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OPENSEQ.org
cIV_B_60_cI_L_80_1_human
Genes: A B A+B
Length: 227 603 824
Sequences: 2677 2111 1693
Seq/Len: 11.79 3.5 2.05
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 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.36
10 0.00 0.00 2.00
20 0.00 0.00 2.02
100 0.00 0.00 2.03
∞ 0.00 0.00 2.04
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 1.76 0.97 0.86
155_T 167_A 1.73 0.97 0.85
9_L 132_V 1.56 0.94 0.76
23_F 315_V 1.53 0.92 0.74
27_A 383_M 1.48 0.91 0.70
140_N 104_S 1.42 0.88 0.65
61_M 524_N 1.35 0.84 0.58
110_Y 302_V 1.33 0.84 0.57
156_S 588_F 1.31 0.82 0.54
150_I 177_I 1.29 0.81 0.53
213_L 426_M 1.27 0.79 0.51
160_L 383_M 1.26 0.79 0.50
75_L 327_L 1.26 0.78 0.50
28_L 426_M 1.24 0.77 0.47
72_I 404_T 1.23 0.76 0.47
165_V 495_F 1.21 0.75 0.45
123_L 500_T 1.21 0.74 0.45
156_S 277_T 1.17 0.71 0.41
8_G 460_G 1.17 0.71 0.41
6_Q 341_M 1.17 0.71 0.40
52_N 530_P 1.17 0.70 0.40
153_M 559_E 1.16 0.69 0.39
67_I 532_I 1.15 0.69 0.38
9_L 74_T 1.15 0.69 0.38
144_L 104_S 1.14 0.68 0.37
107_T 352_N 1.14 0.68 0.37
140_N 72_Q 1.14 0.68 0.37
154_I 199_Q 1.13 0.67 0.37
167_T 505_N 1.13 0.67 0.37
193_Y 131_L 1.12 0.66 0.35
9_L 571_I 1.12 0.66 0.35
9_L 421_A 1.11 0.65 0.34
44_L 390_Y 1.11 0.65 0.34
64_V 469_T 1.10 0.64 0.33
192_Y 20_L 1.10 0.64 0.33
127_F 370_S 1.08 0.62 0.32
167_T 568_Q 1.08 0.61 0.31
92_D 540_L 1.07 0.61 0.31
167_T 195_S 1.07 0.61 0.31
100_I 579_T 1.07 0.61 0.31
155_T 36_V 1.07 0.61 0.31
100_I 27_N 1.06 0.59 0.29
170_L 115_N 1.05 0.59 0.29
127_F 566_I 1.05 0.58 0.29
165_V 48_L 1.05 0.58 0.28
167_T 46_I 1.04 0.58 0.28
185_T 552_L 1.03 0.57 0.27
8_G 376_G 1.03 0.56 0.27
214_I 352_N 1.02 0.56 0.26
86_M 588_F 1.02 0.55 0.26
155_T 63_I 1.01 0.55 0.26
160_L 509_N 1.01 0.54 0.25
186_A 82_L 1.01 0.54 0.25
100_I 595_L 1.00 0.53 0.25
20_L 137_L 1.00 0.53 0.24
193_Y 185_A 1.00 0.53 0.24
154_I 564_K 0.99 0.52 0.24
192_Y 555_L 0.98 0.51 0.23
156_S 466_F 0.98 0.51 0.23
27_A 136_N 0.98 0.51 0.23
9_L 488_L 0.98 0.51 0.23
27_A 571_I 0.98 0.51 0.23
63_T 574_S 0.97 0.50 0.22
86_M 416_T 0.97 0.50 0.22
49_K 375_I 0.97 0.50 0.22
217_K 70_T 0.97 0.50 0.22
220_E 327_L 0.97 0.50 0.22
73_L 584_I 0.97 0.50 0.22
113_Y 158_W 0.97 0.50 0.22
223_P 270_S 0.97 0.50 0.22
100_I 426_M 0.97 0.49 0.22
70_A 261_I 0.97 0.49 0.22
192_Y 159_Y 0.96 0.49 0.21
188_R 186_L 0.96 0.49 0.21
97_I 44_F 0.96 0.48 0.21
133_L 447_N 0.96 0.48 0.21
76_I 195_S 0.96 0.48 0.21
73_L 428_L 0.96 0.48 0.21
74_V 490_A 0.95 0.47 0.20
168_L 553_L 0.95 0.47 0.20
154_I 46_I 0.95 0.47 0.20
153_M 585_K 0.95 0.47 0.20
154_I 553_L 0.95 0.47 0.20
167_T 556_T 0.94 0.47 0.20
213_L 172_I 0.94 0.47 0.20
30_I 503_D 0.94 0.46 0.20
224_V 496_L 0.94 0.46 0.20
71_I 267_A 0.94 0.46 0.20
64_V 204_L 0.94 0.46 0.20
140_N 205_N 0.93 0.46 0.19
153_M 564_K 0.93 0.45 0.19
155_T 541_G 0.93 0.45 0.19
218_I 564_K 0.93 0.45 0.18
154_I 379_A 0.92 0.45 0.18
51_T 567_S 0.92 0.44 0.18
202_A 390_Y 0.92 0.44 0.18
43_F 410_S 0.92 0.44 0.18
220_E 158_W 0.92 0.44 0.18
224_V 17_P 0.92 0.44 0.18
211_L 82_L 0.92 0.44 0.18
100_I 201_M 0.92 0.44 0.18
41_A 584_I 0.91 0.43 0.18
10_Q 136_N 0.91 0.43 0.17
221_M 593_F 0.91 0.43 0.17
148_T 476_S 0.91 0.42 0.17
40_Y 292_A 0.91 0.42 0.17
23_F 300_K 0.91 0.42 0.17
111_T 173_L 0.90 0.42 0.17
100_I 590_S 0.90 0.42 0.17
27_A 78_L 0.90 0.42 0.17
154_I 424_T 0.90 0.42 0.17
116_L 516_P 0.90 0.42 0.17
163_W 405_N 0.90 0.42 0.17
192_Y 552_L 0.90 0.42 0.17
186_A 378_L 0.90 0.42 0.17
162_S 122_L 0.90 0.41 0.17
138_V 39_I 0.90 0.41 0.17
2_A 552_L 0.89 0.41 0.16
143_V 266_L 0.89 0.41 0.16
71_I 532_I 0.89 0.41 0.16
52_N 418_L 0.89 0.41 0.16
224_V 23_L 0.89 0.40 0.16
63_T 570_Q 0.88 0.40 0.16
186_A 486_L 0.88 0.40 0.16
72_I 448_P 0.88 0.40 0.16
40_Y 557_W 0.88 0.40 0.15
72_I 177_I 0.88 0.40 0.15
63_T 555_L 0.88 0.40 0.15
192_Y 504_L 0.88 0.39 0.15
29_M 376_G 0.88 0.39 0.15
123_L 16_I 0.87 0.39 0.15
72_I 318_G 0.87 0.39 0.15
193_Y 341_M 0.87 0.39 0.15
89_E 111_D 0.87 0.39 0.15
156_S 387_T 0.87 0.39 0.15
67_I 449_T 0.87 0.39 0.15
115_G 566_I 0.87 0.39 0.15
100_I 574_S 0.87 0.39 0.15
214_I 600_L 0.87 0.38 0.15
115_G 504_L 0.87 0.38 0.15
16_I 544_T 0.87 0.38 0.15
12_A 106_W 0.87 0.38 0.15
115_G 42_S 0.87 0.38 0.15
202_A 450_L 0.87 0.38 0.15
148_T 235_S 0.87 0.38 0.15
160_L 413_L 0.87 0.38 0.15
67_I 54_F 0.86 0.38 0.14
30_I 527_G 0.86 0.38 0.14
58_A 264_H 0.86 0.38 0.14
182_T 601_L 0.86 0.38 0.14
87_T 258_F 0.86 0.37 0.14
9_L 118_F 0.85 0.37 0.14
154_I 481_T 0.85 0.37 0.14
165_V 109_N 0.85 0.37 0.14
127_F 213_L 0.85 0.37 0.14
213_L 27_N 0.85 0.37 0.14
11_D 330_C 0.85 0.36 0.14
167_T 500_T 0.85 0.36 0.14
143_V 317_I 0.85 0.36 0.14
7_V 122_L 0.85 0.36 0.14
71_I 70_T 0.84 0.36 0.13
188_R 136_N 0.84 0.36 0.13
205_S 300_K 0.84 0.36 0.13
168_L 211_T 0.84 0.36 0.13
199_I 385_F 0.84 0.36 0.13
138_V 540_L 0.84 0.36 0.13
43_F 424_T 0.84 0.36 0.13
188_R 580_Q 0.84 0.36 0.13
45_T 221_A 0.84 0.36 0.13
132_D 418_L 0.84 0.36 0.13
64_V 272_L 0.84 0.35 0.13
140_N 433_G 0.84 0.35 0.13
75_L 182_F 0.84 0.35 0.13
127_F 78_L 0.84 0.35 0.13
123_L 68_W 0.84 0.35 0.13
175_I 349_N 0.83 0.35 0.13
214_I 597_L 0.83 0.35 0.13
215_P 550_L 0.83 0.35 0.13
180_N 284_T 0.83 0.35 0.13
23_F 137_L 0.83 0.35 0.13
61_M 474_P 0.83 0.35 0.13
10_Q 262_R 0.83 0.35 0.13
156_S 290_V 0.83 0.35 0.13
150_I 63_I 0.83 0.34 0.12
185_T 191_L 0.83 0.34 0.12
127_F 203_L 0.83 0.34 0.12
168_L 218_L 0.83 0.34 0.12
129_E 496_L 0.83 0.34 0.12
37_L 286_L 0.83 0.34 0.12
192_Y 182_F 0.83 0.34 0.12
55_I 390_Y 0.83 0.34 0.12
142_V 424_T 0.83 0.34 0.12
9_L 461_S 0.83 0.34 0.12
90_V 383_M 0.83 0.34 0.12
165_V 528_F 0.83 0.34 0.12
8_G 421_A 0.82 0.34 0.12
9_L 518_C 0.82 0.34 0.12
183_T 321_Q 0.82 0.34 0.12
90_V 362_L 0.82 0.34 0.12
148_T 74_T 0.82 0.34 0.12
170_L 198_P 0.82 0.34 0.12
73_L 551_L 0.82 0.34 0.12
61_M 101_M 0.82 0.34 0.12
137_D 127_T 0.82 0.33 0.12
155_T 505_N 0.82 0.33 0.12
64_V 173_L 0.82 0.33 0.12
113_Y 139_Q 0.82 0.33 0.12
150_I 268_E 0.82 0.33 0.12
9_L 279_C 0.82 0.33 0.12
211_L 101_M 0.82 0.33 0.12
6_Q 353_E 0.82 0.33 0.12
148_T 182_F 0.82 0.33 0.12
150_I 70_T 0.82 0.33 0.12
213_L 191_L 0.82 0.33 0.12
58_A 555_L 0.81 0.33 0.12
23_F 391_S 0.81 0.33 0.12
217_K 496_L 0.81 0.33 0.12
143_V 495_F 0.81 0.33 0.12
37_L 99_S 0.81 0.33 0.12
9_L 418_L 0.81 0.33 0.12
152_M 245_A 0.81 0.33 0.12
30_I 363_L 0.81 0.33 0.12
64_V 119_K 0.81 0.33 0.12
16_I 364_K 0.81 0.33 0.12
27_A 387_T 0.81 0.33 0.12
165_V 177_I 0.81 0.33 0.12
107_T 428_L 0.81 0.33 0.12
182_T 427_I 0.81 0.33 0.12
165_V 399_A 0.81 0.32 0.11
99_S 290_V 0.81 0.32 0.11
117_I 26_P 0.81 0.32 0.11
78_L 322_P 0.81 0.32 0.11
123_L 137_L 0.81 0.32 0.11
2_A 376_G 0.81 0.32 0.11
221_M 596_I 0.81 0.32 0.11
220_E 555_L 0.81 0.32 0.11
175_I 543_L 0.80 0.32 0.11
140_N 587_Y 0.80 0.32 0.11
51_T 135_N 0.80 0.32 0.11
165_V 417_S 0.80 0.32 0.11
214_I 504_L 0.80 0.32 0.11
71_I 515_S 0.80 0.32 0.11
63_T 582_G 0.80 0.32 0.11
38_V 501_A 0.80 0.32 0.11
10_Q 83_D 0.80 0.32 0.11
187_T 597_L 0.80 0.32 0.11
38_V 327_L 0.80 0.31 0.11
19_E 181_G 0.80 0.31 0.11
226_T 371_T 0.80 0.31 0.11
131_G 161_R 0.80 0.31 0.11
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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