May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_C_4_cI_M_60_Pdenitr
Genes: A B A+B
Length: 273 513 729
Sequences: 2888 12268 2869
Seq/Len: 10.58 23.91 3.94
MirrorTree (Pazo et al. 2001) 0.46
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 0.57 0.12
2 0.00 0.61 1.26
5 0.00 0.66 2.71
10 0.00 0.67 3.00
20 0.00 0.68 3.05
100 0.00 0.68 3.15
∞ 0.01 0.68 3.65
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
201_A 287_Y 1.27 0.92 0.34
208_A 273_S 1.02 0.75 0.17
8_Y 190_T 0.98 0.71 0.15
266_V 113_Y 0.97 0.69 0.14
265_F 290_W 0.90 0.60 0.11
205_Y 360_I 0.89 0.60 0.11
235_L 412_V 0.88 0.59 0.11
114_Y 84_I 0.88 0.58 0.10
265_F 255_V 0.87 0.57 0.10
138_W 255_V 0.87 0.56 0.10
121_P 293_A 0.86 0.56 0.10
242_K 227_A 0.86 0.56 0.10
10_I 382_Y 0.86 0.55 0.10
123_K 223_L 0.84 0.54 0.09
130_E 435_L 0.84 0.54 0.09
121_P 100_I 0.84 0.53 0.09
147_I 130_A 0.83 0.52 0.09
121_P 50_L 0.82 0.51 0.09
136_D 283_V 0.82 0.51 0.08
33_A 329_F 0.81 0.49 0.08
155_V 151_I 0.81 0.49 0.08
51_F 43_T 0.81 0.49 0.08
108_F 169_Y 0.81 0.49 0.08
179_V 463_W 0.81 0.49 0.08
225_I 345_S 0.81 0.49 0.08
183_V 42_T 0.80 0.48 0.08
239_M 457_M 0.80 0.47 0.08
98_V 93_T 0.80 0.47 0.07
201_A 422_V 0.79 0.47 0.07
172_I 94_F 0.79 0.47 0.07
13_P 240_T 0.79 0.47 0.07
48_P 407_L 0.79 0.46 0.07
53_I 449_E 0.79 0.46 0.07
35_M 365_H 0.79 0.46 0.07
208_A 288_V 0.78 0.45 0.07
165_E 426_G 0.78 0.45 0.07
242_K 463_W 0.78 0.45 0.07
25_F 184_M 0.78 0.45 0.07
201_A 369_I 0.78 0.45 0.07
211_M 89_V 0.78 0.45 0.07
51_F 365_H 0.78 0.44 0.07
27_M 386_F 0.77 0.44 0.07
26_V 183_A 0.77 0.43 0.07
195_H 322_G 0.76 0.43 0.07
61_V 383_A 0.76 0.43 0.07
262_L 186_R 0.76 0.43 0.07
158_A 71_W 0.76 0.42 0.07
61_V 391_M 0.76 0.42 0.07
60_Y 53_L 0.76 0.42 0.06
260_V 266_G 0.76 0.42 0.06
162_F 182_I 0.75 0.42 0.06
7_D 113_Y 0.75 0.41 0.06
181_L 410_M 0.75 0.41 0.06
196_A 169_Y 0.75 0.41 0.06
237_G 276_M 0.75 0.41 0.06
150_L 386_F 0.75 0.41 0.06
169_K 48_I 0.74 0.41 0.06
56_V 377_N 0.74 0.40 0.06
8_Y 438_Y 0.74 0.40 0.06
166_G 100_I 0.74 0.40 0.06
48_P 474_I 0.74 0.40 0.06
99_M 126_G 0.73 0.39 0.06
232_I 283_V 0.73 0.39 0.06
8_Y 188_A 0.73 0.39 0.06
27_M 272_F 0.73 0.39 0.06
30_G 396_L 0.73 0.38 0.06
53_I 369_I 0.73 0.38 0.06
134_T 79_M 0.72 0.38 0.06
103_A 130_A 0.72 0.37 0.06
237_G 335_G 0.72 0.37 0.05
56_V 138_L 0.72 0.37 0.05
8_Y 429_L 0.72 0.37 0.05
262_L 167_F 0.72 0.37 0.05
183_V 58_P 0.72 0.37 0.05
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.68 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
4052 3.95 cIV_C_6_cI_M_80_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
3192 2.03 cIV_C_4_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3191 1.88 cIV_C_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3190 0.82 cIV_C_4_cI_M_60_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3189 3.94 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
3188 4.24 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3187 4.42 cIV_C_4_cI_M_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
Page generated in 0.0293 seconds.