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OPENSEQ.org
cIp_9_40_cIV_II_40_human
Genes: A B A+B
Length: 210 227 384
Sequences: 638 5832 307
Seq/Len: 3.04 25.69 0.8
MirrorTree (Pazo et al. 2001) 0.40
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 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.02
100 0.00 0.00 0.06
∞ 0.00 0.01 0.70
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
120_I 211_L 1.41 0.63 0.00
63_E 79_P 1.31 0.56 0.00
194_K 205_S 1.31 0.55 0.00
186_E 99_S 1.16 0.42 0.00
52_T 47_T 1.15 0.41 0.00
208_L 181_Q 1.12 0.39 0.00
83_N 57_D 1.12 0.38 0.00
80_A 148_A 1.08 0.36 0.00
91_L 87_T 1.01 0.30 0.00
56_A 225_F 0.99 0.29 0.00
171_F 92_D 0.98 0.28 0.00
203_I 182_T 0.97 0.28 0.00
77_R 153_M 0.97 0.27 0.00
82_I 61_M 0.97 0.27 0.00
173_F 223_P 0.95 0.26 0.00
59_L 23_F 0.94 0.25 0.00
54_R 99_S 0.91 0.23 0.00
152_Y 52_N 0.91 0.23 0.00
137_S 212_E 0.91 0.23 0.00
84_Y 217_K 0.90 0.23 0.00
73_S 219_F 0.90 0.23 0.00
59_L 78_L 0.89 0.22 0.00
129_E 172_T 0.89 0.22 0.00
75_L 13_T 0.89 0.22 0.00
181_L 152_M 0.89 0.22 0.00
198_E 20_L 0.84 0.19 0.00
68_L 218_I 0.84 0.19 0.00
64_L 99_S 0.84 0.19 0.00
105_P 39_L 0.84 0.19 0.00
120_I 44_L 0.84 0.19 0.00
186_E 185_T 0.83 0.19 0.00
65_F 144_L 0.83 0.19 0.00
183_Y 142_V 0.83 0.18 0.00
89_G 109_E 0.83 0.18 0.00
204_Q 147_E 0.82 0.18 0.00
84_Y 28_L 0.82 0.18 0.00
164_A 20_L 0.81 0.18 0.00
80_A 92_D 0.81 0.17 0.00
124_Q 9_L 0.80 0.17 0.00
204_Q 82_R 0.80 0.17 0.00
64_L 22_T 0.80 0.17 0.00
91_L 215_P 0.80 0.17 0.00
59_L 11_D 0.79 0.17 0.00
74_Y 29_M 0.79 0.17 0.00
74_Y 33_L 0.79 0.16 0.00
155_F 61_M 0.78 0.16 0.00
174_S 218_I 0.78 0.16 0.00
137_S 202_A 0.78 0.16 0.00
137_S 88_D 0.78 0.16 0.00
129_E 167_T 0.78 0.16 0.00
59_L 16_I 0.77 0.16 0.00
187_K 15_P 0.77 0.16 0.00
207_Y 68_L 0.77 0.16 0.00
204_Q 188_R 0.76 0.15 0.00
51_V 216_L 0.76 0.15 0.00
134_T 182_T 0.76 0.15 0.00
141_T 74_V 0.76 0.15 0.00
173_F 12_A 0.76 0.15 0.00
193_D 219_F 0.76 0.15 0.00
169_P 68_L 0.75 0.15 0.00
208_L 147_E 0.75 0.15 0.00
124_Q 215_P 0.75 0.15 0.00
152_Y 109_E 0.75 0.15 0.00
71_T 68_L 0.75 0.15 0.00
180_E 180_N 0.74 0.15 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
5690 0.6 cIp_9_4_cIV_II_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5689 0.8 cIp_9_40_cIV_II_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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