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OPENSEQ.org
cIp_1_4_cIV_C_4
Genes: A B A+B
Length: 438 274 696
Sequences: 2218 2529 300
Seq/Len: 5.06 9.23 0.43
MirrorTree (Pazo et al. 2001) 0.25
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 0.00 0.00
10 0.02 0.00 0.00
20 0.02 0.00 0.01
100 0.04 0.00 0.05
∞ 0.12 0.00 0.42
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
308_D 211_Y 1.40 0.44 0.00
251_L 52_F 1.22 0.32 0.00
231_M 52_F 1.04 0.22 0.00
134_V 151_L 1.04 0.22 0.00
155_R 181_I 1.02 0.21 0.00
425_A 22_A 1.01 0.20 0.00
54_I 26_F 1.00 0.20 0.00
414_L 33_V 1.00 0.20 0.00
171_L 25_A 0.97 0.18 0.00
28_T 141_L 0.97 0.18 0.00
50_P 211_Y 0.96 0.18 0.00
235_A 47_E 0.95 0.17 0.00
179_A 232_L 0.94 0.17 0.00
412_G 143_L 0.94 0.17 0.00
29_L 192_Y 0.94 0.17 0.00
209_S 222_I 0.93 0.17 0.00
270_T 141_L 0.93 0.16 0.00
30_D 54_I 0.93 0.16 0.00
218_I 266_F 0.92 0.16 0.00
300_L 57_V 0.92 0.16 0.00
115_I 48_G 0.91 0.16 0.00
195_L 232_L 0.89 0.15 0.00
149_I 117_M 0.89 0.15 0.00
51_D 56_L 0.88 0.15 0.00
166_D 241_T 0.88 0.14 0.00
384_V 180_V 0.87 0.14 0.00
391_L 181_I 0.87 0.14 0.00
107_L 50_W 0.87 0.14 0.00
289_A 20_F 0.87 0.14 0.00
218_I 250_A 0.87 0.14 0.00
274_E 138_P 0.86 0.14 0.00
328_V 233_I 0.86 0.14 0.00
134_V 34_A 0.86 0.14 0.00
209_S 167_G 0.86 0.14 0.00
33_L 51_M 0.86 0.14 0.00
23_K 180_V 0.85 0.14 0.00
160_K 226_I 0.85 0.14 0.00
376_T 211_Y 0.85 0.14 0.00
49_T 229_F 0.85 0.13 0.00
59_R 143_L 0.85 0.13 0.00
300_L 87_L 0.84 0.13 0.00
302_F 178_V 0.84 0.13 0.00
240_Q 24_G 0.84 0.13 0.00
179_A 176_L 0.84 0.13 0.00
166_D 21_G 0.84 0.13 0.00
415_R 33_V 0.84 0.13 0.00
115_I 50_W 0.84 0.13 0.00
223_T 141_L 0.83 0.13 0.00
158_L 93_L 0.83 0.13 0.00
326_G 137_D 0.83 0.13 0.00
30_D 23_I 0.83 0.13 0.00
389_A 233_I 0.83 0.13 0.00
313_Y 148_I 0.82 0.13 0.00
333_E 74_G 0.82 0.12 0.00
168_S 177_I 0.82 0.12 0.00
53_V 251_A 0.82 0.12 0.00
274_E 167_G 0.81 0.12 0.00
101_F 232_L 0.81 0.12 0.00
318_A 51_M 0.81 0.12 0.00
236_D 148_I 0.81 0.12 0.00
317_Q 28_M 0.81 0.12 0.00
373_K 162_A 0.81 0.12 0.00
171_L 225_T 0.81 0.12 0.00
157_Y 211_Y 0.81 0.12 0.00
187_A 20_F 0.80 0.12 0.00
30_D 34_A 0.80 0.12 0.00
30_D 28_M 0.80 0.12 0.00
143_D 19_F 0.79 0.12 0.00
213_G 145_N 0.79 0.12 0.00
156_G 242_Q 0.79 0.11 0.00
173_V 168_D 0.79 0.11 0.00
308_D 177_I 0.78 0.11 0.00
227_V 54_I 0.78 0.11 0.00
339_D 153_G 0.78 0.11 0.00
300_L 60_L 0.77 0.11 0.00
55_E 74_G 0.77 0.11 0.00
33_L 68_A 0.77 0.11 0.00
260_R 202_A 0.77 0.11 0.00
186_T 60_L 0.77 0.11 0.00
429_R 85_I 0.77 0.11 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
4034 0.43 cIp_1_4_cIV_C_4 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4033 0.58 cIp_1_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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