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OPENSEQ.org
cIV_B_10_cIII_isp_60_Pdenitr
Genes: A B A+B
Length: 252 190 428
Sequences: 4618 508 151
Seq/Len: 18.33 2.67 0.35
MirrorTree (Pazo et al. 2001) 0.13
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 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.01
100 0.02 0.01 0.06
∞ 0.04 0.02 0.34
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
195_V 88_A 1.29 0.32 0.00
53_L 49_Q 1.27 0.30 0.00
51_L 68_T 1.24 0.29 0.00
44_A 9_G 1.15 0.24 0.00
45_V 54_I 1.10 0.22 0.00
51_L 96_Q 1.09 0.21 0.00
145_A 35_A 1.08 0.21 0.00
110_P 34_A 1.06 0.20 0.00
167_G 61_V 1.04 0.19 0.00
77_I 35_A 1.03 0.18 0.00
114_I 67_L 1.03 0.18 0.00
59_R 93_D 1.00 0.17 0.00
202_L 26_A 1.00 0.17 0.00
222_I 42_M 1.00 0.17 0.00
185_I 38_L 0.99 0.17 0.00
146_D 184_D 0.98 0.17 0.00
237_E 19_L 0.97 0.16 0.00
143_A 59_S 0.97 0.16 0.00
118_G 176_I 0.96 0.16 0.00
174_V 19_L 0.94 0.15 0.00
114_I 138_V 0.93 0.15 0.00
64_A 138_V 0.93 0.15 0.00
240_E 38_L 0.93 0.15 0.00
117_I 28_T 0.93 0.15 0.00
114_I 57_D 0.93 0.15 0.00
199_I 174_L 0.93 0.14 0.00
83_L 176_I 0.93 0.14 0.00
114_I 32_G 0.93 0.14 0.00
183_W 93_D 0.92 0.14 0.00
114_I 28_T 0.90 0.14 0.00
60_F 78_I 0.90 0.14 0.00
124_S 42_M 0.90 0.14 0.00
138_M 98_I 0.89 0.13 0.00
175_T 76_V 0.89 0.13 0.00
194_A 71_W 0.89 0.13 0.00
45_V 78_I 0.88 0.13 0.00
136_A 147_F 0.88 0.13 0.00
167_G 91_E 0.88 0.13 0.00
189_A 81_R 0.88 0.13 0.00
238_K 148_G 0.87 0.13 0.00
29_H 61_V 0.87 0.13 0.00
161_P 182_L 0.87 0.12 0.00
51_L 67_L 0.86 0.12 0.00
225_A 92_V 0.86 0.12 0.00
104_Q 45_S 0.86 0.12 0.00
246_A 88_A 0.86 0.12 0.00
94_A 40_N 0.85 0.12 0.00
235_S 95_G 0.85 0.12 0.00
77_I 33_A 0.84 0.12 0.00
187_A 127_V 0.84 0.12 0.00
117_I 140_I 0.84 0.12 0.00
97_L 48_V 0.84 0.12 0.00
84_V 113_T 0.83 0.12 0.00
47_I 88_A 0.83 0.12 0.00
103_S 67_L 0.83 0.11 0.00
170_V 31_A 0.83 0.11 0.00
20_F 124_E 0.82 0.11 0.00
143_A 147_F 0.82 0.11 0.00
22_P 83_E 0.81 0.11 0.00
208_Q 115_E 0.81 0.11 0.00
91_A 118_T 0.81 0.11 0.00
83_L 158_H 0.80 0.11 0.00
176_A 21_Y 0.80 0.11 0.00
161_P 45_S 0.80 0.10 0.00
169_K 138_V 0.80 0.10 0.00
222_I 71_W 0.79 0.10 0.00
51_L 39_V 0.79 0.10 0.00
53_L 93_D 0.79 0.10 0.00
243_L 27_G 0.79 0.10 0.00
167_G 62_E 0.79 0.10 0.00
43_T 174_L 0.78 0.10 0.00
84_V 88_A 0.78 0.10 0.00
112_L 138_V 0.78 0.10 0.00
183_W 39_V 0.78 0.10 0.00
55_I 52_A 0.78 0.10 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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