May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIp_5_6_cIV_B_6
Genes: A B A+B
Length: 207 298 464
Sequences: 1076 2942 471
Seq/Len: 5.2 9.87 1.02
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 0.08
20 0.00 0.02 0.13
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 1.97 0.95 0.73
137_I 241_Y 1.35 0.66 0.25
124_F 99_R 1.30 0.61 0.21
91_I 145_A 1.26 0.58 0.19
124_F 273_A 1.20 0.53 0.15
100_D 146_I 1.08 0.42 0.10
162_W 119_V 1.07 0.41 0.10
48_E 195_V 1.07 0.41 0.10
126_I 274_G 1.06 0.40 0.09
36_V 104_T 1.03 0.37 0.08
53_D 118_L 1.01 0.35 0.08
63_D 218_A 0.98 0.33 0.07
46_L 146_I 0.95 0.30 0.06
106_L 272_L 0.94 0.30 0.06
124_F 88_R 0.93 0.29 0.06
129_S 116_L 0.91 0.27 0.05
109_V 191_V 0.90 0.27 0.05
114_N 108_V 0.87 0.24 0.04
170_V 74_V 0.87 0.24 0.04
123_L 109_I 0.86 0.24 0.04
43_V 171_E 0.81 0.21 0.03
123_L 69_Y 0.81 0.20 0.03
64_I 202_Q 0.81 0.20 0.03
82_L 214_I 0.81 0.20 0.03
17_I 196_G 0.81 0.20 0.03
154_T 211_A 0.80 0.20 0.03
91_I 141_L 0.80 0.20 0.03
41_S 35_D 0.80 0.20 0.03
110_F 242_F 0.79 0.19 0.03
32_G 270_A 0.79 0.19 0.03
126_I 182_E 0.79 0.19 0.03
123_L 113_V 0.79 0.19 0.03
151_D 150_W 0.78 0.19 0.03
93_V 155_E 0.78 0.19 0.03
163_S 112_L 0.78 0.19 0.03
85_M 145_A 0.78 0.18 0.03
124_F 86_I 0.77 0.18 0.03
109_V 108_V 0.77 0.18 0.03
120_V 270_A 0.77 0.18 0.03
108_G 113_V 0.77 0.18 0.03
137_I 163_F 0.76 0.18 0.03
15_E 141_L 0.76 0.18 0.03
97_V 238_E 0.76 0.18 0.03
17_I 170_K 0.76 0.18 0.03
112_G 67_V 0.76 0.18 0.02
32_G 76_I 0.76 0.18 0.02
126_I 191_V 0.75 0.17 0.02
118_R 156_Y 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
Page generated in 0.9525 seconds.