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OPENSEQ.org
cIV_A_4_cI_M_4_1_human
Genes: A B A+B
Length: 513 459 965
Sequences: 4483 6767 2952
Seq/Len: 8.74 14.74 3.06
MirrorTree (Pazo et al. 2001) 0.55
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 0.23 0.03
2 0.01 0.23 0.08
5 0.02 0.27 0.27
10 0.02 0.27 1.79
20 0.03 0.27 1.88
100 0.05 0.28 2.10
∞ 0.08 0.29 3.04
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
265_K 250_L 1.14 0.79 0.05
229_I 410_M 0.94 0.58 0.03
391_G 195_M 0.93 0.57 0.03
476_F 197_L 0.89 0.53 0.02
473_W 291_I 0.85 0.47 0.02
350_V 199_Y 0.82 0.44 0.02
391_G 155_V 0.82 0.43 0.02
193_I 395_L 0.82 0.43 0.02
137_S 124_T 0.81 0.41 0.02
7_L 67_M 0.78 0.38 0.02
461_S 285_L 0.78 0.38 0.02
466_M 437_M 0.78 0.38 0.02
87_I 264_L 0.75 0.35 0.01
476_F 163_A 0.75 0.35 0.01
159_L 377_G 0.75 0.35 0.01
356_I 292_S 0.74 0.34 0.01
375_A 341_I 0.74 0.34 0.01
331_N 368_A 0.74 0.34 0.01
279_S 262_L 0.74 0.34 0.01
359_A 309_F 0.73 0.33 0.01
108_S 386_F 0.73 0.33 0.01
83_V 262_L 0.73 0.33 0.01
397_F 72_L 0.73 0.33 0.01
341_A 202_A 0.72 0.32 0.01
335_S 199_Y 0.72 0.32 0.01
419_I 306_P 0.72 0.32 0.01
443_Y 121_F 0.72 0.32 0.01
320_V 312_A 0.72 0.31 0.01
391_G 30_H 0.72 0.31 0.01
85_L 66_L 0.72 0.31 0.01
356_I 234_V 0.71 0.31 0.01
501_P 368_A 0.71 0.30 0.01
286_I 250_L 0.71 0.30 0.01
260_Y 382_L 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
4418 1.62 cIV_A_80_cI_M_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4416 1.15 cIV_A_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4415 1.17 cIV_A_80_1_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 1) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4414 1.15 cIV_A_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4413 1.62 cIV_A_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.17 Done - Shared
4408 2.75 cIV_A_20_cI_M_20_1_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4405 3.06 cIV_A_4_cI_M_4_1_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4398 2.38 cIV_A_40_cI_M_40_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.04 Done - Shared
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