May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_B_80_cI_L_60_1_human
Genes: A B A+B
Length: 227 603 821
Sequences: 1814 2957 2364
Seq/Len: 7.99 4.9 2.88
MirrorTree (Pazo et al. 2001) 0.86
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 0.00 0.02
2 0.00 0.00 0.03
5 0.00 0.00 1.10
10 0.00 0.00 2.81
20 0.00 0.00 2.83
100 0.00 0.00 2.84
∞ 0.00 0.00 2.85
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
61_M 167_A 1.34 0.90 0.35
143_V 495_F 1.25 0.86 0.28
27_A 404_T 1.14 0.78 0.21
144_L 104_S 1.13 0.77 0.20
140_N 104_S 1.13 0.77 0.20
97_I 122_L 1.10 0.74 0.19
99_S 153_L 1.08 0.72 0.18
156_S 588_F 1.08 0.72 0.17
82_R 337_A 1.08 0.72 0.17
38_V 337_A 1.07 0.71 0.17
61_M 316_T 1.06 0.70 0.17
9_L 132_V 1.04 0.68 0.15
9_L 341_M 1.02 0.65 0.14
153_M 324_L 1.00 0.64 0.14
74_V 356_I 1.00 0.63 0.13
86_M 416_T 1.00 0.63 0.13
23_F 315_V 1.00 0.63 0.13
76_I 152_F 0.99 0.63 0.13
153_M 180_I 0.99 0.62 0.13
86_M 396_I 0.98 0.61 0.13
165_V 177_I 0.98 0.61 0.12
156_S 394_H 0.97 0.60 0.12
72_I 404_T 0.97 0.60 0.12
9_L 74_T 0.96 0.58 0.12
43_F 510_K 0.96 0.58 0.11
84_L 345_S 0.96 0.58 0.11
107_T 95_F 0.95 0.57 0.11
129_E 496_L 0.94 0.57 0.11
160_L 95_F 0.93 0.56 0.10
26_H 337_A 0.93 0.55 0.10
42_L 432_T 0.92 0.54 0.10
33_L 583_M 0.92 0.54 0.10
8_G 460_G 0.92 0.53 0.10
67_I 379_A 0.91 0.53 0.10
174_A 407_W 0.91 0.53 0.10
154_I 199_Q 0.91 0.53 0.10
100_I 27_N 0.90 0.52 0.09
149_P 152_F 0.90 0.52 0.09
175_I 412_T 0.90 0.51 0.09
64_V 564_K 0.90 0.51 0.09
32_F 312_L 0.89 0.51 0.09
188_R 136_N 0.89 0.51 0.09
21_I 379_A 0.88 0.49 0.09
155_T 541_G 0.88 0.49 0.09
75_L 327_L 0.88 0.49 0.09
72_I 448_P 0.87 0.48 0.08
156_S 282_A 0.87 0.47 0.08
160_L 477_H 0.86 0.47 0.08
156_S 387_T 0.86 0.46 0.08
61_M 101_M 0.86 0.46 0.08
214_I 399_A 0.86 0.46 0.08
210_V 356_I 0.86 0.46 0.08
167_T 46_I 0.85 0.46 0.08
100_I 426_M 0.85 0.46 0.08
165_V 508_T 0.85 0.46 0.08
164_A 454_I 0.85 0.45 0.08
189_P 370_S 0.84 0.45 0.07
41_A 296_N 0.84 0.45 0.07
82_R 324_L 0.84 0.45 0.07
160_L 383_M 0.84 0.44 0.07
92_D 540_L 0.84 0.44 0.07
21_I 257_I 0.84 0.44 0.07
160_L 153_L 0.84 0.44 0.07
167_T 195_S 0.84 0.44 0.07
215_P 376_G 0.83 0.43 0.07
154_I 46_I 0.83 0.43 0.07
64_V 469_T 0.83 0.43 0.07
63_T 430_T 0.83 0.43 0.07
26_H 150_M 0.83 0.43 0.07
9_L 371_T 0.83 0.43 0.07
97_I 55_M 0.83 0.42 0.07
192_Y 488_L 0.82 0.42 0.07
129_E 411_I 0.82 0.42 0.07
52_N 530_P 0.82 0.42 0.07
27_A 383_M 0.82 0.42 0.07
189_P 591_F 0.82 0.42 0.07
87_T 420_S 0.82 0.42 0.07
215_P 550_L 0.82 0.41 0.07
172_T 375_I 0.82 0.41 0.07
128_L 275_T 0.81 0.41 0.07
155_T 167_A 0.81 0.41 0.07
124_P 289_A 0.81 0.41 0.07
193_Y 551_L 0.81 0.41 0.07
74_V 521_Y 0.81 0.40 0.06
90_V 472_I 0.81 0.40 0.06
7_V 69_A 0.81 0.40 0.06
64_V 565_T 0.81 0.40 0.06
64_V 53_M 0.81 0.40 0.06
9_L 421_A 0.80 0.40 0.06
61_M 524_N 0.80 0.39 0.06
71_I 260_L 0.80 0.39 0.06
160_L 325_A 0.80 0.39 0.06
116_L 55_M 0.80 0.39 0.06
28_L 69_A 0.80 0.39 0.06
90_V 281_G 0.80 0.39 0.06
160_L 478_F 0.80 0.39 0.06
100_I 189_F 0.80 0.39 0.06
2_A 534_H 0.80 0.39 0.06
7_V 556_T 0.80 0.39 0.06
43_F 596_I 0.80 0.39 0.06
202_A 433_G 0.79 0.39 0.06
76_I 195_S 0.79 0.39 0.06
114_G 245_A 0.79 0.39 0.06
210_V 137_L 0.79 0.38 0.06
137_D 260_L 0.79 0.38 0.06
27_A 131_L 0.79 0.38 0.06
126_L 55_M 0.79 0.38 0.06
43_F 80_F 0.79 0.38 0.06
160_L 464_A 0.79 0.38 0.06
172_T 431_L 0.79 0.38 0.06
95_L 440_L 0.79 0.38 0.06
58_A 267_A 0.79 0.38 0.06
153_M 215_G 0.78 0.37 0.06
33_L 396_I 0.78 0.37 0.06
38_V 361_G 0.78 0.37 0.06
189_P 321_Q 0.78 0.37 0.06
53_T 556_T 0.78 0.37 0.06
36_F 101_M 0.78 0.37 0.06
193_Y 341_M 0.78 0.37 0.06
143_V 561_L 0.78 0.37 0.06
156_S 277_T 0.78 0.37 0.06
167_T 267_A 0.78 0.36 0.06
132_D 418_L 0.77 0.36 0.06
100_I 579_T 0.77 0.36 0.06
185_T 552_L 0.77 0.36 0.06
96_T 68_W 0.77 0.36 0.06
170_L 263_F 0.76 0.35 0.05
56_S 131_L 0.76 0.35 0.05
38_V 343_S 0.76 0.35 0.05
170_L 464_A 0.76 0.35 0.05
155_T 36_V 0.76 0.35 0.05
123_L 463_F 0.76 0.35 0.05
182_T 601_L 0.76 0.35 0.05
84_L 396_I 0.76 0.34 0.05
131_G 458_A 0.76 0.34 0.05
121_Y 361_G 0.76 0.34 0.05
223_P 270_S 0.75 0.34 0.05
146_I 54_F 0.75 0.34 0.05
116_L 321_Q 0.75 0.34 0.05
144_L 418_L 0.75 0.34 0.05
193_Y 275_T 0.75 0.34 0.05
29_M 375_I 0.75 0.34 0.05
142_V 100_I 0.75 0.34 0.05
193_Y 109_N 0.75 0.34 0.05
192_Y 555_L 0.75 0.34 0.05
170_L 115_N 0.75 0.34 0.05
97_I 592_F 0.75 0.34 0.05
99_S 298_I 0.75 0.33 0.05
217_K 472_I 0.75 0.33 0.05
221_M 575_I 0.75 0.33 0.05
32_F 290_V 0.74 0.33 0.05
41_A 130_I 0.74 0.33 0.05
124_P 291_C 0.74 0.33 0.05
29_M 346_I 0.74 0.33 0.05
217_K 518_C 0.74 0.33 0.05
193_Y 273_I 0.74 0.32 0.05
142_V 552_L 0.74 0.32 0.05
43_F 410_S 0.74 0.32 0.05
89_E 337_A 0.74 0.32 0.05
117_I 26_P 0.73 0.32 0.05
154_I 398_T 0.73 0.32 0.05
8_G 376_G 0.73 0.31 0.05
172_T 365_T 0.73 0.31 0.05
30_I 503_D 0.73 0.31 0.05
113_Y 158_W 0.73 0.31 0.05
99_S 587_Y 0.73 0.31 0.05
9_L 518_C 0.73 0.31 0.05
214_I 506_Y 0.73 0.31 0.05
72_I 364_K 0.73 0.31 0.05
181_Q 347_I 0.73 0.31 0.04
27_A 387_T 0.73 0.31 0.04
153_M 314_M 0.73 0.31 0.04
220_E 327_L 0.73 0.31 0.04
167_T 500_T 0.72 0.31 0.04
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
4657 2.9 cIV_B_60_cI_L_80_2_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.24 Done - Shared
4656 3.62 cIV_B_60_cI_L_80_2_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 2) msa: Jackhmmer (2015_06) 0.26 Done - Shared
4655 3.34 cIV_B_80_cI_L_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 2) msa: Jackhmmer (2015_06) 0.46 Done - Shared
4449 2.05 cIV_B_60_cI_L_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4448 2.88 cIV_B_80_cI_L_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.35 Done - Shared
4447 2.04 cIV_B_80_cI_L_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.91 Done - Shared
Page generated in 0.6668 seconds.