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OPENSEQ.org
cIp_1_40_cIV_A_40
Genes: A B A+B
Length: 438 558 958
Sequences: 2218 3242 753
Seq/Len: 5.06 5.81 0.79
MirrorTree (Pazo et al. 2001) 0.09
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 0.00
2 0.01 0.00 0.00
5 0.01 0.01 0.00
10 0.02 0.01 0.01
20 0.02 0.02 0.02
100 0.04 0.03 0.13
∞ 0.12 0.06 0.76
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
171_L 294_I 1.18 0.44 0.00
132_I 447_L 1.09 0.36 0.00
107_L 426_A 0.97 0.27 0.00
134_V 398_L 0.96 0.27 0.00
189_M 293_V 0.94 0.25 0.00
53_V 184_F 0.94 0.25 0.00
202_K 399_D 0.92 0.24 0.00
149_I 446_Q 0.91 0.23 0.00
131_Y 298_A 0.91 0.23 0.00
43_R 535_P 0.88 0.21 0.00
251_L 504_I 0.85 0.20 0.00
310_P 298_A 0.85 0.20 0.00
231_M 116_M 0.85 0.19 0.00
371_F 314_A 0.84 0.19 0.00
42_K 186_V 0.83 0.18 0.00
173_V 346_T 0.82 0.18 0.00
163_F 217_V 0.82 0.18 0.00
313_Y 454_I 0.81 0.18 0.00
318_A 451_M 0.80 0.17 0.00
72_T 490_S 0.79 0.16 0.00
51_D 202_T 0.79 0.16 0.00
260_R 454_I 0.78 0.16 0.00
120_L 52_Y 0.78 0.16 0.00
155_R 349_V 0.78 0.16 0.00
155_R 438_R 0.77 0.16 0.00
382_K 445_G 0.75 0.15 0.00
238_F 495_I 0.75 0.14 0.00
171_L 426_A 0.74 0.14 0.00
166_D 369_F 0.74 0.14 0.00
223_T 97_L 0.73 0.14 0.00
192_L 384_T 0.73 0.14 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
4031 1.16 cIp_1_40_cIV_A_40 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4030 0.79 cIp_1_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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