May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIp_1_4_cIV_B_4
Genes: A B A+B
Length: 455 227 650
Sequences: 2643 5082 854
Seq/Len: 5.81 22.39 1.31
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.01 0.01
20 0.03 0.01 0.02
100 0.05 0.02 0.15
∞ 0.14 0.04 1.25
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
352_T 219_F 0.88 0.30 0.00
122_L 162_S 0.85 0.27 0.00
435_P 224_V 0.84 0.27 0.00
188_V 32_F 0.84 0.26 0.00
436_E 147_E 0.84 0.26 0.00
337_Q 163_W 0.83 0.25 0.00
389_R 142_V 0.80 0.23 0.00
266_L 148_A 0.80 0.23 0.00
74_S 61_M 0.79 0.23 0.00
233_V 138_V 0.77 0.21 0.00
238_T 115_G 0.77 0.21 0.00
138_R 192_Y 0.76 0.21 0.00
169_E 97_I 0.75 0.20 0.00
250_G 146_I 0.75 0.20 0.00
45_K 43_F 0.73 0.19 0.00
233_V 175_I 0.71 0.18 0.00
401_D 225_F 0.71 0.17 0.00
129_L 19_E 0.70 0.17 0.00
186_V 146_I 0.70 0.17 0.00
286_P 225_F 0.70 0.17 0.00
392_R 37_L 0.70 0.17 0.00
135_V 18_E 0.69 0.17 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
4046 1.31 cIp_1_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4044 0.94 cIp_1_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 0.3852 seconds.