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OPENSEQ.org
cI_D_cIII_cytb_Pdenitr
Genes: A B A+B
Length: 412 440 816
Sequences: 3488 3290 603
Seq/Len: 8.47 7.48 0.74
MirrorTree (Pazo et al. 2001) 0.28
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 0.01
5 0.03 0.00 0.02
10 0.04 0.00 0.05
20 0.05 0.00 0.07
100 0.06 0.00 0.16
∞ 0.13 0.01 0.71
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
253_Q 61_T 1.39 0.59 0.00
53_V 284_N 1.37 0.58 0.00
53_V 44_W 1.24 0.47 0.00
236_T 274_L 1.21 0.44 0.00
29_I 398_A 1.19 0.43 0.00
106_T 171_G 1.18 0.42 0.00
53_V 128_T 1.09 0.35 0.00
98_W 50_V 1.08 0.34 0.00
279_C 262_V 1.06 0.32 0.00
326_S 340_I 1.03 0.30 0.00
260_E 137_L 1.00 0.28 0.00
259_D 110_I 0.99 0.27 0.00
262_D 169_I 0.99 0.27 0.00
335_T 20_H 0.98 0.27 0.00
98_W 209_V 0.97 0.26 0.00
29_I 284_N 0.94 0.24 0.00
110_I 178_T 0.94 0.24 0.00
295_V 282_E 0.94 0.24 0.00
265_I 50_V 0.93 0.23 0.00
29_I 134_L 0.92 0.23 0.00
399_I 195_F 0.92 0.23 0.00
54_E 372_V 0.91 0.22 0.00
120_L 56_V 0.91 0.22 0.00
196_E 334_I 0.91 0.22 0.00
74_R 91_Y 0.91 0.22 0.00
120_L 392_I 0.91 0.22 0.00
167_A 298_F 0.90 0.22 0.00
367_K 63_I 0.90 0.21 0.00
384_I 282_E 0.90 0.21 0.00
223_G 106_L 0.89 0.21 0.00
284_M 209_V 0.89 0.21 0.00
202_V 243_P 0.88 0.21 0.00
371_A 160_T 0.87 0.20 0.00
208_L 413_I 0.86 0.20 0.00
108_T 60_A 0.86 0.20 0.00
281_M 264_F 0.86 0.19 0.00
127_I 402_A 0.86 0.19 0.00
117_I 388_I 0.84 0.18 0.00
102_I 267_V 0.84 0.18 0.00
231_L 341_L 0.83 0.18 0.00
295_V 205_I 0.83 0.18 0.00
127_I 341_L 0.83 0.18 0.00
343_G 122_K 0.83 0.18 0.00
297_K 262_V 0.83 0.18 0.00
382_Q 171_G 0.82 0.17 0.00
98_W 349_L 0.82 0.17 0.00
313_T 64_V 0.82 0.17 0.00
361_V 395_A 0.82 0.17 0.00
197_R 334_I 0.81 0.17 0.00
274_Y 164_G 0.81 0.17 0.00
79_N 298_F 0.81 0.17 0.00
267_V 211_V 0.81 0.17 0.00
158_M 334_I 0.81 0.17 0.00
112_R 204_V 0.80 0.17 0.00
134_V 342_V 0.80 0.16 0.00
312_L 419_A 0.80 0.16 0.00
225_V 211_V 0.80 0.16 0.00
388_S 106_L 0.80 0.16 0.00
322_R 172_V 0.80 0.16 0.00
388_S 394_L 0.80 0.16 0.00
349_V 112_I 0.80 0.16 0.00
326_S 256_L 0.80 0.16 0.00
228_A 397_S 0.80 0.16 0.00
53_V 389_Y 0.79 0.16 0.00
297_K 25_I 0.79 0.16 0.00
370_R 174_E 0.79 0.16 0.00
76_Y 210_V 0.79 0.16 0.00
164_A 366_W 0.79 0.16 0.00
393_L 206_A 0.79 0.16 0.00
102_I 334_I 0.78 0.16 0.00
292_Q 284_N 0.78 0.15 0.00
98_W 107_A 0.78 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
3015 0.74 cI_D_2_cIII_cytb_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3014 0.75 cI_D_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2804 0.74 cI_D_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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