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OPENSEQ.org
cIV_C_80_cI_H_80_human
Genes: A B A+B
Length: 261 318 576
Sequences: 2234 3641 2113
Seq/Len: 8.56 11.45 3.67
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 0.07
2 0.00 0.00 0.21
5 0.00 0.00 0.44
10 0.00 0.00 3.16
20 0.00 0.00 3.25
100 0.00 0.01 3.32
∞ 0.00 0.02 3.65
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
142_V 270_F 1.13 0.83 0.08
12_K 52_A 1.11 0.81 0.07
135_S 187_I 1.10 0.80 0.07
127_L 126_N 1.08 0.79 0.07
129_V 277_Y 1.08 0.79 0.07
172_Y 200_L 1.02 0.73 0.06
96_G 196_T 0.96 0.67 0.05
78_G 151_L 0.96 0.67 0.05
217_I 177_P 0.96 0.66 0.05
54_M 304_H 0.96 0.66 0.05
135_S 154_L 0.95 0.65 0.04
33_M 232_I 0.94 0.63 0.04
50_N 190_L 0.92 0.61 0.04
92_L 146_L 0.92 0.61 0.04
255_S 280_F 0.91 0.60 0.04
8_Y 184_M 0.91 0.60 0.04
21_A 132_A 0.91 0.59 0.04
199_V 33_L 0.90 0.59 0.04
25_L 132_A 0.90 0.58 0.04
35_F 29_G 0.88 0.56 0.04
25_L 77_L 0.88 0.56 0.04
107_A 217_A 0.87 0.55 0.03
164_L 154_L 0.87 0.54 0.03
198_F 276_A 0.85 0.53 0.03
175_L 162_L 0.85 0.53 0.03
165_I 265_L 0.85 0.52 0.03
5_S 126_N 0.84 0.52 0.03
128_E 33_L 0.84 0.51 0.03
21_A 229_T 0.84 0.51 0.03
172_Y 139_T 0.84 0.51 0.03
212_S 9_L 0.84 0.51 0.03
6_H 46_L 0.83 0.50 0.03
13_P 109_S 0.83 0.49 0.03
178_A 296_L 0.83 0.49 0.03
124_L 196_T 0.82 0.49 0.03
22_L 115_S 0.82 0.49 0.03
101_F 100_L 0.82 0.48 0.03
250_L 17_M 0.81 0.47 0.03
34_W 42_P 0.81 0.47 0.03
23_S 63_P 0.81 0.47 0.03
22_L 52_A 0.81 0.47 0.03
253_Y 79_L 0.80 0.46 0.03
48_L 83_L 0.80 0.46 0.03
170_G 203_G 0.80 0.46 0.03
187_T 150_L 0.79 0.45 0.03
213_T 89_L 0.79 0.45 0.03
6_H 49_F 0.79 0.45 0.03
165_I 6_L 0.79 0.44 0.03
238_A 263_T 0.79 0.44 0.03
38_H 230_N 0.79 0.44 0.03
38_H 213_I 0.79 0.44 0.03
193_Y 302_M 0.78 0.44 0.03
68_Q 22_L 0.78 0.44 0.03
104_S 238_T 0.78 0.43 0.03
80_R 232_I 0.78 0.43 0.02
23_S 61_L 0.78 0.43 0.02
20_G 50_A 0.78 0.43 0.02
27_M 107_A 0.78 0.43 0.02
109_T 280_F 0.78 0.42 0.02
200_A 145_T 0.77 0.42 0.02
31_L 257_T 0.77 0.42 0.02
122_T 140_I 0.77 0.42 0.02
52_L 106_L 0.77 0.42 0.02
31_L 119_S 0.77 0.41 0.02
70_H 184_M 0.77 0.41 0.02
253_Y 126_N 0.77 0.41 0.02
3_H 15_I 0.77 0.41 0.02
154_N 263_T 0.76 0.41 0.02
203_F 286_M 0.76 0.40 0.02
143_S 301_L 0.76 0.40 0.02
95_A 64_A 0.76 0.40 0.02
76_Q 236_T 0.76 0.40 0.02
44_M 183_M 0.75 0.39 0.02
107_A 149_I 0.75 0.39 0.02
210_I 304_H 0.75 0.39 0.02
92_L 89_L 0.75 0.39 0.02
77_K 89_L 0.75 0.39 0.02
179_S 91_M 0.75 0.39 0.02
254_V 176_L 0.75 0.39 0.02
48_L 8_L 0.74 0.39 0.02
83_M 45_L 0.74 0.38 0.02
40_M 305_V 0.74 0.38 0.02
112_L 60_P 0.74 0.38 0.02
80_R 136_V 0.74 0.38 0.02
214_F 294_L 0.74 0.38 0.02
31_L 309_I 0.74 0.38 0.02
70_H 146_L 0.74 0.38 0.02
25_L 168_T 0.74 0.38 0.02
80_R 298_L 0.73 0.37 0.02
256_I 22_L 0.73 0.37 0.02
8_Y 147_A 0.73 0.37 0.02
182_F 111_L 0.73 0.37 0.02
54_M 21_M 0.73 0.37 0.02
73_P 45_L 0.73 0.37 0.02
147_A 32_Q 0.73 0.37 0.02
93_F 286_M 0.73 0.36 0.02
37_F 115_S 0.73 0.36 0.02
104_S 107_A 0.73 0.36 0.02
88_T 96_V 0.73 0.36 0.02
226_H 43_Y 0.72 0.36 0.02
135_S 150_L 0.72 0.35 0.02
138_L 158_G 0.72 0.35 0.02
97_F 274_R 0.72 0.35 0.02
115_H 76_T 0.72 0.35 0.02
189_S 169_Q 0.72 0.35 0.02
120_G 280_F 0.72 0.35 0.02
240_W 144_V 0.72 0.35 0.02
18_L 10_I 0.72 0.35 0.02
79_L 126_N 0.72 0.35 0.02
6_H 213_I 0.72 0.35 0.02
128_E 238_T 0.72 0.35 0.02
168_L 4_A 0.71 0.35 0.02
195_S 93_N 0.71 0.35 0.02
77_K 144_V 0.71 0.35 0.02
45_L 179_W 0.71 0.35 0.02
28_T 238_T 0.71 0.35 0.02
72_T 233_M 0.71 0.34 0.02
131_L 28_L 0.71 0.34 0.02
239_A 139_T 0.71 0.34 0.02
157_N 11_V 0.71 0.34 0.02
33_M 150_L 0.71 0.34 0.02
91_V 10_I 0.71 0.34 0.02
27_M 15_I 0.71 0.34 0.02
24_A 157_S 0.71 0.34 0.02
125_N 315_P 0.70 0.34 0.02
100_A 12_P 0.70 0.34 0.02
199_V 280_F 0.70 0.34 0.02
27_M 63_P 0.70 0.34 0.02
159_M 29_G 0.70 0.34 0.02
171_L 108_T 0.70 0.33 0.02
138_L 230_N 0.70 0.33 0.02
216_T 87_T 0.70 0.33 0.02
122_T 237_L 0.70 0.33 0.02
27_M 70_L 0.70 0.33 0.02
134_T 245_T 0.70 0.33 0.02
7_A 132_A 0.70 0.33 0.02
212_S 82_A 0.70 0.33 0.02
101_F 213_I 0.69 0.33 0.02
127_L 164_T 0.69 0.33 0.02
73_P 15_I 0.69 0.32 0.02
44_M 4_A 0.69 0.32 0.02
138_L 128_A 0.69 0.32 0.02
189_S 292_N 0.69 0.32 0.02
193_Y 155_L 0.69 0.32 0.02
25_L 246_T 0.69 0.32 0.02
215_L 94_P 0.69 0.32 0.02
144_I 32_Q 0.69 0.32 0.02
72_T 162_L 0.69 0.32 0.02
77_K 84_L 0.69 0.32 0.02
95_A 246_T 0.69 0.32 0.02
255_S 16_A 0.69 0.32 0.02
156_R 223_F 0.69 0.32 0.02
150_S 148_I 0.69 0.32 0.02
32_A 27_I 0.69 0.32 0.02
213_T 4_A 0.69 0.32 0.02
152_M 307_M 0.69 0.32 0.02
217_I 101_G 0.69 0.32 0.02
70_H 243_L 0.69 0.32 0.02
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
4586 3.98 cIV_C_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
4584 3.93 cIV_C_60_cI_H_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
4582 3.67 cIV_C_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
4581 3.95 cIV_C_60_cI_H_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
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