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OPENSEQ.org
cIp_4_4_cytb_4_human
Genes: A B A+B
Length: 463 379 771
Sequences: 3882 4482 729
Seq/Len: 8.38 11.83 0.95
MirrorTree (Pazo et al. 2001) 0.33
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 0.01
2 0.00 0.00 0.02
5 0.00 0.00 0.03
10 0.00 0.00 0.06
20 0.00 0.00 0.09
100 0.01 0.00 0.19
∞ 0.07 0.00 0.87
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
280_A 48_T 1.25 0.55 0.00
127_K 78_W 1.13 0.44 0.00
332_C 239_S 1.12 0.43 0.00
416_S 156_Y 1.05 0.37 0.00
444_L 307_I 1.03 0.35 0.00
167_A 46_I 1.00 0.33 0.00
106_V 365_I 0.97 0.31 0.00
377_S 299_I 0.94 0.28 0.00
155_V 293_L 0.94 0.28 0.00
386_T 6_R 0.92 0.27 0.00
212_E 190_I 0.91 0.26 0.00
264_N 376_K 0.91 0.26 0.00
439_S 93_I 0.91 0.26 0.00
342_R 225_Y 0.90 0.26 0.00
348_L 355_A 0.90 0.26 0.00
227_I 237_I 0.90 0.25 0.00
165_P 334_L 0.90 0.25 0.00
418_R 50_L 0.89 0.25 0.00
82_L 261_N 0.89 0.24 0.00
152_S 347_P 0.89 0.24 0.00
173_L 43_I 0.88 0.24 0.00
412_V 48_T 0.88 0.24 0.00
262_L 181_T 0.87 0.23 0.00
334_V 241_M 0.87 0.23 0.00
230_G 155_P 0.87 0.23 0.00
279_T 48_T 0.86 0.23 0.00
106_V 113_T 0.86 0.23 0.00
338_R 29_S 0.86 0.23 0.00
342_R 361_T 0.85 0.22 0.00
151_Y 37_L 0.85 0.22 0.00
414_D 192_A 0.84 0.21 0.00
341_L 239_S 0.84 0.21 0.00
281_E 290_G 0.84 0.21 0.00
187_V 301_I 0.83 0.21 0.00
142_V 54_M 0.83 0.21 0.00
411_L 164_W 0.83 0.21 0.00
315_E 122_L 0.83 0.21 0.00
170_I 351_I 0.82 0.20 0.00
249_K 361_T 0.82 0.20 0.00
109_C 47_T 0.82 0.20 0.00
338_R 370_I 0.82 0.20 0.00
163_P 165_I 0.81 0.20 0.00
451_I 192_A 0.81 0.20 0.00
274_D 90_M 0.81 0.20 0.00
298_I 11_L 0.81 0.20 0.00
249_K 304_M 0.81 0.20 0.00
220_A 275_F 0.81 0.20 0.00
155_V 339_I 0.81 0.20 0.00
248_S 194_A 0.81 0.19 0.00
217_V 154_I 0.81 0.19 0.00
106_V 94_C 0.80 0.19 0.00
355_E 191_A 0.80 0.19 0.00
298_I 261_N 0.80 0.19 0.00
106_V 60_A 0.80 0.19 0.00
82_L 235_L 0.80 0.19 0.00
289_S 251_L 0.80 0.19 0.00
281_E 239_S 0.79 0.18 0.00
427_P 193_L 0.79 0.18 0.00
422_C 145_T 0.78 0.18 0.00
203_L 120_L 0.78 0.18 0.00
393_P 305_I 0.78 0.18 0.00
396_T 119_I 0.78 0.18 0.00
155_V 295_L 0.78 0.18 0.00
194_L 96_F 0.78 0.18 0.00
317_D 121_L 0.78 0.18 0.00
328_D 330_A 0.78 0.18 0.00
211_F 263_L 0.78 0.18 0.00
81_T 240_L 0.77 0.18 0.00
162_R 83_L 0.77 0.17 0.00
332_C 304_M 0.77 0.17 0.00
102_S 243_L 0.77 0.17 0.00
438_M 121_L 0.77 0.17 0.00
252_S 109_L 0.77 0.17 0.00
448_V 196_L 0.76 0.17 0.00
244_I 348_F 0.76 0.17 0.00
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
5881 0.87 cIp_4_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5879 0.95 cIp_4_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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