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OPENSEQ.org
cIm_J_2_cyt1_2_human
Genes: A B A+B
Length: 174 325 425
Sequences: 8320 747 143
Seq/Len: 47.82 2.3 0.34
MirrorTree (Pazo et al. 2001) 0.30
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.00
100 0.00 0.02 0.02
∞ 0.01 0.02 0.29
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
135_I 168_P 1.63 0.54 0.00
57_L 286_K 1.51 0.46 0.00
76_E 138_V 1.40 0.38 0.00
145_L 264_S 1.36 0.36 0.00
102_L 307_K 1.31 0.33 0.00
53_L 105_L 1.27 0.30 0.00
97_A 83_S 1.26 0.30 0.00
14_M 110_I 1.26 0.30 0.00
77_E 132_Y 1.26 0.30 0.00
102_L 144_E 1.25 0.29 0.00
156_T 109_S 1.22 0.28 0.00
31_V 281_E 1.21 0.27 0.00
76_E 139_C 1.20 0.26 0.00
96_L 126_S 1.19 0.26 0.00
94_V 200_I 1.19 0.26 0.00
20_S 93_S 1.17 0.25 0.00
76_E 98_H 1.16 0.24 0.00
92_V 104_S 1.14 0.23 0.00
4_A 266_I 1.13 0.23 0.00
9_S 139_C 1.13 0.23 0.00
35_S 267_A 1.13 0.23 0.00
156_T 126_S 1.11 0.21 0.00
156_T 159_N 1.10 0.21 0.00
79_P 132_Y 1.09 0.21 0.00
4_A 205_H 1.09 0.21 0.00
38_V 307_K 1.09 0.21 0.00
4_A 98_H 1.08 0.20 0.00
16_F 287_R 1.08 0.20 0.00
22_K 104_S 1.07 0.20 0.00
13_V 306_I 1.06 0.20 0.00
148_Y 199_Y 1.06 0.19 0.00
56_F 314_L 1.05 0.19 0.00
90_V 78_L 1.05 0.19 0.00
80_E 290_L 1.04 0.19 0.00
4_A 307_K 1.04 0.18 0.00
90_V 297_A 1.04 0.18 0.00
45_N 299_L 1.02 0.18 0.00
92_V 174_Y 1.02 0.18 0.00
11_G 245_A 1.01 0.17 0.00
28_G 227_L 1.01 0.17 0.00
56_F 303_V 1.01 0.17 0.00
106_V 264_S 1.01 0.17 0.00
30_L 101_L 1.00 0.17 0.00
106_V 163_E 1.00 0.17 0.00
103_V 166_M 0.99 0.17 0.00
104_L 214_L 0.99 0.17 0.00
38_V 190_N 0.99 0.16 0.00
17_V 174_Y 0.98 0.16 0.00
159_T 179_Y 0.98 0.16 0.00
20_S 101_L 0.98 0.16 0.00
13_V 211_V 0.98 0.16 0.00
144_A 180_P 0.98 0.16 0.00
159_T 160_E 0.97 0.16 0.00
77_E 262_T 0.97 0.16 0.00
172_R 98_H 0.96 0.15 0.00
95_G 307_K 0.96 0.15 0.00
159_T 265_Q 0.95 0.15 0.00
95_G 153_E 0.95 0.15 0.00
114_V 115_Q 0.94 0.15 0.00
22_K 89_L 0.94 0.15 0.00
85_G 186_R 0.94 0.15 0.00
53_L 302_L 0.94 0.15 0.00
23_P 131_A 0.94 0.15 0.00
11_G 256_D 0.94 0.15 0.00
46_F 242_I 0.94 0.15 0.00
135_I 126_S 0.94 0.14 0.00
57_L 129_F 0.93 0.14 0.00
144_A 284_H 0.93 0.14 0.00
41_V 143_D 0.93 0.14 0.00
17_V 177_K 0.93 0.14 0.00
51_M 286_K 0.92 0.14 0.00
38_V 240_Q 0.92 0.14 0.00
133_G 73_G 0.92 0.14 0.00
165_Y 286_K 0.92 0.14 0.00
143_G 303_V 0.92 0.14 0.00
40_C 199_Y 0.92 0.14 0.00
10_V 174_Y 0.91 0.14 0.00
150_R 75_A 0.91 0.14 0.00
94_V 75_A 0.91 0.14 0.00
100_V 310_K 0.91 0.14 0.00
135_I 153_E 0.91 0.14 0.00
144_A 260_P 0.91 0.14 0.00
98_M 116_V 0.90 0.14 0.00
28_G 176_P 0.90 0.14 0.00
15_G 247_P 0.90 0.14 0.00
97_A 271_C 0.90 0.14 0.00
79_P 109_S 0.90 0.13 0.00
159_T 190_N 0.89 0.13 0.00
124_W 251_D 0.89 0.13 0.00
87_E 290_L 0.89 0.13 0.00
135_I 94_Y 0.89 0.13 0.00
156_T 71_G 0.89 0.13 0.00
97_A 102_L 0.89 0.13 0.00
46_F 86_D 0.89 0.13 0.00
46_F 108_T 0.89 0.13 0.00
148_Y 127_M 0.88 0.13 0.00
9_S 130_V 0.88 0.13 0.00
173_G 190_N 0.88 0.13 0.00
21_S 314_L 0.88 0.13 0.00
102_L 180_P 0.87 0.12 0.00
145_L 140_Y 0.86 0.12 0.00
156_T 263_M 0.86 0.12 0.00
100_V 261_A 0.86 0.12 0.00
103_V 142_E 0.86 0.12 0.00
126_I 174_Y 0.85 0.12 0.00
56_F 245_A 0.85 0.12 0.00
40_C 294_M 0.85 0.12 0.00
134_L 115_Q 0.85 0.12 0.00
107_K 171_L 0.85 0.12 0.00
90_V 72_A 0.85 0.12 0.00
82_W 172_F 0.84 0.12 0.00
83_G 168_P 0.84 0.12 0.00
7_L 271_C 0.84 0.12 0.00
165_Y 305_T 0.84 0.12 0.00
82_W 188_A 0.84 0.12 0.00
92_V 260_P 0.84 0.12 0.00
22_K 233_F 0.84 0.11 0.00
128_E 252_V 0.84 0.11 0.00
95_G 201_V 0.84 0.11 0.00
79_P 302_L 0.83 0.11 0.00
98_M 235_P 0.83 0.11 0.00
172_R 137_G 0.83 0.11 0.00
83_G 186_R 0.83 0.11 0.00
150_R 127_M 0.83 0.11 0.00
76_E 199_Y 0.83 0.11 0.00
3_Y 145_A 0.83 0.11 0.00
44_L 298_L 0.83 0.11 0.00
100_V 248_I 0.83 0.11 0.00
4_A 99_R 0.83 0.11 0.00
20_S 242_I 0.83 0.11 0.00
95_G 157_G 0.82 0.11 0.00
38_V 139_C 0.82 0.11 0.00
54_M 111_R 0.82 0.11 0.00
22_K 151_E 0.82 0.11 0.00
23_P 268_K 0.81 0.11 0.00
150_R 168_P 0.81 0.11 0.00
27_Y 200_I 0.81 0.11 0.00
18_G 158_P 0.81 0.11 0.00
11_G 140_Y 0.81 0.11 0.00
127_Y 175_F 0.81 0.11 0.00
161_F 147_E 0.81 0.11 0.00
10_V 228_R 0.81 0.11 0.00
104_L 267_A 0.81 0.11 0.00
83_G 308_R 0.81 0.11 0.00
40_C 150_A 0.80 0.10 0.00
145_L 297_A 0.80 0.10 0.00
144_A 172_F 0.80 0.10 0.00
79_P 312_S 0.80 0.10 0.00
95_G 158_P 0.80 0.10 0.00
134_L 242_I 0.80 0.10 0.00
132_S 316_S 0.80 0.10 0.00
90_V 197_L 0.79 0.10 0.00
65_V 302_L 0.79 0.10 0.00
28_G 267_A 0.79 0.10 0.00
10_V 136_V 0.79 0.10 0.00
71_T 145_A 0.79 0.10 0.00
9_S 169_G 0.79 0.10 0.00
79_P 176_P 0.79 0.10 0.00
96_L 248_I 0.78 0.10 0.00
131_G 114_F 0.78 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
5767 0.36 cIm_J_4_cyt1_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5766 0.34 cIm_J_2_cyt1_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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