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OPENSEQ.org
cIp_4_40_cIV_1_40
Genes: A B A+B
Length: 463 513 907
Sequences: 2150 3286 800
Seq/Len: 4.64 6.41 0.88
MirrorTree (Pazo et al. 2001) 0.23
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 0.00 0.00
2 0.00 0.00 0.01
5 0.01 0.01 0.02
10 0.01 0.01 0.04
20 0.02 0.01 0.07
100 0.03 0.02 0.19
∞ 0.09 0.06 0.82
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
348_L 193_V 1.21 0.49 0.00
438_M 97_M 1.07 0.37 0.00
284_L 104_L 1.00 0.32 0.00
398_T 9_S 0.97 0.29 0.00
106_V 192_A 0.95 0.28 0.00
355_E 161_A 0.93 0.26 0.00
344_I 180_Q 0.93 0.26 0.00
411_L 64_V 0.93 0.26 0.00
280_A 393_F 0.92 0.25 0.00
162_R 152_L 0.85 0.21 0.00
399_A 332_M 0.85 0.21 0.00
440_K 484_M 0.85 0.21 0.00
411_L 20_L 0.85 0.21 0.00
412_V 166_T 0.84 0.20 0.00
272_T 363_L 0.84 0.20 0.00
222_M 162_I 0.82 0.20 0.00
360_D 350_V 0.82 0.19 0.00
332_C 464_A 0.79 0.18 0.00
180_L 32_A 0.79 0.18 0.00
167_A 279_S 0.79 0.17 0.00
351_M 464_A 0.78 0.17 0.00
343_I 30_G 0.78 0.17 0.00
82_L 110_L 0.76 0.16 0.00
143_S 48_L 0.76 0.16 0.00
334_V 100_M 0.76 0.16 0.00
332_C 320_V 0.76 0.16 0.00
342_R 198_S 0.76 0.16 0.00
173_L 62_A 0.75 0.16 0.00
143_S 370_T 0.75 0.16 0.00
390_Q 220_F 0.75 0.16 0.00
315_E 419_I 0.75 0.15 0.00
281_E 461_S 0.75 0.15 0.00
339_Q 409_Y 0.74 0.15 0.00
249_K 456_V 0.74 0.15 0.00
317_D 284_G 0.74 0.15 0.00
274_D 436_M 0.74 0.15 0.00
339_Q 481_K 0.74 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
4306 1.31 cIp_4_40_cIV_1_40 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4296 0.88 cIp_4_40_cIV_1_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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