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OPENSEQ.org
cIm_J_4_cyt1_4_human
Genes: A B A+B
Length: 174 325 423
Sequences: 7718 829 154
Seq/Len: 44.36 2.55 0.36
MirrorTree (Pazo et al. 2001) 0.43
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 0.03
∞ 0.01 0.02 0.31
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
76_E 138_V 1.63 0.56 0.00
57_L 286_K 1.51 0.47 0.00
53_L 105_L 1.44 0.43 0.00
76_E 139_C 1.36 0.37 0.00
136_R 168_P 1.35 0.36 0.00
77_E 132_Y 1.34 0.35 0.00
156_T 159_N 1.32 0.35 0.00
28_G 176_P 1.26 0.31 0.00
9_S 139_C 1.26 0.31 0.00
161_F 147_E 1.24 0.29 0.00
92_V 104_S 1.24 0.29 0.00
148_Y 199_Y 1.21 0.28 0.00
38_V 190_N 1.21 0.28 0.00
38_V 307_K 1.21 0.28 0.00
94_V 200_I 1.21 0.28 0.00
20_S 93_S 1.20 0.27 0.00
99_E 148_L 1.18 0.26 0.00
22_K 104_S 1.14 0.24 0.00
9_S 131_A 1.13 0.24 0.00
20_S 101_L 1.13 0.23 0.00
136_R 126_S 1.13 0.23 0.00
172_R 98_H 1.11 0.23 0.00
13_V 306_I 1.11 0.23 0.00
57_L 129_F 1.10 0.22 0.00
145_L 264_S 1.09 0.22 0.00
154_V 239_G 1.09 0.21 0.00
56_F 314_L 1.09 0.21 0.00
156_T 263_M 1.08 0.21 0.00
104_L 267_A 1.08 0.21 0.00
31_V 281_E 1.08 0.21 0.00
51_M 286_K 1.08 0.21 0.00
40_C 199_Y 1.08 0.21 0.00
76_E 98_H 1.08 0.21 0.00
18_G 205_H 1.06 0.20 0.00
78_Y 272_T 1.06 0.20 0.00
104_L 214_L 1.05 0.20 0.00
4_A 266_I 1.05 0.20 0.00
20_S 70_G 1.05 0.20 0.00
141_G 174_Y 1.04 0.19 0.00
56_F 303_V 1.03 0.19 0.00
145_L 75_A 1.02 0.18 0.00
99_E 300_V 1.01 0.18 0.00
3_Y 89_L 1.01 0.18 0.00
4_A 205_H 1.01 0.18 0.00
156_T 126_S 1.00 0.18 0.00
156_T 109_S 1.00 0.18 0.00
13_V 211_V 1.00 0.18 0.00
17_V 72_A 0.99 0.17 0.00
159_T 118_K 0.99 0.17 0.00
46_F 242_I 0.97 0.16 0.00
90_V 197_L 0.97 0.16 0.00
43_I 191_G 0.96 0.16 0.00
4_A 98_H 0.96 0.16 0.00
128_E 299_L 0.96 0.16 0.00
41_V 143_D 0.96 0.16 0.00
12_L 146_K 0.96 0.16 0.00
10_V 136_V 0.96 0.16 0.00
119_N 105_L 0.95 0.16 0.00
97_A 107_H 0.95 0.16 0.00
46_F 134_H 0.95 0.15 0.00
40_C 150_A 0.95 0.15 0.00
57_L 105_L 0.94 0.15 0.00
136_R 94_Y 0.94 0.15 0.00
144_A 172_F 0.94 0.15 0.00
57_L 293_L 0.94 0.15 0.00
99_E 136_V 0.93 0.15 0.00
165_Y 67_L 0.93 0.15 0.00
79_P 109_S 0.93 0.15 0.00
98_M 235_P 0.93 0.15 0.00
22_K 102_L 0.92 0.15 0.00
16_F 215_L 0.92 0.14 0.00
13_V 145_A 0.92 0.14 0.00
138_D 130_V 0.91 0.14 0.00
95_G 158_P 0.91 0.14 0.00
56_F 245_A 0.91 0.14 0.00
102_L 307_K 0.91 0.14 0.00
165_Y 286_K 0.90 0.14 0.00
144_A 180_P 0.90 0.14 0.00
14_M 110_I 0.90 0.14 0.00
79_P 259_T 0.90 0.14 0.00
126_I 180_P 0.90 0.14 0.00
113_V 69_A 0.90 0.14 0.00
156_T 212_F 0.90 0.14 0.00
81_A 250_T 0.90 0.14 0.00
16_F 201_V 0.90 0.14 0.00
141_G 206_G 0.90 0.14 0.00
172_R 309_H 0.89 0.14 0.00
76_E 290_L 0.89 0.14 0.00
9_S 169_G 0.89 0.14 0.00
21_S 197_L 0.89 0.14 0.00
53_L 254_E 0.89 0.14 0.00
11_G 75_A 0.89 0.13 0.00
76_E 199_Y 0.89 0.13 0.00
96_L 279_E 0.88 0.13 0.00
92_V 159_N 0.88 0.13 0.00
94_V 316_S 0.88 0.13 0.00
128_E 227_L 0.88 0.13 0.00
83_G 186_R 0.88 0.13 0.00
85_G 186_R 0.87 0.13 0.00
22_K 308_R 0.87 0.13 0.00
11_G 245_A 0.87 0.13 0.00
100_V 193_L 0.87 0.13 0.00
133_G 76_M 0.87 0.13 0.00
102_L 180_P 0.87 0.13 0.00
97_A 86_D 0.86 0.13 0.00
4_A 99_R 0.86 0.12 0.00
20_S 242_I 0.86 0.12 0.00
90_V 94_Y 0.86 0.12 0.00
44_L 137_G 0.86 0.12 0.00
38_V 139_C 0.86 0.12 0.00
136_R 284_H 0.85 0.12 0.00
150_R 117_Y 0.85 0.12 0.00
21_S 274_L 0.85 0.12 0.00
103_V 108_T 0.85 0.12 0.00
80_E 245_A 0.85 0.12 0.00
53_L 302_L 0.85 0.12 0.00
143_G 288_M 0.84 0.12 0.00
4_A 307_K 0.84 0.12 0.00
28_G 227_L 0.84 0.12 0.00
95_G 307_K 0.84 0.12 0.00
97_A 70_G 0.84 0.12 0.00
99_E 235_P 0.84 0.12 0.00
94_V 90_H 0.83 0.12 0.00
85_G 140_Y 0.83 0.12 0.00
96_L 188_A 0.83 0.12 0.00
108_E 282_H 0.83 0.12 0.00
109_Y 256_D 0.83 0.12 0.00
38_V 240_Q 0.83 0.12 0.00
109_Y 115_Q 0.83 0.12 0.00
45_N 203_A 0.82 0.12 0.00
108_E 186_R 0.82 0.11 0.00
141_G 156_D 0.82 0.11 0.00
156_T 71_G 0.82 0.11 0.00
159_T 265_Q 0.82 0.11 0.00
20_S 313_V 0.82 0.11 0.00
39_G 277_A 0.82 0.11 0.00
96_L 126_S 0.82 0.11 0.00
95_G 153_E 0.82 0.11 0.00
19_F 191_G 0.81 0.11 0.00
21_S 314_L 0.81 0.11 0.00
45_N 214_L 0.81 0.11 0.00
155_V 117_Y 0.81 0.11 0.00
100_V 254_E 0.81 0.11 0.00
44_L 298_L 0.81 0.11 0.00
22_K 89_L 0.81 0.11 0.00
144_A 298_L 0.81 0.11 0.00
13_V 71_G 0.81 0.11 0.00
100_V 248_I 0.81 0.11 0.00
102_L 144_E 0.81 0.11 0.00
135_I 242_I 0.81 0.11 0.00
144_A 127_M 0.81 0.11 0.00
45_N 199_Y 0.80 0.11 0.00
83_G 190_N 0.80 0.11 0.00
11_G 70_G 0.80 0.11 0.00
105_W 240_Q 0.80 0.11 0.00
11_G 197_L 0.80 0.11 0.00
3_Y 293_L 0.80 0.11 0.00
103_V 142_E 0.80 0.11 0.00
135_I 115_Q 0.80 0.11 0.00
106_V 300_V 0.80 0.11 0.00
154_V 97_S 0.79 0.11 0.00
99_E 73_G 0.79 0.11 0.00
76_E 145_A 0.79 0.11 0.00
104_L 137_G 0.79 0.11 0.00
17_V 177_K 0.79 0.10 0.00
23_P 277_A 0.79 0.10 0.00
44_L 81_A 0.79 0.10 0.00
3_Y 208_E 0.79 0.10 0.00
79_P 288_M 0.79 0.10 0.00
110_D 298_L 0.79 0.10 0.00
7_L 81_A 0.79 0.10 0.00
123_S 150_A 0.79 0.10 0.00
159_T 313_V 0.79 0.10 0.00
159_T 305_T 0.78 0.10 0.00
30_L 101_L 0.78 0.10 0.00
7_L 271_C 0.78 0.10 0.00
105_W 256_D 0.78 0.10 0.00
35_S 267_A 0.78 0.10 0.00
4_A 275_R 0.78 0.10 0.00
135_I 78_L 0.78 0.10 0.00
156_T 316_S 0.78 0.10 0.00
13_V 163_E 0.78 0.10 0.00
21_S 312_S 0.78 0.10 0.00
37_V 161_D 0.77 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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