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OPENSEQ.org
cIp_9_4_cIV_III_4_human
Genes: A B A+B
Length: 210 261 463
Sequences: 1680 4217 77
Seq/Len: 8 16.16 0.17
MirrorTree (Pazo et al. 2001) 0.19
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 0.00
10 0.00 0.00 0.01
20 0.00 0.00 0.01
100 0.00 0.00 0.02
∞ 0.02 0.01 0.16
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
178_H 225_F 1.16 0.16 0.00
183_Y 255_S 1.15 0.15 0.00
27_L 141_G 1.09 0.14 0.00
66_R 68_Q 1.06 0.13 0.00
24_G 176_L 1.04 0.12 0.00
126_I 225_F 1.03 0.12 0.00
32_V 217_I 1.03 0.12 0.00
94_R 157_N 1.03 0.12 0.00
44_P 142_V 1.00 0.11 0.00
75_L 198_F 1.00 0.11 0.00
77_R 171_L 1.00 0.11 0.00
23_G 51_T 0.96 0.10 0.00
183_Y 81_Y 0.95 0.10 0.00
84_Y 237_A 0.95 0.10 0.00
148_T 213_T 0.94 0.10 0.00
64_L 54_M 0.94 0.10 0.00
52_T 127_L 0.94 0.10 0.00
64_L 168_L 0.94 0.10 0.00
120_I 170_G 0.93 0.10 0.00
72_L 31_L 0.91 0.09 0.00
76_F 193_Y 0.90 0.09 0.00
130_A 151_L 0.89 0.09 0.00
57_R 39_S 0.89 0.09 0.00
40_N 12_K 0.89 0.09 0.00
115_K 150_S 0.88 0.09 0.00
110_R 165_I 0.87 0.09 0.00
48_M 214_F 0.87 0.09 0.00
165_I 165_I 0.86 0.09 0.00
94_R 62_T 0.86 0.08 0.00
179_E 182_F 0.86 0.08 0.00
92_S 214_F 0.86 0.08 0.00
138_R 256_I 0.86 0.08 0.00
200_A 35_F 0.85 0.08 0.00
132_P 183_E 0.85 0.08 0.00
181_L 22_L 0.85 0.08 0.00
105_P 213_T 0.85 0.08 0.00
53_D 237_A 0.83 0.08 0.00
33_A 102_Y 0.83 0.08 0.00
72_L 154_N 0.83 0.08 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
6073 0.6 cIp_9_60_cIV_III_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.13 Done - Shared
6070 0.14 cIp_9_40_cIV_III_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5699 0.58 cIp_9_40_cIV_III_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b) 0.10 Done - Shared
5696 0.62 cIp_9_40_cIV_III_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5693 0.58 cIp_9_20_cIV_III_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.09 Done - Shared
5692 0.6 cIp_9_40_cIV_III_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.14 Done - Shared
5691 0.17 cIp_9_4_cIV_III_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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