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OPENSEQ.org
cIV_A_4_cI_J_6_Pdenitr
Genes: A B A+B
Length: 538 200 696
Sequences: 4477 4916 2137
Seq/Len: 8.32 24.58 3.07
MirrorTree (Pazo et al. 2001) 0.20
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 0.01 0.00 0.01
2 0.01 0.00 0.05
5 0.02 0.00 0.20
10 0.03 0.00 1.61
20 0.03 0.00 1.70
100 0.05 0.01 1.87
∞ 0.08 0.02 2.90
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
376_V 66_V 1.42 0.94 0.58
5_R 60_Y 1.33 0.91 0.49
351_I 136_G 1.12 0.78 0.31
99_F 158_M 1.08 0.74 0.28
26_V 161_A 1.08 0.74 0.27
227_T 38_L 1.07 0.73 0.27
35_V 148_Q 1.06 0.72 0.26
434_W 136_G 1.00 0.65 0.21
531_P 33_L 0.97 0.62 0.20
127_A 41_A 0.95 0.60 0.18
394_A 14_C 0.94 0.58 0.17
5_R 74_M 0.94 0.58 0.17
479_I 106_I 0.93 0.57 0.17
438_I 21_V 0.93 0.57 0.17
517_T 60_Y 0.91 0.55 0.16
35_V 58_V 0.90 0.53 0.15
472_I 38_L 0.90 0.53 0.15
428_A 147_F 0.87 0.50 0.14
175_A 66_V 0.87 0.50 0.13
501_V 150_A 0.87 0.50 0.13
474_S 98_V 0.87 0.49 0.13
104_I 163_V 0.86 0.49 0.13
289_Y 49_A 0.86 0.48 0.13
278_I 16_A 0.85 0.48 0.12
4_T 60_Y 0.83 0.45 0.12
42_Q 21_V 0.82 0.43 0.11
297_A 93_A 0.82 0.43 0.11
486_F 138_V 0.82 0.43 0.11
524_E 72_V 0.82 0.43 0.11
526_T 60_Y 0.82 0.43 0.11
483_S 164_L 0.81 0.41 0.10
442_L 139_L 0.80 0.41 0.10
514_L 69_L 0.80 0.41 0.10
243_A 40_A 0.80 0.41 0.10
360_A 160_G 0.79 0.40 0.10
486_F 94_L 0.79 0.40 0.10
28_L 8_L 0.79 0.39 0.09
99_F 59_V 0.78 0.39 0.09
356_P 34_I 0.78 0.38 0.09
488_I 51_F 0.77 0.37 0.09
35_V 47_Q 0.77 0.37 0.09
337_I 151_G 0.77 0.37 0.09
100_M 72_V 0.76 0.36 0.08
431_L 132_T 0.76 0.36 0.08
506_Y 42_G 0.76 0.36 0.08
501_V 72_V 0.76 0.36 0.08
523_P 41_A 0.75 0.35 0.08
429_G 73_M 0.75 0.35 0.08
359_W 32_W 0.75 0.35 0.08
29_I 125_V 0.75 0.35 0.08
71_W 127_A 0.75 0.35 0.08
375_V 43_L 0.75 0.35 0.08
472_I 50_E 0.75 0.35 0.08
413_Y 63_A 0.74 0.34 0.08
360_A 136_G 0.74 0.34 0.08
74_M 21_V 0.74 0.34 0.08
485_L 121_R 0.74 0.34 0.08
135_A 95_V 0.74 0.34 0.08
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
3468 3.07 cIV_A_4_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.58 Done - Shared
3385 1.55 cIV_A_6_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3384 3.98 cIV_A_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
3380 3.97 cIV_A_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
3378 3.98 cIV_A_10_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3377 3.07 cIV_A_10_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.42 Done - Shared
3372 3.08 cIV_A_6_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.67 Done - Shared
3370 3.98 cIV_A_6_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3369 3.99 cIV_A_6_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
3368 0.61 cIV_A_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3367 4 cIV_A_4_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
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