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OPENSEQ.org
cIp_1_4_cIV_1_4
Genes: A B A+B
Length: 455 513 939
Sequences: 2247 3286 747
Seq/Len: 4.94 6.41 0.8
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 0.00
2 0.01 0.00 0.00
5 0.01 0.01 0.00
10 0.02 0.01 0.01
20 0.02 0.01 0.02
100 0.04 0.02 0.14
∞ 0.12 0.06 0.77
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
147_I 412_I 1.34 0.58 0.00
186_V 258_V 1.21 0.46 0.00
164_I 411_K 1.02 0.31 0.00
217_K 364_D 1.01 0.30 0.00
204_I 257_I 0.96 0.26 0.00
67_I 148_F 0.95 0.26 0.00
149_I 363_L 0.93 0.25 0.00
122_L 391_G 0.93 0.24 0.00
178_C 181_T 0.90 0.22 0.00
99_G 458_S 0.83 0.19 0.00
246_C 83_V 0.83 0.18 0.00
266_L 469_I 0.82 0.18 0.00
330_F 419_I 0.82 0.18 0.00
387_M 279_S 0.82 0.18 0.00
60_L 484_M 0.80 0.17 0.00
327_L 262_S 0.80 0.17 0.00
146_Y 262_S 0.80 0.17 0.00
130_L 262_S 0.79 0.17 0.00
335_Q 416_I 0.79 0.17 0.00
121_I 193_V 0.77 0.16 0.00
164_I 463_T 0.77 0.16 0.00
238_T 64_V 0.76 0.15 0.00
86_T 455_S 0.76 0.15 0.00
287_L 456_V 0.75 0.15 0.00
146_Y 314_I 0.75 0.15 0.00
176_N 81_W 0.74 0.15 0.00
99_G 177_T 0.74 0.15 0.00
101_P 357_V 0.74 0.14 0.00
57_K 150_L 0.74 0.14 0.00
162_V 481_K 0.74 0.14 0.00
135_V 36_L 0.74 0.14 0.00
251_T 395_H 0.74 0.14 0.00
61_L 313_A 0.73 0.14 0.00
58_E 497_G 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
4168 0.8 cIp_1_4_cIV_1_4 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4167 1.17 cIp_1_4_cIV_1_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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