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OPENSEQ.org
cIV_B_80_cI_L_80_1_human
Genes: A B A+B
Length: 227 603 823
Sequences: 1814 2111 1678
Seq/Len: 7.99 3.5 2.04
MirrorTree (Pazo et al. 2001) 0.85
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 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.35
10 0.00 0.00 1.99
20 0.00 0.00 2.01
100 0.00 0.00 2.02
∞ 0.00 0.00 2.02
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
155_T 167_A 1.83 0.98 0.91
61_M 167_A 1.82 0.98 0.90
23_F 315_V 1.64 0.95 0.83
27_A 383_M 1.55 0.93 0.78
9_L 132_V 1.43 0.89 0.69
140_N 104_S 1.43 0.88 0.69
110_Y 302_V 1.42 0.88 0.68
213_L 426_M 1.38 0.86 0.65
165_V 495_F 1.36 0.85 0.63
28_L 426_M 1.35 0.85 0.62
61_M 524_N 1.35 0.85 0.62
156_S 588_F 1.34 0.84 0.61
150_I 177_I 1.32 0.83 0.59
160_L 383_M 1.28 0.80 0.55
144_L 104_S 1.24 0.76 0.51
72_I 404_T 1.22 0.75 0.49
52_N 530_P 1.22 0.75 0.49
75_L 327_L 1.21 0.74 0.48
214_I 352_N 1.20 0.73 0.47
156_S 277_T 1.20 0.73 0.47
67_I 532_I 1.19 0.72 0.45
107_T 352_N 1.18 0.71 0.44
154_I 379_A 1.17 0.71 0.44
9_L 421_A 1.15 0.69 0.42
92_D 540_L 1.14 0.68 0.41
100_I 579_T 1.13 0.67 0.40
6_Q 341_M 1.13 0.67 0.40
140_N 72_Q 1.13 0.67 0.40
154_I 199_Q 1.11 0.64 0.37
8_G 460_G 1.10 0.64 0.36
64_V 469_T 1.10 0.64 0.36
8_G 376_G 1.10 0.64 0.36
153_M 559_E 1.10 0.63 0.36
123_L 500_T 1.10 0.63 0.36
87_T 258_F 1.09 0.62 0.35
167_T 195_S 1.09 0.62 0.35
100_I 27_N 1.08 0.62 0.35
167_T 505_N 1.08 0.61 0.34
167_T 568_Q 1.07 0.60 0.33
213_L 172_I 1.06 0.59 0.32
20_L 137_L 1.05 0.59 0.32
154_I 424_T 1.05 0.59 0.32
170_L 198_P 1.05 0.58 0.32
193_Y 185_A 1.05 0.58 0.31
127_F 370_S 1.05 0.58 0.31
9_L 74_T 1.05 0.58 0.31
97_I 44_F 1.04 0.58 0.31
165_V 48_L 1.04 0.58 0.31
211_L 82_L 1.04 0.57 0.31
111_T 173_L 1.04 0.57 0.30
44_L 390_Y 1.03 0.56 0.30
193_Y 131_L 1.03 0.56 0.30
160_L 509_N 1.03 0.56 0.29
113_Y 158_W 1.03 0.56 0.29
155_T 63_I 1.03 0.56 0.29
155_T 36_V 1.03 0.56 0.29
100_I 595_L 1.02 0.55 0.28
220_E 327_L 1.01 0.55 0.28
167_T 46_I 1.01 0.55 0.28
9_L 571_I 1.01 0.54 0.28
154_I 46_I 1.01 0.54 0.28
86_M 588_F 1.01 0.54 0.28
73_L 584_I 1.00 0.53 0.27
27_A 571_I 1.00 0.52 0.26
186_A 82_L 0.99 0.52 0.26
49_K 375_I 0.99 0.51 0.25
220_E 158_W 0.98 0.51 0.25
70_A 261_I 0.98 0.50 0.25
27_A 136_N 0.98 0.50 0.25
76_I 195_S 0.97 0.50 0.24
143_V 57_L 0.97 0.49 0.24
100_I 426_M 0.97 0.49 0.24
86_M 416_T 0.97 0.49 0.24
73_L 428_L 0.96 0.49 0.24
170_L 115_N 0.96 0.48 0.23
154_I 564_K 0.96 0.48 0.23
138_V 39_I 0.96 0.48 0.23
143_V 495_F 0.96 0.48 0.23
186_A 486_L 0.96 0.48 0.23
153_M 564_K 0.96 0.48 0.23
153_M 585_K 0.95 0.48 0.23
55_I 390_Y 0.95 0.47 0.22
100_I 201_M 0.95 0.47 0.22
30_I 503_D 0.95 0.47 0.22
127_F 566_I 0.95 0.47 0.22
217_K 70_T 0.95 0.47 0.22
37_L 286_L 0.94 0.47 0.22
192_Y 182_F 0.94 0.47 0.22
64_V 173_L 0.94 0.47 0.22
185_T 552_L 0.94 0.46 0.22
133_L 447_N 0.94 0.46 0.22
64_V 183_I 0.94 0.46 0.21
52_N 418_L 0.94 0.46 0.21
218_I 564_K 0.94 0.46 0.21
41_A 584_I 0.93 0.46 0.21
154_I 553_L 0.93 0.46 0.21
143_V 266_L 0.93 0.45 0.21
16_I 544_T 0.93 0.45 0.21
37_L 451_L 0.93 0.45 0.21
27_A 78_L 0.93 0.45 0.21
100_I 590_S 0.93 0.45 0.20
43_F 410_S 0.93 0.45 0.20
182_T 427_I 0.93 0.45 0.20
165_V 528_F 0.92 0.44 0.20
38_V 337_A 0.92 0.44 0.20
192_Y 552_L 0.92 0.44 0.20
202_A 450_L 0.92 0.44 0.20
163_W 405_N 0.92 0.44 0.20
202_A 390_Y 0.92 0.44 0.20
167_T 556_T 0.91 0.43 0.20
224_V 17_P 0.91 0.43 0.19
140_N 205_N 0.91 0.42 0.19
12_A 106_W 0.91 0.42 0.19
214_I 597_L 0.90 0.42 0.19
90_V 362_L 0.90 0.42 0.19
63_T 574_S 0.90 0.42 0.19
116_L 516_P 0.90 0.42 0.19
45_T 221_A 0.90 0.42 0.19
40_Y 292_A 0.90 0.42 0.18
192_Y 555_L 0.90 0.41 0.18
29_M 376_G 0.90 0.41 0.18
224_V 496_L 0.90 0.41 0.18
40_Y 557_W 0.90 0.41 0.18
74_V 490_A 0.90 0.41 0.18
155_T 541_G 0.90 0.41 0.18
156_S 404_T 0.90 0.41 0.18
182_T 601_L 0.89 0.41 0.18
2_A 552_L 0.89 0.41 0.18
63_T 555_L 0.89 0.41 0.18
23_F 137_L 0.89 0.41 0.18
115_G 566_I 0.89 0.41 0.18
51_T 284_T 0.89 0.40 0.18
22_T 317_I 0.89 0.40 0.18
148_T 235_S 0.89 0.40 0.17
132_D 418_L 0.89 0.40 0.17
223_P 270_S 0.89 0.40 0.17
114_G 414_I 0.88 0.40 0.17
33_L 486_L 0.88 0.40 0.17
148_T 476_S 0.88 0.40 0.17
72_I 343_S 0.88 0.39 0.17
221_M 593_F 0.88 0.39 0.17
10_Q 83_D 0.88 0.39 0.17
58_A 264_H 0.88 0.39 0.17
61_M 201_M 0.87 0.39 0.17
67_I 449_T 0.87 0.39 0.17
100_I 267_A 0.87 0.39 0.16
193_Y 346_I 0.87 0.39 0.16
168_L 211_T 0.87 0.39 0.16
214_I 600_L 0.87 0.39 0.16
150_I 137_L 0.87 0.39 0.16
37_L 99_S 0.87 0.39 0.16
2_A 376_G 0.87 0.38 0.16
168_L 218_L 0.87 0.38 0.16
72_I 318_G 0.86 0.38 0.16
117_I 26_P 0.86 0.38 0.16
188_R 580_Q 0.86 0.38 0.16
140_N 587_Y 0.86 0.38 0.16
148_T 74_T 0.86 0.37 0.16
17_M 176_R 0.86 0.37 0.15
193_Y 341_M 0.86 0.37 0.15
127_F 78_L 0.86 0.37 0.15
192_Y 159_Y 0.86 0.37 0.15
72_I 448_P 0.86 0.37 0.15
192_Y 20_L 0.85 0.37 0.15
186_A 378_L 0.85 0.37 0.15
154_I 208_P 0.85 0.37 0.15
215_P 550_L 0.85 0.37 0.15
10_Q 262_R 0.85 0.37 0.15
73_L 551_L 0.85 0.37 0.15
63_T 570_Q 0.85 0.37 0.15
67_I 54_F 0.85 0.37 0.15
10_Q 136_N 0.85 0.37 0.15
29_M 346_I 0.85 0.36 0.15
27_A 387_T 0.85 0.36 0.15
71_I 14_S 0.85 0.36 0.15
127_F 203_L 0.85 0.36 0.15
61_M 101_M 0.85 0.36 0.15
99_S 290_V 0.84 0.36 0.15
156_S 466_F 0.84 0.36 0.15
6_Q 353_E 0.84 0.36 0.14
148_T 182_F 0.84 0.36 0.14
143_V 203_L 0.84 0.35 0.14
41_A 130_I 0.84 0.35 0.14
35_C 296_N 0.84 0.35 0.14
138_V 540_L 0.84 0.35 0.14
23_F 391_S 0.84 0.35 0.14
140_N 327_L 0.83 0.35 0.14
214_I 504_L 0.83 0.35 0.14
89_E 83_D 0.83 0.35 0.14
9_L 118_F 0.83 0.35 0.14
113_Y 139_Q 0.83 0.35 0.14
71_I 346_I 0.83 0.34 0.14
64_V 59_Q 0.83 0.34 0.14
30_I 527_G 0.83 0.34 0.14
19_E 181_G 0.83 0.34 0.14
89_E 262_R 0.83 0.34 0.14
155_T 46_I 0.82 0.34 0.13
95_L 596_I 0.82 0.34 0.13
74_V 521_Y 0.82 0.34 0.13
51_T 135_N 0.82 0.34 0.13
19_E 174_Y 0.82 0.33 0.13
127_F 185_A 0.82 0.33 0.13
167_T 431_L 0.82 0.33 0.13
123_L 137_L 0.82 0.33 0.13
168_L 553_L 0.82 0.33 0.13
167_T 570_Q 0.82 0.33 0.13
127_F 375_I 0.82 0.33 0.13
70_A 457_L 0.82 0.33 0.13
170_L 533_T 0.82 0.33 0.13
90_V 383_M 0.82 0.33 0.13
64_V 204_L 0.81 0.33 0.13
180_N 284_T 0.81 0.33 0.13
71_I 267_A 0.81 0.33 0.13
175_I 349_N 0.81 0.33 0.13
43_F 82_L 0.81 0.33 0.13
210_V 137_L 0.81 0.33 0.13
150_I 63_I 0.81 0.33 0.13
156_S 387_T 0.81 0.33 0.13
100_I 562_L 0.81 0.33 0.13
217_K 576_I 0.81 0.33 0.13
47_S 525_M 0.81 0.33 0.13
213_L 27_N 0.81 0.32 0.13
75_L 182_F 0.81 0.32 0.13
112_D 558_L 0.81 0.32 0.13
138_V 104_S 0.81 0.32 0.12
116_L 350_L 0.81 0.32 0.12
30_I 363_L 0.81 0.32 0.12
167_T 411_I 0.81 0.32 0.12
27_A 276_L 0.81 0.32 0.12
162_S 122_L 0.81 0.32 0.12
71_I 515_S 0.81 0.32 0.12
43_F 424_T 0.81 0.32 0.12
9_L 518_C 0.81 0.32 0.12
100_I 528_F 0.81 0.32 0.12
165_V 177_I 0.80 0.32 0.12
107_T 389_F 0.80 0.32 0.12
71_I 532_I 0.80 0.32 0.12
52_N 53_M 0.80 0.32 0.12
205_S 300_K 0.80 0.32 0.12
174_A 158_W 0.80 0.32 0.12
115_G 42_S 0.80 0.31 0.12
51_T 567_S 0.80 0.31 0.12
187_T 473_S 0.80 0.31 0.12
11_D 330_C 0.80 0.31 0.12
189_P 90_I 0.80 0.31 0.12
38_V 501_A 0.80 0.31 0.12
150_I 26_P 0.80 0.31 0.12
154_I 573_T 0.80 0.31 0.12
8_G 421_A 0.79 0.31 0.12
16_I 364_K 0.79 0.31 0.12
187_T 597_L 0.79 0.31 0.12
7_V 271_P 0.79 0.31 0.12
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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