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OPENSEQ.org
cIV_A_6_cI_J_10_Pdenitr
Genes: A B A+B
Length: 538 200 713
Sequences: 4449 2223 1106
Seq/Len: 8.27 11.12 1.55
MirrorTree (Pazo et al. 2001) 0.08
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 0.03
5 0.02 0.01 0.12
10 0.02 0.01 0.23
20 0.03 0.01 0.32
100 0.04 0.02 0.49
∞ 0.08 0.03 1.50
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
412_V 159_I 1.10 0.56 0.00
438_I 21_V 1.09 0.55 0.00
130_V 57_V 1.02 0.47 0.00
227_T 38_L 1.01 0.46 0.00
39_M 157_A 0.98 0.43 0.00
99_F 158_M 0.97 0.42 0.00
442_L 159_I 0.96 0.41 0.00
431_L 132_T 0.96 0.41 0.00
301_I 57_V 0.94 0.39 0.00
326_L 52_V 0.94 0.39 0.00
216_L 106_I 0.94 0.39 0.00
23_A 47_Q 0.91 0.36 0.00
359_W 32_W 0.91 0.36 0.00
106_A 161_A 0.90 0.35 0.00
394_A 93_A 0.89 0.34 0.00
483_S 21_V 0.88 0.34 0.00
127_A 41_A 0.88 0.33 0.00
37_M 41_A 0.88 0.33 0.00
21_F 136_G 0.87 0.32 0.00
479_I 106_I 0.86 0.32 0.00
378_S 20_V 0.86 0.31 0.00
81_L 158_M 0.86 0.31 0.00
35_V 139_L 0.86 0.31 0.00
277_V 132_T 0.85 0.31 0.00
28_L 8_L 0.82 0.28 0.00
343_I 29_S 0.82 0.28 0.00
189_L 101_L 0.81 0.27 0.00
25_I 46_L 0.81 0.27 0.00
485_L 72_V 0.80 0.26 0.00
410_A 41_A 0.80 0.26 0.00
351_I 83_K 0.79 0.25 0.00
378_S 38_L 0.79 0.25 0.00
381_P 66_V 0.78 0.25 0.00
297_A 27_V 0.78 0.24 0.00
286_I 55_L 0.78 0.24 0.00
217_L 135_L 0.78 0.24 0.00
482_A 5_A 0.77 0.24 0.00
519_P 38_L 0.77 0.24 0.00
249_V 12_S 0.77 0.24 0.00
99_F 59_V 0.77 0.23 0.00
436_M 150_A 0.76 0.23 0.00
425_P 9_F 0.76 0.23 0.00
81_L 98_V 0.76 0.23 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
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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