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OPENSEQ.org
cIV_B_6_cIII_isp_40_Pdenitr
Genes: A B A+B
Length: 252 190 426
Sequences: 4627 1013 382
Seq/Len: 18.36 5.33 0.9
MirrorTree (Pazo et al. 2001) 0.24
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.01
10 0.01 0.01 0.02
20 0.01 0.01 0.03
100 0.02 0.01 0.14
∞ 0.04 0.02 0.86
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
114_I 28_T 1.57 0.79 0.03
59_R 187_I 1.18 0.47 0.01
112_L 59_S 1.14 0.43 0.01
248_E 184_D 1.08 0.38 0.01
47_I 140_I 1.06 0.36 0.01
246_A 88_A 0.99 0.31 0.01
45_V 78_I 0.98 0.30 0.01
53_L 49_Q 0.97 0.29 0.01
51_L 96_Q 0.97 0.29 0.01
64_A 176_I 0.95 0.28 0.00
80_I 29_V 0.94 0.27 0.00
247_K 189_L 0.93 0.27 0.00
45_V 54_I 0.93 0.26 0.00
225_A 168_G 0.92 0.26 0.00
175_T 76_V 0.90 0.25 0.00
76_P 31_A 0.87 0.23 0.00
166_V 69_V 0.87 0.22 0.00
77_I 35_A 0.86 0.22 0.00
59_R 115_E 0.85 0.21 0.00
44_A 187_I 0.85 0.21 0.00
243_L 187_I 0.84 0.21 0.00
87_L 83_E 0.84 0.21 0.00
114_I 187_I 0.83 0.20 0.00
132_V 35_A 0.83 0.20 0.00
143_A 59_S 0.82 0.20 0.00
222_I 42_M 0.82 0.19 0.00
176_A 38_L 0.82 0.19 0.00
20_F 131_V 0.81 0.19 0.00
235_S 93_D 0.81 0.19 0.00
118_G 176_I 0.80 0.19 0.00
222_I 187_I 0.80 0.19 0.00
188_F 145_G 0.80 0.18 0.00
195_V 59_S 0.79 0.18 0.00
84_V 29_V 0.79 0.18 0.00
21_Q 47_D 0.79 0.18 0.00
51_L 68_T 0.79 0.18 0.00
118_G 47_D 0.77 0.17 0.00
238_K 34_A 0.77 0.17 0.00
64_A 183_D 0.76 0.16 0.00
185_I 38_L 0.76 0.16 0.00
185_I 69_V 0.76 0.16 0.00
40_Y 122_A 0.75 0.16 0.00
44_A 167_R 0.75 0.16 0.00
40_Y 79_R 0.75 0.16 0.00
105_E 176_I 0.75 0.16 0.00
11_G 185_T 0.75 0.16 0.00
114_I 67_L 0.74 0.15 0.00
195_V 88_A 0.74 0.15 0.00
185_I 76_V 0.73 0.15 0.00
84_V 88_A 0.73 0.15 0.00
209_E 176_I 0.73 0.15 0.00
131_G 95_G 0.73 0.15 0.00
94_A 144_A 0.73 0.15 0.00
217_S 78_I 0.73 0.15 0.00
75_T 78_I 0.73 0.15 0.00
167_G 91_E 0.72 0.15 0.00
114_I 138_V 0.72 0.15 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
3113 0.9 cIV_B_6_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3112 0.35 cIV_B_10_cIII_isp_60_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3111 0.9 cIV_B_10_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.24 Done - Shared
3110 1.66 cIV_B_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3109 0.91 cIV_B_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
3108 1.65 cIV_B_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3107 0.8 cIV_B_40_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3106 1.7 cIV_B_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3099 0.9 cIV_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
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