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OPENSEQ.org
cIp_5_4_cIV_B_4
Genes: A B A+B
Length: 207 298 464
Sequences: 1036 3243 471
Seq/Len: 5 10.88 1.02
MirrorTree (Pazo et al. 2001) 0.32
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 0.02
5 0.00 0.00 0.04
10 0.00 0.01 0.07
20 0.00 0.01 0.12
100 0.00 0.03 0.20
∞ 0.01 0.06 0.93
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
110_F 205_A 1.89 0.94 0.60
91_I 145_A 1.42 0.71 0.24
137_I 241_Y 1.31 0.62 0.17
124_F 99_R 1.24 0.56 0.14
124_F 273_A 1.18 0.50 0.11
53_D 118_L 1.16 0.48 0.10
129_S 116_L 1.15 0.47 0.10
105_S 44_N 1.02 0.36 0.06
48_E 195_V 1.02 0.36 0.06
162_W 119_V 1.01 0.35 0.06
126_I 274_G 1.00 0.34 0.06
123_L 109_I 1.00 0.34 0.06
41_S 35_D 0.97 0.32 0.05
46_L 146_I 0.96 0.31 0.05
63_D 218_A 0.95 0.30 0.05
154_T 211_A 0.95 0.30 0.05
46_L 76_I 0.94 0.29 0.04
109_V 191_V 0.93 0.29 0.04
85_M 145_A 0.91 0.27 0.04
114_N 108_V 0.90 0.27 0.04
43_V 171_E 0.88 0.25 0.03
97_V 238_E 0.88 0.25 0.03
17_I 196_G 0.88 0.25 0.03
34_L 199_V 0.87 0.25 0.03
126_I 191_V 0.87 0.24 0.03
124_F 88_R 0.86 0.24 0.03
94_K 106_I 0.85 0.23 0.03
111_P 158_N 0.85 0.23 0.03
36_V 104_T 0.85 0.23 0.03
17_I 170_K 0.84 0.23 0.03
11_L 143_I 0.84 0.23 0.03
115_W 152_W 0.81 0.21 0.03
85_M 261_K 0.80 0.20 0.02
103_V 89_F 0.80 0.20 0.02
47_I 145_A 0.79 0.19 0.02
123_L 69_Y 0.78 0.19 0.02
137_I 163_F 0.78 0.19 0.02
61_L 272_L 0.78 0.19 0.02
105_S 63_L 0.77 0.18 0.02
57_R 116_L 0.77 0.18 0.02
91_I 143_I 0.77 0.18 0.02
91_I 77_F 0.76 0.18 0.02
25_V 266_E 0.76 0.18 0.02
82_L 214_I 0.76 0.18 0.02
25_V 37_P 0.76 0.18 0.02
120_V 270_A 0.76 0.18 0.02
74_A 141_L 0.76 0.18 0.02
15_E 195_V 0.76 0.18 0.02
17_I 205_A 0.76 0.18 0.02
110_F 242_F 0.76 0.17 0.02
100_D 146_I 0.75 0.17 0.02
82_L 141_L 0.75 0.17 0.02
95_V 223_A 0.75 0.17 0.02
109_V 35_D 0.75 0.17 0.02
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
3990 1.01 cIp_5_2_cIV_B_6 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.42 Done - Shared
3989 1.02 cIp_5_6_cIV_B_6 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.73 Done - Shared
3988 1.01 cIp_5_4_cIV_B_10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.57 Done - Shared
3983 1.01 cIp_5_4_cIV_B_6 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.77 Done - Shared
3981 1.02 cIp_5_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.60 Done - Shared
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