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OPENSEQ.org
cIp_9_4_cIV_II_4_human
Genes: A B A+B
Length: 210 227 425
Sequences: 1680 7221 257
Seq/Len: 8 31.81 0.6
MirrorTree (Pazo et al. 2001) 0.21
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 0.03
100 0.00 0.01 0.06
∞ 0.02 0.02 0.59
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
92_S 211_L 1.08 0.29 0.00
124_Q 218_I 0.95 0.21 0.00
42_Q 40_Y 0.94 0.21 0.00
19_A 63_T 0.91 0.19 0.00
135_D 215_P 0.87 0.17 0.00
35_T 101_G 0.87 0.17 0.00
37_K 112_D 0.86 0.17 0.00
35_T 192_Y 0.85 0.17 0.00
85_P 167_T 0.83 0.15 0.00
7_P 197_S 0.82 0.15 0.00
7_P 215_P 0.82 0.15 0.00
164_A 156_S 0.80 0.14 0.00
24_G 30_I 0.79 0.14 0.00
120_I 67_I 0.79 0.14 0.00
124_Q 43_F 0.78 0.14 0.00
92_S 72_I 0.77 0.13 0.00
7_P 165_V 0.76 0.13 0.00
108_E 153_M 0.76 0.13 0.00
109_E 39_L 0.76 0.13 0.00
92_S 20_L 0.76 0.13 0.00
159_A 170_L 0.74 0.12 0.00
133_R 146_I 0.74 0.12 0.00
183_Y 174_A 0.74 0.12 0.00
46_M 23_F 0.73 0.12 0.00
120_I 65_W 0.73 0.12 0.00
11_R 77_A 0.72 0.12 0.00
68_L 170_L 0.72 0.11 0.00
59_L 71_I 0.72 0.11 0.00
35_T 9_L 0.71 0.11 0.00
30_S 74_V 0.71 0.11 0.00
183_Y 99_S 0.71 0.11 0.00
159_A 156_S 0.70 0.11 0.00
58_T 165_V 0.70 0.11 0.00
108_E 225_F 0.70 0.11 0.00
92_S 106_W 0.70 0.11 0.00
68_L 97_I 0.69 0.10 0.00
172_E 58_A 0.69 0.10 0.00
178_H 99_S 0.68 0.10 0.00
90_P 214_I 0.68 0.10 0.00
20_G 226_T 0.67 0.10 0.00
108_E 155_T 0.67 0.10 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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