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cIV_A_80_cI_L_80_human
Genes: A B A+B
Length: 513 603 1109
Sequences: 3286 10702 3453
Seq/Len: 6.41 17.75 3.11
MirrorTree (Pazo et al. 2001) 0.66
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 0.31 0.03
2 0.00 0.33 0.12
5 0.01 0.37 0.37
10 0.01 0.38 1.97
20 0.01 0.38 2.04
100 0.02 0.39 2.22
∞ 0.06 0.39 3.09
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
26_A 281_G 1.07 0.74 0.02
453_L 375_I 0.94 0.59 0.02
391_G 362_L 0.89 0.52 0.01
413_H 387_T 0.86 0.48 0.01
5_R 221_A 0.84 0.46 0.01
193_V 430_T 0.84 0.46 0.01
187_S 341_M 0.83 0.45 0.01
286_I 501_A 0.82 0.44 0.01
470_F 281_G 0.82 0.44 0.01
476_F 219_A 0.82 0.44 0.01
465_V 86_S 0.81 0.42 0.01
27_G 152_F 0.81 0.42 0.01
257_I 452_N 0.79 0.40 0.01
374_V 430_T 0.79 0.39 0.01
35_L 500_T 0.78 0.39 0.01
488_P 185_A 0.77 0.38 0.01
27_G 366_M 0.77 0.38 0.01
480_R 20_L 0.77 0.37 0.01
400_F 326_F 0.76 0.36 0.01
409_Y 212_P 0.75 0.35 0.01
464_A 76_L 0.74 0.35 0.01
419_I 549_P 0.74 0.34 0.01
466_M 362_L 0.74 0.34 0.01
85_L 183_I 0.74 0.34 0.01
54_Y 201_M 0.73 0.34 0.01
314_I 334_F 0.73 0.33 0.01
176_M 288_A 0.73 0.33 0.01
270_Y 582_G 0.73 0.33 0.01
498_C 587_Y 0.73 0.33 0.01
460_I 288_A 0.72 0.33 0.01
359_A 379_A 0.72 0.32 0.01
155_V 518_C 0.72 0.32 0.01
97_M 399_A 0.72 0.32 0.01
447_Y 185_A 0.71 0.31 0.01
505_F 152_F 0.71 0.31 0.01
97_M 324_L 0.71 0.31 0.01
332_M 182_F 0.71 0.30 0.01
7_L 168_A 0.70 0.30 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
4654 2.53 cIV_A_80_cI_L_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 2) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4652 3.11 cIV_A_80_cI_L_80_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4453 1.1 cIV_A_60_cI_L_80_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4452 1.11 cIV_A_60_cI_L_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.98 Done - Shared
4451 1.1 cIV_A_80_cI_L_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.97 Done - Shared
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