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OPENSEQ.org
cIV_A_80_cI_N_60_1_human
Genes: A B A+B
Length: 513 347 857
Sequences: 3020 5821 2413
Seq/Len: 5.89 16.78 2.82
MirrorTree (Pazo et al. 2001) 0.63
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 0.00 1.47
2 0.00 0.01 1.53
5 0.01 0.01 1.62
10 0.01 0.01 1.75
20 0.01 0.01 1.92
100 0.02 0.02 2.03
∞ 0.05 0.03 2.81
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
510_Y 188_G 1.16 0.79 0.05
334_W 176_R 1.06 0.70 0.04
146_T 35_M 1.00 0.62 0.03
187_S 197_N 0.98 0.61 0.03
314_I 283_A 0.98 0.60 0.03
33_L 33_L 0.98 0.60 0.03
270_Y 117_E 0.96 0.58 0.03
114_A 266_I 0.96 0.58 0.03
356_I 39_A 0.96 0.58 0.03
130_P 6_Q 0.95 0.57 0.03
453_L 18_L 0.94 0.56 0.03
258_V 248_F 0.94 0.55 0.03
258_V 95_S 0.94 0.55 0.03
447_Y 159_I 0.93 0.55 0.03
175_A 117_E 0.93 0.54 0.03
270_Y 188_G 0.93 0.54 0.03
166_T 26_W 0.92 0.54 0.03
223_A 164_A 0.92 0.53 0.03
12_H 54_E 0.91 0.52 0.03
463_T 227_T 0.90 0.51 0.02
7_L 244_I 0.90 0.50 0.02
54_Y 295_R 0.89 0.50 0.02
231_Y 107_G 0.89 0.49 0.02
265_K 121_G 0.88 0.48 0.02
409_Y 66_A 0.87 0.48 0.02
314_I 116_P 0.87 0.47 0.02
168_I 300_T 0.87 0.47 0.02
169_I 267_I 0.86 0.47 0.02
339_L 38_L 0.86 0.46 0.02
495_L 117_E 0.86 0.46 0.02
174_P 117_E 0.86 0.46 0.02
463_T 69_I 0.85 0.45 0.02
356_I 278_I 0.84 0.44 0.02
354_T 30_W 0.84 0.44 0.02
395_H 289_N 0.84 0.43 0.02
320_V 324_P 0.83 0.43 0.02
423_L 157_L 0.83 0.42 0.02
407_Q 193_V 0.83 0.42 0.02
282_F 158_S 0.82 0.42 0.02
133_A 52_S 0.82 0.41 0.02
410_A 289_N 0.82 0.41 0.02
193_I 162_I 0.81 0.40 0.02
229_I 175_L 0.81 0.40 0.02
479_K 52_S 0.80 0.39 0.02
434_S 117_E 0.80 0.39 0.02
87_I 141_I 0.80 0.39 0.02
407_Q 188_G 0.79 0.38 0.02
270_Y 62_T 0.79 0.38 0.02
482_V 329_L 0.79 0.38 0.02
453_L 239_W 0.79 0.38 0.02
286_I 101_A 0.79 0.37 0.02
83_V 43_V 0.79 0.37 0.02
7_L 136_L 0.78 0.37 0.02
506_E 284_T 0.78 0.37 0.02
419_I 167_W 0.78 0.37 0.02
278_M 212_T 0.78 0.36 0.02
475_A 72_M 0.77 0.36 0.02
297_M 68_M 0.77 0.35 0.01
405_L 75_L 0.77 0.35 0.01
490_M 194_L 0.77 0.35 0.01
133_A 181_Y 0.77 0.35 0.01
400_F 55_A 0.77 0.35 0.01
460_I 331_A 0.77 0.35 0.01
50_N 331_A 0.77 0.35 0.01
359_A 187_M 0.76 0.35 0.01
449_T 56_A 0.76 0.34 0.01
173_P 193_V 0.75 0.34 0.01
279_S 181_Y 0.75 0.34 0.01
489_S 216_F 0.75 0.33 0.01
25_W 57_I 0.75 0.33 0.01
391_G 187_M 0.74 0.33 0.01
320_V 257_L 0.74 0.33 0.01
464_A 15_A 0.74 0.32 0.01
350_V 203_L 0.74 0.32 0.01
330_S 216_F 0.74 0.32 0.01
278_M 67_S 0.74 0.32 0.01
470_F 207_I 0.73 0.32 0.01
413_H 126_S 0.73 0.31 0.01
460_I 309_N 0.73 0.31 0.01
5_R 117_E 0.73 0.31 0.01
286_I 20_T 0.73 0.31 0.01
42_G 294_L 0.73 0.31 0.01
215_L 29_T 0.73 0.31 0.01
487_E 232_R 0.73 0.31 0.01
204_A 288_L 0.73 0.31 0.01
294_T 61_L 0.73 0.31 0.01
466_M 11_S 0.73 0.31 0.01
466_M 194_L 0.73 0.31 0.01
295_V 31_V 0.73 0.31 0.01
279_S 38_L 0.73 0.31 0.01
189_L 71_L 0.73 0.31 0.01
391_G 68_M 0.73 0.31 0.01
35_L 61_L 0.72 0.30 0.01
54_Y 249_L 0.72 0.30 0.01
356_I 15_A 0.72 0.30 0.01
308_A 87_T 0.72 0.30 0.01
206_I 131_L 0.72 0.30 0.01
258_V 233_T 0.72 0.30 0.01
492_L 73_A 0.72 0.30 0.01
487_E 117_E 0.72 0.30 0.01
262_S 310_N 0.72 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
4548 0.73 cIV_A_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.51 Done - Shared
4546 0.73 cIV_A_60_cI_N_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.51 Done - Shared
4539 2.82 cIV_A_80_cI_N_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4536 1.63 cIV_A_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.29 Done - Shared
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