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OPENSEQ.org
cIV_C_60_cI_L_60_1_human
Genes: A B A+B
Length: 261 603 858
Sequences: 2363 2957 2374
Seq/Len: 9.05 4.9 2.77
MirrorTree (Pazo et al. 2001) 0.82
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 0.05
2 0.00 0.00 0.97
5 0.00 0.00 2.54
10 0.00 0.00 2.72
20 0.00 0.00 2.74
100 0.00 0.00 2.74
∞ 0.00 0.00 2.75
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
28_T 460_G 1.28 0.86 0.19
112_L 413_L 1.18 0.80 0.14
8_Y 469_T 1.18 0.80 0.14
127_L 379_A 1.16 0.78 0.13
61_V 451_L 1.14 0.77 0.13
91_V 281_G 1.13 0.75 0.12
167_I 302_V 1.08 0.71 0.11
154_N 322_P 1.07 0.70 0.10
230_K 245_A 1.06 0.69 0.10
209_I 494_T 1.05 0.68 0.10
21_A 188_W 1.05 0.68 0.10
101_F 174_Y 1.00 0.62 0.08
220_I 499_L 0.99 0.62 0.08
185_P 588_F 0.99 0.61 0.08
6_H 134_A 0.97 0.59 0.07
216_T 205_N 0.97 0.58 0.07
62_T 130_I 0.97 0.58 0.07
22_L 591_F 0.97 0.58 0.07
48_L 45_I 0.97 0.58 0.07
53_T 580_Q 0.96 0.58 0.07
61_V 564_K 0.94 0.55 0.07
216_T 592_F 0.94 0.55 0.07
13_P 231_P 0.93 0.54 0.06
125_N 486_L 0.92 0.53 0.06
91_V 410_S 0.92 0.53 0.06
152_M 150_M 0.92 0.53 0.06
167_I 494_T 0.92 0.52 0.06
196_T 379_A 0.91 0.52 0.06
189_S 555_L 0.91 0.51 0.06
55_Y 80_F 0.91 0.51 0.06
42_L 503_D 0.90 0.50 0.06
209_I 364_K 0.90 0.50 0.06
51_T 573_T 0.90 0.50 0.06
192_I 184_L 0.90 0.50 0.06
103_H 327_L 0.89 0.49 0.06
233_F 379_A 0.89 0.49 0.06
220_I 184_L 0.89 0.49 0.06
48_L 567_S 0.89 0.49 0.06
125_N 459_A 0.89 0.49 0.06
96_G 152_F 0.88 0.48 0.05
230_K 130_I 0.88 0.48 0.05
112_L 80_F 0.87 0.47 0.05
27_M 184_L 0.87 0.47 0.05
40_M 463_F 0.87 0.46 0.05
127_L 558_L 0.86 0.46 0.05
125_N 19_I 0.86 0.45 0.05
55_Y 565_T 0.86 0.45 0.05
50_N 447_N 0.86 0.45 0.05
220_I 592_F 0.85 0.45 0.05
174_T 529_Y 0.85 0.44 0.05
139_A 314_M 0.85 0.44 0.05
183_E 311_G 0.85 0.44 0.05
62_T 548_L 0.85 0.44 0.05
65_S 430_T 0.85 0.44 0.05
22_L 528_F 0.84 0.43 0.05
61_V 71_T 0.84 0.43 0.05
27_M 421_A 0.84 0.43 0.05
222_Q 319_I 0.84 0.43 0.04
110_P 424_T 0.83 0.42 0.04
239_A 121_L 0.83 0.42 0.04
191_G 418_L 0.83 0.42 0.04
203_F 314_M 0.83 0.42 0.04
91_V 123_I 0.83 0.42 0.04
48_L 496_L 0.82 0.41 0.04
48_L 283_I 0.82 0.41 0.04
199_V 317_I 0.82 0.41 0.04
65_S 540_L 0.82 0.40 0.04
162_A 130_I 0.82 0.40 0.04
212_S 371_T 0.81 0.40 0.04
217_I 373_L 0.81 0.40 0.04
50_N 581_K 0.81 0.40 0.04
81_Y 186_L 0.81 0.40 0.04
7_A 387_T 0.81 0.40 0.04
153_E 169_I 0.81 0.40 0.04
21_A 231_P 0.81 0.40 0.04
25_L 82_L 0.81 0.40 0.04
47_L 411_I 0.81 0.39 0.04
48_L 500_T 0.81 0.39 0.04
151_L 86_S 0.81 0.39 0.04
217_I 590_S 0.81 0.39 0.04
169_L 397_E 0.81 0.39 0.04
121_I 195_S 0.81 0.39 0.04
143_S 182_F 0.80 0.39 0.04
19_T 321_Q 0.80 0.38 0.04
47_L 548_L 0.80 0.38 0.04
72_T 243_V 0.79 0.37 0.04
223_L 593_F 0.79 0.37 0.04
250_L 136_N 0.79 0.37 0.04
189_S 351_N 0.79 0.37 0.04
80_R 114_I 0.79 0.37 0.04
129_V 103_F 0.78 0.36 0.04
18_L 184_L 0.78 0.36 0.04
61_V 500_T 0.78 0.36 0.04
220_I 79_S 0.78 0.36 0.04
144_I 496_L 0.78 0.36 0.04
218_C 337_A 0.78 0.36 0.04
28_T 231_P 0.78 0.36 0.04
74_P 368_L 0.77 0.35 0.04
76_Q 281_G 0.77 0.35 0.04
29_S 558_L 0.77 0.35 0.04
199_V 387_T 0.77 0.35 0.04
167_I 26_P 0.77 0.35 0.03
25_L 88_M 0.77 0.35 0.03
109_T 71_T 0.77 0.35 0.03
138_L 418_L 0.77 0.34 0.03
256_I 423_S 0.77 0.34 0.03
144_I 123_I 0.76 0.34 0.03
52_L 515_S 0.76 0.34 0.03
96_G 134_A 0.76 0.34 0.03
4_Q 458_A 0.76 0.34 0.03
168_L 17_P 0.76 0.34 0.03
195_S 273_I 0.76 0.34 0.03
144_I 352_N 0.76 0.34 0.03
164_L 172_I 0.76 0.34 0.03
235_F 346_I 0.76 0.34 0.03
53_T 461_S 0.76 0.34 0.03
164_L 506_Y 0.76 0.33 0.03
151_L 327_L 0.75 0.33 0.03
19_T 66_W 0.75 0.33 0.03
192_I 592_F 0.75 0.33 0.03
189_S 417_S 0.75 0.33 0.03
35_F 183_I 0.75 0.33 0.03
52_L 278_L 0.75 0.33 0.03
61_V 123_I 0.75 0.33 0.03
61_V 434_Q 0.75 0.33 0.03
107_A 595_L 0.75 0.33 0.03
160_I 352_N 0.75 0.33 0.03
171_L 167_A 0.75 0.33 0.03
67_Y 500_T 0.75 0.32 0.03
255_S 483_P 0.75 0.32 0.03
55_Y 489_T 0.75 0.32 0.03
103_H 377_S 0.74 0.32 0.03
21_A 396_I 0.74 0.32 0.03
112_L 430_T 0.74 0.32 0.03
28_T 453_P 0.74 0.32 0.03
88_T 461_S 0.74 0.32 0.03
91_V 444_N 0.74 0.32 0.03
253_Y 337_A 0.74 0.32 0.03
61_V 484_L 0.74 0.32 0.03
172_Y 235_S 0.74 0.32 0.03
128_E 150_M 0.74 0.31 0.03
48_L 593_F 0.74 0.31 0.03
104_S 558_L 0.74 0.31 0.03
43_L 463_F 0.74 0.31 0.03
155_N 31_S 0.73 0.31 0.03
261_S 286_L 0.73 0.31 0.03
175_L 414_I 0.73 0.31 0.03
124_L 103_F 0.73 0.31 0.03
48_L 596_I 0.73 0.31 0.03
225_F 214_L 0.73 0.31 0.03
92_L 81_K 0.73 0.31 0.03
135_S 288_A 0.73 0.31 0.03
162_A 123_I 0.73 0.31 0.03
45_L 343_S 0.73 0.31 0.03
5_S 134_A 0.73 0.31 0.03
158_Q 426_M 0.73 0.30 0.03
159_M 510_K 0.73 0.30 0.03
261_S 399_A 0.73 0.30 0.03
209_I 193_S 0.73 0.30 0.03
109_T 353_E 0.72 0.30 0.03
56_Q 342_C 0.72 0.30 0.03
228_T 120_Y 0.72 0.30 0.03
138_L 490_A 0.72 0.30 0.03
182_F 203_L 0.72 0.30 0.03
25_L 521_Y 0.72 0.30 0.03
143_S 424_T 0.72 0.29 0.03
191_G 132_V 0.72 0.29 0.03
101_F 330_C 0.72 0.29 0.03
147_A 499_L 0.72 0.29 0.03
189_S 375_I 0.72 0.29 0.03
162_A 584_I 0.72 0.29 0.03
50_N 588_F 0.71 0.29 0.03
131_L 457_L 0.71 0.29 0.03
162_A 476_S 0.71 0.29 0.03
74_P 488_L 0.71 0.29 0.03
144_I 198_P 0.71 0.29 0.03
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
4446 1.95 cIV_C_20_cI_L_80_1_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.84 Done - Shared
4444 1.94 cIV_C_40_cI_L_80_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.84 Done - Shared
4443 1.94 cIV_C_60_cI_L_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.83 Done - Shared
4442 1.94 cIV_C_80_cI_L_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.69 Done - Shared
4441 2.77 cIV_C_60_cI_L_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.19 Done - Shared
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