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OPENSEQ.org
cIV_B_60_cI_J_20_human
Genes: A B A+B
Length: 227 174 390
Sequences: 2677 1614 1054
Seq/Len: 11.79 9.28 2.7
MirrorTree (Pazo et al. 2001) 0.68
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 0.01
5 0.00 0.00 0.06
10 0.00 0.00 2.62
20 0.00 0.00 2.63
100 0.00 0.00 2.63
∞ 0.00 0.00 2.63
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
149_P 138_D 1.34 0.89 0.31
213_L 154_V 1.34 0.89 0.31
53_T 157_G 1.32 0.88 0.30
57_D 29_G 1.32 0.88 0.29
16_I 24_S 1.29 0.86 0.27
64_V 94_V 1.28 0.86 0.27
73_L 8_L 1.26 0.85 0.26
52_N 29_G 1.21 0.81 0.22
137_D 89_L 1.19 0.80 0.21
9_L 33_I 1.18 0.79 0.20
97_I 51_M 1.17 0.79 0.20
94_S 27_Y 1.16 0.77 0.19
95_L 28_G 1.15 0.77 0.19
68_L 64_M 1.15 0.77 0.18
154_I 132_S 1.15 0.76 0.18
73_L 73_M 1.15 0.76 0.18
132_D 51_M 1.10 0.72 0.16
188_R 131_G 1.09 0.71 0.15
3_H 167_V 1.06 0.68 0.14
156_S 95_G 1.06 0.68 0.14
110_Y 48_G 1.06 0.68 0.14
141_R 52_G 1.05 0.67 0.14
63_T 52_G 1.05 0.67 0.14
143_V 18_G 1.05 0.67 0.14
97_I 16_F 1.05 0.67 0.13
115_G 145_L 1.04 0.66 0.13
9_L 52_G 1.04 0.66 0.13
46_L 157_G 1.03 0.65 0.13
184_F 55_V 1.02 0.64 0.12
133_L 52_G 1.02 0.64 0.12
186_A 74_A 1.02 0.63 0.12
16_I 128_E 1.01 0.62 0.12
191_V 35_S 1.00 0.61 0.11
23_F 52_G 0.99 0.61 0.11
144_L 162_V 0.99 0.60 0.11
52_N 28_G 0.98 0.60 0.11
64_V 24_S 0.98 0.59 0.11
123_L 154_V 0.98 0.59 0.11
9_L 162_V 0.97 0.57 0.10
42_L 165_Y 0.96 0.57 0.10
154_I 106_V 0.96 0.57 0.10
129_E 93_L 0.96 0.57 0.10
61_M 17_V 0.96 0.56 0.10
58_A 157_G 0.96 0.56 0.10
99_S 109_Y 0.95 0.56 0.10
112_D 41_V 0.95 0.55 0.10
138_V 157_G 0.94 0.55 0.09
111_T 162_V 0.94 0.55 0.09
41_A 93_L 0.94 0.54 0.09
68_L 48_G 0.94 0.54 0.09
4_A 146_Y 0.93 0.54 0.09
116_L 137_E 0.93 0.53 0.09
187_T 76_E 0.93 0.53 0.09
220_E 72_A 0.93 0.53 0.09
220_E 170_I 0.92 0.52 0.09
11_D 30_L 0.92 0.52 0.09
146_I 94_V 0.91 0.51 0.08
5_A 167_V 0.91 0.50 0.08
224_V 83_G 0.90 0.50 0.08
5_A 27_Y 0.90 0.50 0.08
45_T 148_Y 0.90 0.50 0.08
127_F 14_M 0.90 0.49 0.08
202_A 9_S 0.89 0.49 0.08
127_F 34_V 0.89 0.48 0.08
47_S 21_S 0.89 0.48 0.08
48_T 11_G 0.89 0.48 0.08
57_D 20_S 0.89 0.48 0.08
97_I 3_Y 0.88 0.48 0.07
61_M 145_L 0.88 0.48 0.07
82_R 23_P 0.88 0.47 0.07
111_T 136_R 0.88 0.47 0.07
213_L 138_D 0.88 0.47 0.07
57_D 23_P 0.88 0.47 0.07
133_L 43_I 0.88 0.47 0.07
64_V 7_L 0.87 0.46 0.07
43_F 11_G 0.87 0.46 0.07
133_L 161_F 0.87 0.46 0.07
48_T 167_V 0.87 0.46 0.07
64_V 85_G 0.87 0.46 0.07
74_V 27_Y 0.87 0.46 0.07
191_V 6_F 0.87 0.46 0.07
56_S 27_Y 0.87 0.46 0.07
186_A 3_Y 0.86 0.45 0.07
183_T 82_W 0.86 0.45 0.07
149_P 74_A 0.86 0.44 0.07
110_Y 41_V 0.86 0.44 0.07
53_T 145_L 0.86 0.44 0.07
183_T 52_G 0.85 0.44 0.07
155_T 97_A 0.85 0.44 0.07
155_T 133_G 0.85 0.44 0.07
165_V 44_L 0.85 0.44 0.07
32_F 17_V 0.85 0.44 0.07
170_L 138_D 0.85 0.43 0.07
165_V 106_V 0.84 0.43 0.06
148_T 170_I 0.84 0.43 0.06
140_N 73_M 0.84 0.43 0.06
74_V 5_L 0.84 0.43 0.06
33_L 3_Y 0.84 0.43 0.06
142_V 107_K 0.84 0.42 0.06
167_T 64_M 0.84 0.42 0.06
142_V 171_A 0.84 0.42 0.06
221_M 159_T 0.84 0.42 0.06
164_A 106_V 0.83 0.41 0.06
126_L 90_V 0.83 0.41 0.06
54_N 156_T 0.83 0.41 0.06
67_I 92_V 0.83 0.41 0.06
184_F 2_M 0.83 0.41 0.06
75_L 52_G 0.82 0.41 0.06
165_V 90_V 0.82 0.40 0.06
57_D 30_L 0.82 0.40 0.06
55_I 9_S 0.82 0.40 0.06
94_S 64_M 0.82 0.40 0.06
175_I 170_I 0.81 0.39 0.06
54_N 11_G 0.81 0.39 0.06
116_L 134_L 0.81 0.39 0.06
23_F 78_Y 0.81 0.39 0.06
16_I 123_S 0.81 0.39 0.06
31_I 101_G 0.81 0.39 0.06
154_I 35_S 0.81 0.39 0.06
92_D 11_G 0.81 0.38 0.06
57_D 66_V 0.81 0.38 0.06
155_T 156_T 0.80 0.38 0.05
73_L 156_T 0.80 0.37 0.05
52_N 30_L 0.80 0.37 0.05
147_E 10_V 0.79 0.37 0.05
43_F 157_G 0.79 0.37 0.05
92_D 126_I 0.79 0.37 0.05
63_T 41_V 0.79 0.37 0.05
140_N 35_S 0.79 0.37 0.05
88_D 27_Y 0.79 0.37 0.05
172_T 44_L 0.79 0.36 0.05
111_T 1_M 0.79 0.36 0.05
52_N 128_E 0.79 0.36 0.05
97_I 144_A 0.79 0.36 0.05
110_Y 56_F 0.79 0.36 0.05
27_A 78_Y 0.79 0.36 0.05
50_L 169_E 0.79 0.36 0.05
193_Y 19_F 0.78 0.36 0.05
167_T 12_L 0.78 0.35 0.05
187_T 45_N 0.78 0.35 0.05
147_E 135_I 0.78 0.35 0.05
30_I 41_V 0.78 0.35 0.05
23_F 64_M 0.78 0.35 0.05
86_M 29_G 0.77 0.35 0.05
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
4649 7.41 cIV_B_40_cI_J_6_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
4648 2.8 cIV_B_40_cI_J_10_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 4) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4647 5.35 cIV_B_40_cI_J_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
4646 2.7 cIV_B_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
4645 0.29 cIV_B_60_cI_J_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4644 2.71 cIV_B_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
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