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OPENSEQ.org
cIV_C_40_cI_K_20_4_human
Genes: A B A+B
Length: 261 98 359
Sequences: 2457 1088 643
Seq/Len: 9.41 11.1 1.79
MirrorTree (Pazo et al. 2001) 0.70
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 0.03
2 0.00 0.00 1.74
5 0.00 0.00 1.79
10 0.00 0.00 1.79
20 0.00 0.00 1.79
100 0.00 0.00 1.79
∞ 0.00 0.00 1.79
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
103_H 78_L 2.17 0.99 0.97
189_S 90_V 2.11 0.99 0.97
114_G 78_L 1.90 0.98 0.94
8_Y 17_L 1.68 0.95 0.88
199_V 85_Y 1.59 0.93 0.83
125_N 57_N 1.46 0.88 0.75
37_F 51_T 1.43 0.86 0.72
150_S 33_L 1.42 0.86 0.72
23_S 90_V 1.36 0.82 0.66
189_S 47_M 1.35 0.81 0.66
229_S 33_L 1.34 0.81 0.65
213_T 78_L 1.34 0.81 0.65
182_F 67_A 1.33 0.80 0.64
143_S 73_V 1.33 0.80 0.63
104_S 78_L 1.32 0.80 0.63
135_S 83_N 1.31 0.78 0.61
222_Q 35_G 1.30 0.78 0.61
102_Y 35_G 1.26 0.75 0.57
189_S 27_M 1.26 0.75 0.57
29_S 92_N 1.25 0.74 0.56
10_M 60_P 1.25 0.74 0.56
199_V 67_A 1.24 0.73 0.54
191_G 86_G 1.22 0.71 0.52
79_L 18_G 1.19 0.69 0.49
217_I 92_N 1.19 0.68 0.49
26_L 43_M 1.18 0.68 0.48
139_A 35_G 1.18 0.68 0.48
168_L 45_T 1.18 0.68 0.48
199_V 65_V 1.17 0.67 0.47
122_T 41_F 1.15 0.65 0.45
7_A 62_A 1.15 0.65 0.45
150_S 27_M 1.14 0.64 0.44
20_G 84_T 1.14 0.64 0.43
182_F 41_F 1.13 0.63 0.43
143_S 15_S 1.13 0.63 0.43
112_L 39_S 1.13 0.63 0.43
77_K 17_L 1.13 0.62 0.42
35_F 83_N 1.12 0.62 0.42
49_T 82_S 1.12 0.62 0.42
5_S 22_Y 1.12 0.62 0.41
217_I 79_V 1.11 0.60 0.40
96_G 60_P 1.10 0.60 0.39
112_L 79_V 1.10 0.60 0.39
62_T 48_T 1.10 0.60 0.39
144_I 41_F 1.09 0.59 0.38
112_L 78_L 1.09 0.59 0.38
23_S 81_I 1.09 0.59 0.38
191_G 46_F 1.09 0.58 0.38
47_L 94_N 1.08 0.58 0.38
104_S 79_V 1.08 0.58 0.37
144_I 39_S 1.08 0.58 0.37
162_A 86_G 1.07 0.57 0.36
18_L 76_A 1.07 0.57 0.36
228_T 38_L 1.06 0.56 0.35
96_G 36_M 1.06 0.56 0.35
48_L 21_V 1.06 0.56 0.35
25_L 84_T 1.06 0.56 0.35
61_V 73_V 1.04 0.53 0.33
23_S 20_L 1.04 0.53 0.33
114_G 76_A 1.03 0.53 0.32
195_S 94_N 1.03 0.52 0.32
229_S 86_G 1.03 0.52 0.32
175_L 67_A 1.02 0.52 0.31
96_G 38_L 1.02 0.52 0.31
5_S 19_M 1.01 0.50 0.30
28_T 59_V 1.00 0.49 0.29
216_T 78_L 1.00 0.49 0.29
114_G 65_V 1.00 0.49 0.29
35_F 67_A 1.00 0.49 0.29
65_S 72_A 1.00 0.49 0.29
217_I 13_T 1.00 0.49 0.28
216_T 92_N 1.00 0.49 0.28
199_V 83_N 1.00 0.49 0.28
61_V 92_N 0.99 0.48 0.28
49_T 27_M 0.99 0.48 0.28
228_T 35_G 0.99 0.48 0.28
100_A 64_L 0.99 0.48 0.28
228_T 60_P 0.99 0.48 0.28
156_R 45_T 0.99 0.48 0.28
155_N 33_L 0.98 0.47 0.27
184_S 17_L 0.98 0.47 0.27
151_L 65_V 0.98 0.47 0.27
143_S 84_T 0.98 0.47 0.27
103_H 84_T 0.97 0.46 0.26
212_S 86_G 0.97 0.46 0.26
46_G 23_R 0.97 0.46 0.26
162_A 27_M 0.97 0.46 0.26
162_A 88_D 0.97 0.46 0.26
164_L 14_I 0.97 0.45 0.26
119_T 47_M 0.96 0.45 0.25
212_S 56_A 0.96 0.45 0.25
39_S 8_I 0.96 0.45 0.25
183_E 37_M 0.96 0.45 0.25
43_L 21_V 0.95 0.44 0.25
96_G 35_G 0.95 0.44 0.25
251_F 66_F 0.95 0.44 0.25
151_L 29_S 0.95 0.44 0.24
144_I 73_V 0.95 0.43 0.24
65_S 93_L 0.95 0.43 0.24
61_V 8_I 0.94 0.43 0.23
88_T 66_F 0.94 0.43 0.23
33_M 39_S 0.94 0.43 0.23
199_V 90_V 0.94 0.42 0.23
153_E 20_L 0.94 0.42 0.23
228_T 37_M 0.94 0.42 0.23
19_T 55_L 0.94 0.42 0.23
110_P 60_P 0.94 0.42 0.23
158_Q 88_D 0.93 0.41 0.22
192_I 86_G 0.93 0.41 0.22
188_I 36_M 0.93 0.41 0.22
212_S 36_M 0.92 0.41 0.22
121_I 11_A 0.92 0.41 0.22
191_G 50_N 0.92 0.41 0.21
2_T 40_L 0.91 0.40 0.21
8_Y 61_I 0.91 0.39 0.21
167_I 72_A 0.91 0.39 0.20
224_M 42_I 0.91 0.39 0.20
135_S 85_Y 0.91 0.39 0.20
119_T 33_L 0.90 0.39 0.20
179_S 35_G 0.90 0.38 0.20
55_Y 58_I 0.90 0.38 0.20
79_L 28_S 0.90 0.38 0.20
152_M 36_M 0.90 0.38 0.20
230_K 70_E 0.90 0.38 0.20
139_A 23_R 0.89 0.38 0.19
161_Q 82_S 0.89 0.38 0.19
253_Y 16_L 0.89 0.38 0.19
84_I 61_I 0.89 0.37 0.19
250_L 83_N 0.89 0.37 0.19
25_L 79_V 0.89 0.37 0.19
125_N 58_I 0.89 0.37 0.19
77_K 97_Q 0.88 0.37 0.18
127_L 6_M 0.88 0.37 0.18
7_A 72_A 0.88 0.36 0.18
8_Y 57_N 0.88 0.36 0.18
102_Y 60_P 0.88 0.36 0.18
78_G 23_R 0.88 0.36 0.18
62_T 41_F 0.88 0.36 0.18
76_Q 60_P 0.88 0.36 0.18
229_S 27_M 0.87 0.35 0.17
165_I 83_N 0.86 0.35 0.17
143_S 79_V 0.86 0.35 0.17
65_S 17_L 0.86 0.35 0.17
40_M 61_I 0.86 0.35 0.17
55_Y 98_C 0.86 0.34 0.17
44_M 33_L 0.86 0.34 0.17
184_S 6_M 0.86 0.34 0.17
188_I 92_N 0.86 0.34 0.17
73_P 67_A 0.85 0.34 0.16
223_L 6_M 0.85 0.34 0.16
165_I 80_S 0.85 0.34 0.16
127_L 85_Y 0.85 0.33 0.16
142_V 83_N 0.85 0.33 0.16
112_L 56_A 0.84 0.33 0.16
127_L 65_V 0.84 0.33 0.15
8_Y 10_L 0.84 0.33 0.15
217_I 53_S 0.84 0.32 0.15
102_Y 22_Y 0.84 0.32 0.15
228_T 36_M 0.84 0.32 0.15
103_H 79_V 0.84 0.32 0.15
61_V 6_M 0.83 0.32 0.15
191_G 27_M 0.83 0.32 0.15
139_A 22_Y 0.83 0.32 0.15
27_M 94_N 0.83 0.32 0.15
250_L 87_L 0.83 0.31 0.15
147_A 44_G 0.83 0.31 0.15
76_Q 38_L 0.83 0.31 0.14
114_G 27_M 0.83 0.31 0.14
48_L 15_S 0.83 0.31 0.14
33_M 15_S 0.82 0.31 0.14
103_H 27_M 0.82 0.31 0.14
48_L 16_L 0.82 0.31 0.14
136_V 55_L 0.82 0.31 0.14
24_A 28_S 0.82 0.31 0.14
152_M 35_G 0.82 0.30 0.14
5_S 27_M 0.82 0.30 0.14
13_P 60_P 0.82 0.30 0.14
154_N 80_S 0.81 0.30 0.14
125_N 36_M 0.81 0.30 0.13
115_H 86_G 0.81 0.30 0.13
56_Q 19_M 0.81 0.29 0.13
153_E 51_T 0.81 0.29 0.13
212_S 12_F 0.81 0.29 0.13
216_T 42_I 0.81 0.29 0.13
13_P 38_L 0.81 0.29 0.13
127_L 83_N 0.81 0.29 0.13
154_N 13_T 0.81 0.29 0.13
67_Y 51_T 0.80 0.29 0.13
212_S 45_T 0.80 0.29 0.13
156_R 28_S 0.80 0.29 0.13
154_N 29_S 0.80 0.29 0.13
189_S 63_M 0.80 0.29 0.13
31_L 28_S 0.80 0.29 0.13
250_L 67_A 0.80 0.29 0.13
107_A 92_N 0.80 0.28 0.13
50_N 91_H 0.79 0.28 0.12
73_P 42_I 0.79 0.28 0.12
50_N 67_A 0.79 0.28 0.12
67_Y 63_M 0.79 0.28 0.12
223_L 70_E 0.79 0.28 0.12
81_Y 62_A 0.79 0.28 0.12
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
4504 5.5 cIV_C_40_cI_K_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
4503 1.78 cIV_C_60_cI_K_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4502 1.79 cIV_C_40_cI_K_20_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4501 0.25 cIV_C_40_cI_K_40_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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