.03
81_H 236_D 0.82 0.21 0.02
115_W 152_W 0.82 0.21 0.02
34_L 199_V 0.81 0.21 0.02
46_L 76_I 0.81 0.21 0.02
41_S 35_D 0.81 0.20 0.02
45_G 34_G 0.81 0.20 0.02
82_L 214_I 0.81 0.20 0.02
17_I 205_A 0.81 0.20 0.02
95_V 223_A 0.81 0.20 0.02
107_I 83_L 0.81 0.20 0.02
47_I 159_D 0.81 0.20 0.02
25_V 266_E 0.80 0.20 0.02
11_L 143_I 0.80 0.20 0.02
123_L 69_Y 0.79 0.20 0.02
116_Y 197_K 0.79 0.19 0.02
166_E 267_K 0.79 0.19 0.02
110_F 242_F 0.78 0.18 0.02
100_D 146_I 0.78 0.18 0.02
17_I 196_G 0.77 0.18 0.02
45_G 109_I 0.77 0.18 0.02
35_T 37_P 0.77 0.18 0.02
154_T 211_A 0.76 0.18 0.02
95_V 214_I 0.76 0.18 0.02
130_G 145_A 0.76 0.18 0.02
106_L 108_V 0.76 0.17 0.02
58_F 135_M 0.75 0.17 0.02
15_E 195_V 0.75 0.17 0.02
98_R 272_L 0.75 0.17 0.02
124_F 86_I 0.75 0.17 0.02
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
3990 1.01 cIp_5_2_cIV_B_6 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.42 Done - Shared
3989 1.02 cIp_5_6_cIV_B_6 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.73 Done - Shared
3988 1.01 cIp_5_4_cIV_B_10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.57 Done - Shared
3983 1.01 cIp_5_4_cIV_B_6 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.77 Done - Shared
3981 1.02 cIp_5_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.60 Done - Shared
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