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OPENSEQ.org
cIp_4_4_cIV_B_4
Genes: A B A+B
Length: 412 298 668
Sequences: 3488 3243 824
Seq/Len: 8.47 10.88 1.23
MirrorTree (Pazo et al. 2001) 0.18
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 0.01
2 0.01 0.00 0.02
5 0.03 0.00 0.03
10 0.04 0.01 0.06
20 0.05 0.01 0.09
100 0.06 0.03 0.21
∞ 0.13 0.06 1.16
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
227_E 199_V 1.29 0.66 0.00
394_A 158_N 1.10 0.48 0.00
186_D 143_I 1.03 0.42 0.00
101_A 83_L 1.03 0.41 0.00
52_I 205_A 0.97 0.37 0.00
226_T 105_P 0.95 0.34 0.00
242_G 203_V 0.93 0.33 0.00
265_I 116_L 0.93 0.33 0.00
303_A 195_V 0.93 0.33 0.00
101_A 74_V 0.93 0.32 0.00
389_R 195_V 0.92 0.32 0.00
160_F 241_Y 0.89 0.30 0.00
200_K 76_I 0.87 0.28 0.00
292_Q 199_V 0.86 0.27 0.00
53_V 236_D 0.83 0.25 0.00
288_C 116_L 0.83 0.24 0.00
53_V 127_P 0.81 0.23 0.00
109_V 193_V 0.80 0.22 0.00
289_K 36_L 0.78 0.21 0.00
252_S 63_L 0.78 0.21 0.00
393_L 112_L 0.78 0.21 0.00
49_D 137_N 0.77 0.20 0.00
378_F 113_V 0.76 0.20 0.00
53_V 105_P 0.75 0.19 0.00
196_E 77_F 0.73 0.18 0.00
53_V 268_Y 0.73 0.18 0.00
338_F 160_G 0.73 0.18 0.00
108_T 76_I 0.73 0.18 0.00
226_T 35_D 0.73 0.18 0.00
202_V 120_A 0.73 0.18 0.00
384_I 252_N 0.73 0.18 0.00
112_R 116_L 0.71 0.17 0.00
338_F 57_A 0.71 0.17 0.00
80_L 205_A 0.71 0.17 0.00
295_V 67_V 0.71 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
4002 0.89 cIp_4_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4001 1.23 cIp_4_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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