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OPENSEQ.org
cIp_6_40_cytb_40_human
Genes: A B A+B
Length: 213 379 545
Sequences: 510 4492 73
Seq/Len: 2.39 11.85 0.13
MirrorTree (Pazo et al. 2001) 0.52
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 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.02
∞ 0.00 0.00 0.12
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
144_P 134_L 1.32 0.18 0.00
171_D 274_Y 1.29 0.17 0.00
201_I 219_I 1.28 0.17 0.00
106_F 236_F 1.20 0.14 0.00
79_L 80_I 1.17 0.13 0.00
199_R 302_L 1.16 0.13 0.00
105_R 134_L 1.16 0.13 0.00
63_V 235_L 1.15 0.13 0.00
176_V 274_Y 1.14 0.13 0.00
106_F 201_L 1.13 0.12 0.00
174_V 161_L 1.13 0.12 0.00
122_V 128_A 1.12 0.12 0.00
148_V 191_A 1.12 0.12 0.00
185_P 132_Y 1.12 0.12 0.00
103_M 36_S 1.11 0.12 0.00
204_E 358_L 1.11 0.12 0.00
105_R 56_Y 1.08 0.11 0.00
180_I 275_F 1.08 0.11 0.00
133_A 186_L 1.07 0.11 0.00
56_P 109_L 1.07 0.11 0.00
148_V 365_I 1.07 0.11 0.00
121_I 292_V 1.06 0.11 0.00
72_N 219_I 1.05 0.11 0.00
75_R 187_P 1.04 0.11 0.00
154_A 308_L 1.03 0.10 0.00
121_I 48_T 1.03 0.10 0.00
144_P 56_Y 1.02 0.10 0.00
201_I 13_K 1.02 0.10 0.00
180_I 365_I 1.01 0.10 0.00
180_I 321_L 1.01 0.10 0.00
119_V 293_L 1.00 0.10 0.00
104_D 38_L 0.99 0.10 0.00
58_S 5_M 0.99 0.10 0.00
176_V 179_F 0.98 0.09 0.00
127_T 251_L 0.97 0.09 0.00
62_Y 361_T 0.97 0.09 0.00
181_P 368_P 0.97 0.09 0.00
184_P 132_Y 0.96 0.09 0.00
120_M 187_P 0.96 0.09 0.00
55_K 357_V 0.96 0.09 0.00
205_R 301_I 0.95 0.09 0.00
121_I 148_T 0.95 0.09 0.00
70_L 93_I 0.95 0.09 0.00
143_E 143_G 0.95 0.09 0.00
115_R 132_Y 0.95 0.09 0.00
136_K 175_T 0.95 0.09 0.00
195_L 48_T 0.95 0.09 0.00
60_G 109_L 0.95 0.09 0.00
201_I 324_S 0.94 0.09 0.00
68_D 319_R 0.94 0.09 0.00
145_R 5_M 0.94 0.09 0.00
145_R 186_L 0.93 0.09 0.00
146_Y 323_Q 0.93 0.09 0.00
122_V 292_V 0.93 0.09 0.00
52_V 154_I 0.93 0.09 0.00
79_L 284_S 0.93 0.09 0.00
79_L 252_G 0.92 0.08 0.00
117_S 81_R 0.92 0.08 0.00
50_R 301_I 0.92 0.08 0.00
193_G 9_N 0.92 0.08 0.00
138_Y 155_P 0.91 0.08 0.00
98_A 317_M 0.91 0.08 0.00
145_R 100_G 0.91 0.08 0.00
72_N 5_M 0.91 0.08 0.00
135_R 302_L 0.91 0.08 0.00
148_V 235_L 0.90 0.08 0.00
119_V 149_N 0.90 0.08 0.00
96_M 116_I 0.90 0.08 0.00
151_G 106_G 0.90 0.08 0.00
65_A 123_A 0.90 0.08 0.00
91_V 225_Y 0.90 0.08 0.00
170_C 360_F 0.90 0.08 0.00
113_S 190_I 0.89 0.08 0.00
75_R 175_T 0.89 0.08 0.00
119_V 76_Y 0.88 0.08 0.00
147_V 52_L 0.88 0.08 0.00
104_D 318_F 0.88 0.08 0.00
99_P 334_L 0.88 0.08 0.00
96_M 186_L 0.88 0.08 0.00
179_Y 146_V 0.88 0.08 0.00
110_F 166_W 0.87 0.08 0.00
65_A 115_N 0.87 0.08 0.00
108_V 322_S 0.87 0.07 0.00
149_S 44_L 0.87 0.07 0.00
99_P 121_L 0.87 0.07 0.00
186_T 39_G 0.87 0.07 0.00
68_D 286_P 0.86 0.07 0.00
55_K 373_I 0.86 0.07 0.00
135_R 308_L 0.86 0.07 0.00
145_R 181_T 0.85 0.07 0.00
80_W 87_G 0.85 0.07 0.00
122_V 188_F 0.85 0.07 0.00
174_V 312_K 0.85 0.07 0.00
80_W 225_Y 0.85 0.07 0.00
180_I 154_I 0.85 0.07 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
5954 0.18 cIp_6_4_cytb_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5951 0.13 cIp_6_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5914 0.18 cIp_6_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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