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OPENSEQ.org
cIp_3_40_cIV_2_40
Genes: A B A+B
Length: 727 227 907
Sequences: 1907 4148 603
Seq/Len: 2.62 18.27 0.66
MirrorTree (Pazo et al. 2001) 0.26
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 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.01
10 0.01 0.00 0.01
20 0.01 0.00 0.02
100 0.03 0.01 0.08
∞ 0.09 0.02 0.63
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
60_I 92_D 1.23 0.43 0.00
474_V 47_T 1.22 0.42 0.00
403_V 192_Y 1.13 0.35 0.00
316_Y 94_S 1.13 0.35 0.00
609_A 14_S 1.06 0.30 0.00
405_T 148_A 1.04 0.29 0.00
390_T 97_I 1.03 0.28 0.00
539_K 215_P 1.01 0.27 0.00
336_K 219_F 1.01 0.27 0.00
361_V 97_I 1.01 0.26 0.00
98_K 36_F 1.00 0.26 0.00
153_F 213_L 0.99 0.25 0.00
49_V 203_N 0.96 0.23 0.00
420_K 68_L 0.94 0.22 0.00
394_V 61_M 0.93 0.21 0.00
434_S 97_I 0.92 0.21 0.00
400_V 101_G 0.91 0.20 0.00
206_V 38_V 0.91 0.20 0.00
428_K 36_F 0.90 0.20 0.00
161_E 219_F 0.89 0.20 0.00
552_G 71_I 0.88 0.19 0.00
315_T 219_F 0.88 0.19 0.00
560_L 14_S 0.86 0.18 0.00
292_F 144_L 0.85 0.18 0.00
543_K 131_G 0.85 0.17 0.00
547_L 72_I 0.84 0.17 0.00
45_P 16_I 0.84 0.17 0.00
36_V 95_L 0.83 0.17 0.00
31_L 71_I 0.83 0.16 0.00
357_L 224_V 0.82 0.16 0.00
366_L 191_V 0.82 0.16 0.00
41_V 36_F 0.82 0.16 0.00
593_S 70_A 0.82 0.16 0.00
251_I 226_T 0.82 0.16 0.00
544_V 127_F 0.82 0.16 0.00
333_F 189_P 0.82 0.16 0.00
169_V 33_L 0.81 0.16 0.00
366_L 46_L 0.81 0.16 0.00
470_K 63_T 0.81 0.15 0.00
428_K 72_I 0.81 0.15 0.00
521_S 152_M 0.81 0.15 0.00
612_P 223_P 0.80 0.15 0.00
432_I 63_T 0.80 0.15 0.00
49_V 73_L 0.80 0.15 0.00
633_T 67_I 0.80 0.15 0.00
640_D 192_Y 0.80 0.15 0.00
259_S 168_L 0.80 0.15 0.00
98_K 43_F 0.79 0.15 0.00
474_V 64_V 0.79 0.15 0.00
114_E 37_L 0.79 0.15 0.00
509_D 219_F 0.79 0.15 0.00
596_Y 211_L 0.79 0.15 0.00
404_G 103_Q 0.78 0.14 0.00
551_D 71_I 0.78 0.14 0.00
644_N 36_F 0.78 0.14 0.00
110_K 224_V 0.78 0.14 0.00
366_L 13_T 0.78 0.14 0.00
40_S 192_Y 0.77 0.14 0.00
317_T 205_S 0.77 0.14 0.00
50_L 152_M 0.77 0.14 0.00
69_L 101_G 0.77 0.14 0.00
525_A 202_A 0.77 0.14 0.00
102_I 72_I 0.76 0.14 0.00
153_F 156_S 0.76 0.14 0.00
341_I 34_I 0.76 0.14 0.00
566_I 211_L 0.76 0.14 0.00
544_V 94_S 0.75 0.13 0.00
96_V 183_T 0.75 0.13 0.00
341_I 165_V 0.75 0.13 0.00
41_V 76_I 0.75 0.13 0.00
96_V 144_L 0.75 0.13 0.00
567_I 146_I 0.74 0.13 0.00
432_I 67_I 0.74 0.13 0.00
47_T 217_K 0.74 0.13 0.00
382_R 217_K 0.74 0.13 0.00
314_L 168_L 0.74 0.13 0.00
475_V 147_E 0.74 0.13 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
4191 0.87 cIp_3_4_cIV_2_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4190 0.66 cIp_3_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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