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OPENSEQ.org
cIV_B_40_cI_M_40_1_human
Genes: A B A+B
Length: 227 459 681
Sequences: 4037 3931 2910
Seq/Len: 17.78 8.56 4.27
MirrorTree (Pazo et al. 2001) 0.77
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 0.10
5 0.00 0.00 0.51
10 0.00 0.00 3.50
20 0.00 0.00 3.54
100 0.01 0.00 3.63
∞ 0.01 0.01 4.24
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
76_I 336_R 1.17 0.89 0.16
160_L 282_L 1.17 0.88 0.16
38_V 140_P 1.16 0.88 0.16
83_I 377_G 1.12 0.85 0.14
12_A 72_L 1.06 0.80 0.12
95_L 164_L 1.03 0.78 0.11
192_Y 233_A 0.99 0.74 0.09
82_R 368_A 0.98 0.73 0.09
67_I 158_L 0.95 0.70 0.08
52_N 388_W 0.91 0.64 0.07
46_L 121_F 0.87 0.59 0.06
68_L 116_I 0.87 0.59 0.06
28_L 313_V 0.87 0.59 0.06
49_K 56_F 0.86 0.58 0.06
110_Y 59_D 0.85 0.57 0.06
6_Q 318_A 0.85 0.57 0.06
205_S 148_Y 0.84 0.56 0.06
214_I 402_V 0.83 0.54 0.05
96_T 380_S 0.83 0.54 0.05
127_F 65_L 0.82 0.53 0.05
192_Y 173_S 0.82 0.53 0.05
53_T 411_F 0.81 0.51 0.05
146_I 114_E 0.81 0.51 0.05
97_I 2_L 0.81 0.51 0.05
53_T 403_T 0.80 0.50 0.05
146_I 161_L 0.80 0.50 0.05
13_T 199_Y 0.80 0.50 0.05
43_F 44_Q 0.80 0.50 0.05
143_V 56_F 0.80 0.49 0.05
154_I 61_L 0.80 0.49 0.05
156_S 352_L 0.80 0.49 0.05
160_L 298_V 0.79 0.48 0.04
128_L 243_M 0.79 0.48 0.04
102_H 242_G 0.78 0.47 0.04
75_L 95_Y 0.78 0.47 0.04
210_V 132_I 0.78 0.47 0.04
63_T 406_Y 0.78 0.47 0.04
144_L 388_W 0.77 0.46 0.04
156_S 405_L 0.77 0.46 0.04
121_Y 138_S 0.77 0.45 0.04
144_L 286_I 0.77 0.45 0.04
124_P 330_A 0.77 0.45 0.04
38_V 297_V 0.76 0.45 0.04
157_Q 95_Y 0.76 0.44 0.04
154_I 410_M 0.76 0.44 0.04
28_L 259_Y 0.75 0.44 0.04
162_S 318_A 0.75 0.44 0.04
174_A 398_L 0.75 0.43 0.04
96_T 408_L 0.74 0.42 0.04
32_F 451_P 0.74 0.41 0.04
90_V 78_M 0.73 0.41 0.04
179_L 377_G 0.73 0.41 0.04
184_F 337_T 0.73 0.41 0.04
96_T 197_L 0.73 0.40 0.04
211_L 45_I 0.72 0.40 0.04
132_D 147_T 0.72 0.40 0.04
46_L 109_T 0.72 0.39 0.03
2_A 113_T 0.72 0.39 0.03
19_E 377_G 0.72 0.39 0.03
76_I 326_L 0.72 0.39 0.03
20_L 147_T 0.71 0.39 0.03
175_I 298_V 0.71 0.38 0.03
112_D 59_D 0.71 0.38 0.03
8_G 64_P 0.71 0.38 0.03
31_I 312_A 0.71 0.38 0.03
64_V 444_I 0.71 0.38 0.03
192_Y 95_Y 0.71 0.38 0.03
199_I 66_L 0.71 0.38 0.03
160_L 263_V 0.70 0.37 0.03
153_M 270_I 0.70 0.37 0.03
144_L 181_L 0.70 0.37 0.03
68_L 301_I 0.70 0.36 0.03
67_I 285_L 0.70 0.36 0.03
174_A 65_L 0.69 0.36 0.03
217_K 270_I 0.69 0.36 0.03
121_Y 95_Y 0.69 0.36 0.03
144_L 105_S 0.69 0.36 0.03
217_K 42_F 0.69 0.36 0.03
71_I 39_L 0.69 0.35 0.03
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
4434 3.17 cIV_B_80_cI_M_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.94 Done - Shared
4433 2.51 cIV_B_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.68 Done - Shared
4427 4.27 cIV_B_40_cI_M_40_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.16 Done - Shared
4426 3.25 cIV_B_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4425 2.51 cIV_B_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.72 Done - Shared
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