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OPENSEQ.org
cIV_A_20_cI_K_10_human
Genes: A B A+B
Length: 513 98 608
Sequences: 4412 3525 1707
Seq/Len: 8.6 35.97 2.81
MirrorTree (Pazo et al. 2001) 0.03
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 0.04
2 0.01 0.00 0.07
5 0.02 0.00 0.27
10 0.02 0.00 1.37
20 0.03 0.00 1.45
100 0.04 0.01 1.70
∞ 0.08 0.02 2.79
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
253_M 8_I 1.16 0.79 0.05
168_I 57_N 1.08 0.71 0.04
353_L 32_C 1.06 0.69 0.04
274_V 18_G 1.05 0.68 0.04
314_I 21_V 1.03 0.66 0.04
42_G 24_S 1.02 0.65 0.03
401_S 20_L 1.00 0.63 0.03
21_L 50_N 1.00 0.62 0.03
85_L 96_L 1.00 0.62 0.03
460_I 10_L 0.97 0.59 0.03
416_I 14_I 0.92 0.53 0.02
176_M 31_L 0.88 0.49 0.02
327_L 96_L 0.88 0.48 0.02
375_A 16_L 0.87 0.47 0.02
133_A 98_C 0.87 0.47 0.02
188_V 66_F 0.87 0.47 0.02
169_I 97_Q 0.85 0.44 0.02
42_G 18_G 0.82 0.41 0.02
430_F 86_G 0.82 0.41 0.02
42_G 26_L 0.81 0.39 0.02
413_H 37_M 0.80 0.39 0.02
64_V 65_V 0.79 0.38 0.02
359_A 18_G 0.79 0.38 0.02
257_I 32_C 0.79 0.38 0.02
5_R 67_A 0.78 0.37 0.01
505_F 71_A 0.78 0.36 0.01
501_P 15_S 0.77 0.35 0.01
329_G 86_G 0.77 0.35 0.01
289_A 68_A 0.77 0.35 0.01
36_L 28_S 0.77 0.35 0.01
496_Y 37_M 0.76 0.34 0.01
260_Y 31_L 0.76 0.34 0.01
152_L 54_L 0.76 0.34 0.01
104_L 93_L 0.76 0.34 0.01
433_L 30_L 0.76 0.34 0.01
395_H 45_T 0.75 0.33 0.01
155_V 7_N 0.75 0.33 0.01
100_M 69_C 0.75 0.33 0.01
109_L 42_I 0.75 0.33 0.01
70_V 97_Q 0.75 0.33 0.01
5_R 47_M 0.74 0.32 0.01
361_S 77_L 0.74 0.32 0.01
23_G 28_S 0.73 0.31 0.01
29_L 28_S 0.73 0.31 0.01
390_M 60_P 0.73 0.31 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
4519 2.81 cIV_A_20_cI_K_10_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4518 2.49 cIV_A_60_cI_K_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4517 2.53 cIV_A_40_cI_K_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4516 0.33 cIV_A_40_cI_K_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4515 0.03 cIV_A_40_cI_K_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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