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OPENSEQ.org
cIV_A_80_cI_L_80_human
Genes: A B A+B
Length: 513 603 1108
Sequences: 3037 4961 2799
Seq/Len: 5.92 8.23 2.53
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 0.00 0.03
2 0.00 0.00 0.09
5 0.01 0.00 0.32
10 0.01 0.00 1.87
20 0.01 0.00 1.94
100 0.02 0.01 2.02
∞ 0.05 0.02 2.51
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 1.16 0.76 0.03
466_M 362_L 1.15 0.75 0.03
83_V 442_N 1.13 0.73 0.03
470_F 281_G 1.04 0.64 0.02
119_E 337_A 1.02 0.62 0.02
434_S 281_G 1.01 0.60 0.02
155_V 502_L 0.99 0.59 0.02
460_I 288_A 0.99 0.58 0.02
108_S 298_I 0.98 0.58 0.02
187_S 341_M 0.97 0.56 0.02
187_S 537_I 0.95 0.54 0.02
166_T 359_M 0.94 0.52 0.02
356_I 96_V 0.93 0.51 0.02
229_I 445_E 0.93 0.51 0.02
394_I 153_L 0.91 0.49 0.02
262_S 186_L 0.91 0.49 0.02
5_R 221_A 0.91 0.49 0.02
286_I 396_I 0.91 0.48 0.02
27_G 152_F 0.90 0.47 0.02
400_F 318_G 0.89 0.47 0.01
193_V 430_T 0.88 0.45 0.01
314_I 576_I 0.87 0.44 0.01
320_V 551_L 0.87 0.44 0.01
122_A 188_W 0.86 0.43 0.01
289_A 554_D 0.86 0.43 0.01
5_R 231_P 0.85 0.41 0.01
509_V 341_M 0.85 0.41 0.01
453_L 375_I 0.84 0.41 0.01
338_V 592_F 0.84 0.41 0.01
215_L 316_T 0.84 0.40 0.01
505_F 152_F 0.83 0.40 0.01
492_L 346_I 0.83 0.40 0.01
447_Y 210_L 0.83 0.40 0.01
20_L 87_M 0.83 0.40 0.01
248_L 467_L 0.83 0.40 0.01
341_A 88_M 0.83 0.39 0.01
335_S 217_L 0.83 0.39 0.01
270_Y 582_G 0.83 0.39 0.01
133_A 578_S 0.83 0.39 0.01
261_Y 341_M 0.83 0.39 0.01
465_V 86_S 0.82 0.39 0.01
413_H 566_I 0.82 0.38 0.01
453_L 205_N 0.82 0.38 0.01
423_L 272_L 0.82 0.38 0.01
365_I 167_A 0.82 0.38 0.01
434_S 140_L 0.81 0.37 0.01
115_S 153_L 0.81 0.37 0.01
20_L 341_M 0.81 0.37 0.01
398_P 228_G 0.81 0.37 0.01
83_V 67_H 0.81 0.37 0.01
35_L 500_T 0.80 0.36 0.01
279_S 530_P 0.80 0.36 0.01
33_L 356_I 0.80 0.36 0.01
172_K 217_L 0.80 0.36 0.01
359_A 420_S 0.79 0.35 0.01
83_V 291_C 0.79 0.35 0.01
33_L 298_I 0.79 0.35 0.01
456_V 500_T 0.79 0.35 0.01
289_A 140_L 0.79 0.35 0.01
168_I 366_M 0.79 0.35 0.01
434_S 274_Q 0.78 0.34 0.01
467_L 418_L 0.78 0.34 0.01
155_V 159_Y 0.78 0.34 0.01
97_M 324_L 0.78 0.34 0.01
314_I 376_G 0.78 0.34 0.01
279_S 209_S 0.78 0.34 0.01
463_T 555_L 0.78 0.34 0.01
356_I 525_M 0.78 0.34 0.01
104_L 398_T 0.78 0.34 0.01
296_G 234_P 0.77 0.33 0.01
345_I 267_A 0.77 0.33 0.01
420_G 288_A 0.77 0.33 0.01
487_E 99_S 0.77 0.33 0.01
85_L 183_I 0.77 0.33 0.01
492_L 216_L 0.77 0.33 0.01
122_A 407_W 0.77 0.33 0.01
413_H 387_T 0.77 0.33 0.01
198_S 293_L 0.77 0.33 0.01
453_L 54_F 0.77 0.33 0.01
270_Y 252_M 0.77 0.32 0.01
314_I 468_I 0.76 0.32 0.01
56_V 245_A 0.76 0.32 0.01
274_V 582_G 0.76 0.32 0.01
223_A 289_A 0.76 0.32 0.01
184_F 95_F 0.76 0.32 0.01
258_V 23_L 0.76 0.32 0.01
345_I 152_F 0.76 0.32 0.01
158_I 382_G 0.76 0.32 0.01
111_L 554_D 0.76 0.31 0.01
27_G 366_M 0.75 0.31 0.01
176_M 283_I 0.75 0.31 0.01
489_S 68_W 0.75 0.31 0.01
161_A 82_L 0.75 0.31 0.01
468_M 587_Y 0.75 0.31 0.01
498_C 587_Y 0.75 0.31 0.01
229_I 584_I 0.75 0.31 0.01
259_T 361_G 0.75 0.30 0.01
35_L 458_A 0.74 0.30 0.01
229_I 591_F 0.74 0.30 0.01
398_P 118_F 0.74 0.30 0.01
44_P 260_L 0.74 0.30 0.01
122_A 337_A 0.74 0.30 0.01
463_T 597_L 0.74 0.30 0.01
253_M 349_N 0.74 0.30 0.01
462_L 288_A 0.74 0.30 0.01
258_V 267_A 0.74 0.30 0.01
18_L 112_P 0.74 0.30 0.01
419_I 80_F 0.74 0.30 0.01
171_M 292_A 0.74 0.29 0.01
356_I 453_P 0.74 0.29 0.01
307_S 103_F 0.73 0.29 0.01
36_L 118_F 0.73 0.29 0.01
289_A 382_G 0.73 0.29 0.01
28_V 291_C 0.73 0.29 0.01
392_G 538_P 0.73 0.29 0.01
231_Y 82_L 0.73 0.29 0.01
97_M 220_A 0.73 0.29 0.01
39_A 426_M 0.73 0.29 0.01
162_I 172_I 0.73 0.29 0.01
278_M 349_N 0.73 0.29 0.01
401_S 369_T 0.73 0.29 0.01
7_L 168_A 0.73 0.29 0.01
181_T 318_G 0.73 0.29 0.01
341_A 579_T 0.73 0.29 0.01
327_L 424_T 0.73 0.29 0.01
391_G 362_L 0.73 0.29 0.01
57_I 544_T 0.73 0.29 0.01
447_Y 360_G 0.73 0.28 0.01
488_P 185_A 0.72 0.28 0.01
314_I 440_L 0.72 0.28 0.01
104_L 123_I 0.72 0.28 0.01
318_V 182_F 0.72 0.28 0.01
119_E 172_I 0.72 0.28 0.01
453_L 191_L 0.72 0.28 0.01
261_Y 103_F 0.72 0.28 0.01
460_I 93_A 0.72 0.28 0.01
83_V 243_V 0.71 0.27 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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