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OPENSEQ.org
cIV_C_40_cI_K_10_human
Genes: A B A+B
Length: 261 98 359
Sequences: 2457 3525 1974
Seq/Len: 9.41 35.97 5.5
MirrorTree (Pazo et al. 2001) 0.60
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 0.08
2 0.00 0.00 1.92
5 0.00 0.00 4.15
10 0.00 0.00 4.57
20 0.00 0.00 4.69
100 0.00 0.01 4.88
∞ 0.00 0.02 5.50
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
32_A 48_T 1.23 0.94 0.34
74_P 77_L 1.08 0.88 0.23
124_L 71_A 1.05 0.86 0.21
106_L 86_G 1.05 0.86 0.21
157_N 71_A 1.05 0.85 0.21
192_I 62_A 1.02 0.83 0.19
18_L 97_Q 1.02 0.83 0.19
196_T 20_L 1.00 0.81 0.18
6_H 96_L 1.00 0.81 0.18
53_T 31_L 0.98 0.80 0.17
124_L 63_M 0.96 0.78 0.15
21_A 90_V 0.95 0.77 0.15
6_H 71_A 0.95 0.77 0.15
189_S 27_M 0.94 0.75 0.14
136_V 71_A 0.93 0.75 0.14
40_M 61_I 0.93 0.75 0.14
158_Q 71_A 0.93 0.74 0.14
65_S 38_L 0.93 0.74 0.14
37_F 90_V 0.92 0.73 0.13
101_F 64_L 0.91 0.72 0.13
139_A 28_S 0.90 0.71 0.13
192_I 96_L 0.90 0.71 0.13
83_M 31_L 0.89 0.70 0.12
124_L 68_A 0.88 0.68 0.12
55_Y 97_Q 0.87 0.68 0.11
174_T 76_A 0.87 0.67 0.11
23_S 77_L 0.87 0.67 0.11
184_S 28_S 0.87 0.67 0.11
80_R 90_V 0.87 0.67 0.11
5_S 32_C 0.86 0.66 0.11
91_V 21_V 0.86 0.66 0.11
114_G 29_S 0.86 0.66 0.11
161_Q 66_F 0.85 0.64 0.10
50_N 67_A 0.85 0.64 0.10
121_I 44_G 0.83 0.62 0.10
22_L 77_L 0.82 0.60 0.09
8_Y 42_I 0.81 0.60 0.09
124_L 35_G 0.81 0.59 0.09
77_K 42_I 0.81 0.59 0.09
147_A 65_V 0.81 0.58 0.09
147_A 15_S 0.80 0.58 0.09
259_W 61_I 0.80 0.58 0.09
96_G 35_G 0.80 0.58 0.09
198_F 11_A 0.79 0.57 0.08
129_V 87_L 0.79 0.57 0.08
213_T 47_M 0.79 0.56 0.08
151_L 89_Y 0.79 0.56 0.08
8_Y 96_L 0.78 0.55 0.08
253_Y 58_I 0.78 0.55 0.08
5_S 33_L 0.78 0.55 0.08
172_Y 31_L 0.78 0.54 0.08
61_V 36_M 0.77 0.54 0.08
250_L 67_A 0.77 0.53 0.08
256_I 30_L 0.76 0.52 0.07
10_M 47_M 0.76 0.52 0.07
176_L 79_V 0.76 0.52 0.07
218_C 90_V 0.76 0.52 0.07
72_T 31_L 0.76 0.51 0.07
51_T 14_I 0.76 0.51 0.07
170_G 69_C 0.75 0.50 0.07
230_K 57_N 0.75 0.50 0.07
139_A 29_S 0.75 0.50 0.07
25_L 77_L 0.75 0.50 0.07
91_V 84_T 0.74 0.49 0.07
128_E 90_V 0.74 0.49 0.07
247_V 76_A 0.74 0.49 0.07
167_I 14_I 0.74 0.49 0.07
18_L 89_Y 0.74 0.49 0.07
97_F 64_L 0.74 0.48 0.07
176_L 14_I 0.73 0.48 0.07
13_P 98_C 0.73 0.47 0.06
96_G 68_A 0.73 0.47 0.06
226_H 96_L 0.73 0.47 0.06
24_A 61_I 0.73 0.47 0.06
129_V 92_N 0.73 0.47 0.06
209_I 31_L 0.73 0.47 0.06
156_R 18_G 0.72 0.47 0.06
20_G 86_G 0.72 0.46 0.06
183_E 30_L 0.72 0.46 0.06
155_N 73_V 0.72 0.45 0.06
35_F 39_S 0.71 0.45 0.06
62_T 95_L 0.71 0.45 0.06
91_V 39_S 0.71 0.45 0.06
225_F 67_A 0.71 0.45 0.06
217_I 57_N 0.71 0.45 0.06
213_T 14_I 0.71 0.45 0.06
38_H 36_M 0.71 0.44 0.06
1_M 24_S 0.71 0.44 0.06
49_T 19_M 0.71 0.44 0.06
162_A 93_L 0.70 0.44 0.06
178_A 93_L 0.70 0.43 0.06
110_P 9_M 0.70 0.43 0.06
80_R 61_I 0.70 0.43 0.06
225_F 41_F 0.70 0.43 0.06
160_I 17_L 0.70 0.43 0.06
195_S 5_Y 0.70 0.43 0.06
217_I 62_A 0.70 0.43 0.06
48_L 49_L 0.70 0.43 0.06
21_A 97_Q 0.69 0.42 0.06
48_L 10_L 0.69 0.42 0.06
72_T 95_L 0.69 0.42 0.06
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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