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OPENSEQ.org
cIV_B_60_cI_L_80_2_human
Genes: A B A+B
Length: 227 603 823
Sequences: 2677 2957 2390
Seq/Len: 11.79 4.9 2.9
MirrorTree (Pazo et al. 2001) 0.84
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 1.12
10 0.00 0.00 2.83
20 0.00 0.00 2.85
100 0.00 0.00 2.86
∞ 0.00 0.00 2.88
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 1.29 0.88 0.24
143_V 495_F 1.27 0.87 0.23
140_N 104_S 1.22 0.84 0.20
9_L 132_V 1.06 0.70 0.12
156_S 588_F 1.06 0.70 0.12
27_A 404_T 1.06 0.70 0.12
97_I 122_L 1.05 0.69 0.12
9_L 74_T 1.04 0.68 0.12
144_L 104_S 1.02 0.66 0.11
82_R 337_A 1.02 0.66 0.11
99_S 153_L 1.01 0.65 0.11
175_I 412_T 1.01 0.65 0.11
156_S 394_H 1.01 0.65 0.10
9_L 341_M 1.00 0.64 0.10
156_S 387_T 1.00 0.63 0.10
38_V 337_A 1.00 0.63 0.10
107_T 95_F 0.97 0.61 0.09
86_M 416_T 0.97 0.60 0.09
71_I 260_L 0.97 0.60 0.09
165_V 177_I 0.96 0.59 0.09
74_V 356_I 0.95 0.58 0.09
8_G 460_G 0.95 0.57 0.09
61_M 316_T 0.94 0.56 0.08
64_V 564_K 0.94 0.56 0.08
76_I 152_F 0.94 0.56 0.08
72_I 404_T 0.93 0.55 0.08
21_I 379_A 0.93 0.55 0.08
167_T 46_I 0.92 0.55 0.08
86_M 396_I 0.92 0.54 0.08
154_I 46_I 0.92 0.54 0.08
100_I 426_M 0.92 0.54 0.08
75_L 327_L 0.91 0.53 0.07
23_F 315_V 0.91 0.53 0.07
72_I 448_P 0.91 0.53 0.07
33_L 583_M 0.91 0.53 0.07
43_F 510_K 0.91 0.53 0.07
84_L 345_S 0.90 0.52 0.07
27_A 383_M 0.90 0.52 0.07
61_M 101_M 0.90 0.52 0.07
32_F 312_L 0.90 0.52 0.07
154_I 199_Q 0.90 0.51 0.07
129_E 496_L 0.89 0.50 0.07
153_M 324_L 0.88 0.50 0.07
160_L 477_H 0.88 0.50 0.07
188_R 136_N 0.88 0.49 0.07
172_T 375_I 0.88 0.49 0.07
42_L 432_T 0.88 0.49 0.07
210_V 356_I 0.87 0.48 0.06
9_L 421_A 0.87 0.48 0.06
26_H 150_M 0.87 0.48 0.06
100_I 27_N 0.86 0.47 0.06
189_P 591_F 0.86 0.47 0.06
215_P 376_G 0.86 0.47 0.06
160_L 153_L 0.86 0.46 0.06
210_V 137_L 0.86 0.46 0.06
225_F 537_I 0.86 0.46 0.06
96_T 68_W 0.86 0.46 0.06
67_I 379_A 0.85 0.46 0.06
27_A 131_L 0.85 0.45 0.06
26_H 337_A 0.85 0.45 0.06
149_P 152_F 0.84 0.45 0.06
156_S 277_T 0.84 0.44 0.06
9_L 371_T 0.84 0.44 0.06
221_M 575_I 0.84 0.44 0.06
172_T 431_L 0.84 0.44 0.06
90_V 281_G 0.83 0.43 0.06
192_Y 555_L 0.82 0.42 0.05
160_L 95_F 0.82 0.42 0.05
214_I 399_A 0.82 0.42 0.05
153_M 180_I 0.82 0.41 0.05
61_M 524_N 0.81 0.41 0.05
92_D 540_L 0.81 0.41 0.05
156_S 282_A 0.81 0.41 0.05
84_L 288_A 0.81 0.41 0.05
143_V 90_I 0.81 0.40 0.05
193_Y 551_L 0.81 0.40 0.05
174_A 407_W 0.81 0.40 0.05
155_T 541_G 0.81 0.40 0.05
100_I 189_F 0.80 0.40 0.05
215_P 550_L 0.80 0.40 0.05
2_A 534_H 0.80 0.39 0.05
126_L 55_M 0.80 0.39 0.05
114_G 245_A 0.79 0.39 0.05
28_L 69_A 0.79 0.38 0.05
90_V 472_I 0.79 0.38 0.05
52_N 530_P 0.79 0.38 0.05
156_S 466_F 0.79 0.38 0.05
160_L 325_A 0.79 0.38 0.05
167_T 195_S 0.79 0.38 0.05
32_F 290_V 0.78 0.38 0.04
168_L 500_T 0.78 0.37 0.04
146_I 54_F 0.78 0.37 0.04
47_S 390_Y 0.78 0.37 0.04
41_A 296_N 0.78 0.37 0.04
193_Y 341_M 0.78 0.37 0.04
64_V 53_M 0.78 0.37 0.04
164_A 454_I 0.78 0.37 0.04
38_V 343_S 0.78 0.37 0.04
193_Y 273_I 0.77 0.36 0.04
57_D 150_M 0.77 0.36 0.04
167_T 267_A 0.77 0.36 0.04
64_V 547_N 0.77 0.36 0.04
53_T 556_T 0.77 0.36 0.04
137_D 260_L 0.77 0.36 0.04
33_L 396_I 0.77 0.36 0.04
153_M 215_G 0.77 0.36 0.04
87_T 420_S 0.77 0.36 0.04
63_T 430_T 0.77 0.36 0.04
144_L 418_L 0.77 0.36 0.04
88_D 111_D 0.77 0.36 0.04
95_L 440_L 0.77 0.36 0.04
64_V 317_I 0.77 0.36 0.04
167_T 500_T 0.76 0.35 0.04
151_R 423_S 0.76 0.35 0.04
189_P 321_Q 0.76 0.35 0.04
63_T 100_I 0.76 0.35 0.04
214_I 438_P 0.76 0.35 0.04
211_L 411_I 0.76 0.34 0.04
9_L 518_C 0.76 0.34 0.04
160_L 383_M 0.76 0.34 0.04
202_A 433_G 0.76 0.34 0.04
84_L 386_L 0.76 0.34 0.04
64_V 565_T 0.76 0.34 0.04
155_T 374_T 0.75 0.34 0.04
131_G 99_S 0.75 0.34 0.04
185_T 552_L 0.75 0.34 0.04
99_S 587_Y 0.75 0.34 0.04
56_S 131_L 0.75 0.34 0.04
28_L 301_I 0.75 0.34 0.04
217_K 518_C 0.75 0.34 0.04
165_V 508_T 0.75 0.33 0.04
107_T 352_N 0.75 0.33 0.04
43_F 410_S 0.75 0.33 0.04
127_F 566_I 0.74 0.33 0.04
137_D 402_S 0.74 0.33 0.04
189_P 370_S 0.74 0.33 0.04
97_I 592_F 0.74 0.33 0.04
143_V 561_L 0.74 0.33 0.04
155_T 548_L 0.74 0.33 0.04
116_L 55_M 0.74 0.33 0.04
36_F 101_M 0.74 0.33 0.04
2_A 325_A 0.74 0.33 0.04
182_T 601_L 0.74 0.33 0.04
21_I 257_I 0.74 0.33 0.04
168_L 553_L 0.74 0.33 0.04
153_M 314_M 0.74 0.33 0.04
152_M 399_A 0.74 0.32 0.04
99_S 298_I 0.74 0.32 0.04
51_T 100_I 0.74 0.32 0.04
58_A 267_A 0.74 0.32 0.04
51_T 218_L 0.74 0.32 0.04
193_Y 275_T 0.73 0.32 0.04
76_I 195_S 0.73 0.32 0.04
164_A 486_L 0.73 0.32 0.04
124_P 289_A 0.73 0.32 0.04
64_V 469_T 0.73 0.32 0.04
21_I 217_L 0.73 0.31 0.04
191_V 583_M 0.73 0.31 0.04
215_P 401_M 0.73 0.31 0.04
160_L 478_F 0.72 0.31 0.04
7_V 69_A 0.72 0.31 0.04
97_I 55_M 0.72 0.31 0.04
7_V 556_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
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