May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_C_4_cI_M_20_1_Pdenitr
Genes: A B A+B
Length: 273 513 747
Sequences: 2888 5240 1520
Seq/Len: 10.58 10.21 2.03
MirrorTree (Pazo et al. 2001) 0.72
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 0.06 0.04
2 0.00 0.06 0.10
5 0.00 0.07 1.20
10 0.00 0.08 1.34
20 0.00 0.08 1.40
100 0.00 0.09 1.48
∞ 0.01 0.12 1.93
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
167_D 434_A 1.20 0.73 0.02
232_I 150_I 1.16 0.69 0.02
266_V 113_Y 1.12 0.66 0.02
222_I 313_I 1.12 0.66 0.02
241_Q 132_D 1.06 0.59 0.01
224_T 394_V 1.05 0.58 0.01
58_V 473_L 1.03 0.56 0.01
161_A 348_F 1.01 0.54 0.01
215_F 154_W 1.00 0.53 0.01
23_G 300_S 0.98 0.51 0.01
162_F 429_L 0.98 0.50 0.01
235_L 421_L 0.97 0.49 0.01
136_D 287_Y 0.96 0.48 0.01
203_T 447_I 0.95 0.47 0.01
32_V 260_V 0.94 0.46 0.01
155_V 335_G 0.94 0.46 0.01
121_P 303_A 0.94 0.46 0.01
210_Y 14_V 0.93 0.45 0.01
210_Y 304_L 0.93 0.45 0.01
99_M 251_T 0.93 0.45 0.01
222_I 18_I 0.93 0.44 0.01
53_I 466_I 0.93 0.44 0.01
69_V 180_A 0.93 0.44 0.01
204_V 340_I 0.92 0.44 0.01
235_L 348_F 0.92 0.43 0.01
210_Y 17_I 0.91 0.43 0.01
183_V 276_M 0.91 0.43 0.01
154_A 124_M 0.91 0.42 0.01
180_I 388_F 0.90 0.42 0.01
8_Y 429_L 0.90 0.41 0.01
250_A 159_R 0.90 0.41 0.01
174_G 472_T 0.89 0.41 0.01
228_F 327_G 0.89 0.40 0.01
63_F 81_V 0.89 0.40 0.01
224_T 180_A 0.89 0.40 0.01
201_A 352_A 0.89 0.40 0.01
21_A 220_L 0.88 0.40 0.01
73_G 279_V 0.88 0.39 0.01
140_L 358_G 0.88 0.39 0.01
207_G 163_S 0.88 0.39 0.01
150_L 92_T 0.87 0.38 0.01
140_L 190_T 0.87 0.38 0.01
158_A 365_H 0.86 0.38 0.01
155_V 412_V 0.86 0.38 0.01
135_F 117_F 0.86 0.38 0.01
80_P 189_G 0.86 0.37 0.01
35_M 348_F 0.86 0.37 0.01
57_G 119_V 0.85 0.36 0.01
251_A 396_L 0.85 0.36 0.01
142_L 365_H 0.85 0.36 0.01
150_L 302_V 0.85 0.36 0.01
63_F 196_L 0.85 0.36 0.01
76_G 393_N 0.85 0.36 0.01
206_A 393_N 0.84 0.36 0.01
225_I 221_L 0.84 0.36 0.01
162_F 382_Y 0.84 0.36 0.01
50_M 389_F 0.84 0.35 0.01
218_A 98_L 0.83 0.35 0.01
176_I 392_A 0.83 0.34 0.01
23_G 369_I 0.83 0.34 0.01
135_F 294_I 0.83 0.34 0.01
171_T 400_S 0.82 0.34 0.01
229_V 466_I 0.82 0.33 0.01
260_V 392_A 0.82 0.33 0.01
104_W 265_G 0.81 0.33 0.01
182_G 247_V 0.81 0.33 0.01
162_F 413_F 0.81 0.33 0.01
134_T 399_T 0.81 0.32 0.01
58_V 274_L 0.81 0.32 0.01
187_G 428_I 0.81 0.32 0.01
110_K 273_S 0.81 0.32 0.01
23_G 455_T 0.80 0.32 0.01
18_F 339_A 0.80 0.31 0.01
203_T 472_T 0.80 0.31 0.01
63_F 457_M 0.80 0.31 0.01
207_G 101_L 0.80 0.31 0.01
179_V 150_I 0.80 0.31 0.01
7_D 335_G 0.80 0.31 0.01
108_F 305_A 0.79 0.31 0.01
8_Y 135_L 0.79 0.31 0.01
22_I 187_M 0.79 0.30 0.01
111_N 84_I 0.79 0.30 0.01
8_Y 188_A 0.79 0.30 0.01
57_G 394_V 0.78 0.30 0.01
23_G 226_F 0.78 0.29 0.01
79_T 46_F 0.78 0.29 0.01
27_M 366_T 0.78 0.29 0.01
137_P 420_A 0.78 0.29 0.01
174_G 418_W 0.78 0.29 0.01
58_V 399_T 0.78 0.29 0.01
99_M 270_L 0.77 0.29 0.01
179_V 173_G 0.77 0.29 0.01
177_V 480_R 0.77 0.28 0.01
73_G 272_F 0.77 0.28 0.01
183_V 122_G 0.77 0.28 0.01
166_G 288_V 0.77 0.28 0.01
166_G 458_T 0.77 0.28 0.01
252_W 351_G 0.77 0.28 0.01
204_V 80_G 0.77 0.28 0.01
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
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 0.0655 seconds.