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OPENSEQ.org
cIV_C_4_cI_Ld500_560_20_1_Pdenitr
Genes: A B A+B
Length: 273 642 888
Sequences: 2888 2007 584
Seq/Len: 10.58 3.13 0.66
MirrorTree (Pazo et al. 2001) 0.36
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 0.07
5 0.00 0.00 0.18
10 0.00 0.00 0.29
20 0.00 0.00 0.34
100 0.00 0.01 0.38
∞ 0.01 0.03 0.64
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
34_W 119_F 1.43 0.59 0.00
98_V 293_V 1.35 0.53 0.00
204_V 360_S 1.29 0.48 0.00
90_F 374_Y 1.23 0.43 0.00
221_I 618_L 1.23 0.42 0.00
25_F 618_L 1.22 0.42 0.00
37_G 630_V 1.21 0.41 0.00
179_V 229_F 1.20 0.40 0.00
210_Y 196_S 1.19 0.39 0.00
50_M 476_G 1.18 0.39 0.00
268_I 488_V 1.18 0.39 0.00
158_A 202_I 1.15 0.37 0.00
59_L 74_I 1.14 0.36 0.00
166_G 168_A 1.14 0.35 0.00
52_L 38_L 1.14 0.35 0.00
98_V 297_A 1.11 0.34 0.00
29_T 495_G 1.11 0.33 0.00
90_F 228_G 1.11 0.33 0.00
251_A 86_V 1.10 0.33 0.00
70_V 233_V 1.10 0.32 0.00
50_M 96_M 1.06 0.30 0.00
66_W 273_F 1.05 0.29 0.00
61_V 242_L 1.05 0.29 0.00
33_A 429_W 1.04 0.29 0.00
98_V 444_R 1.04 0.28 0.00
104_W 273_F 1.03 0.28 0.00
84_I 242_L 1.03 0.28 0.00
25_F 286_P 1.03 0.28 0.00
180_I 479_A 1.01 0.27 0.00
64_G 340_A 1.01 0.27 0.00
154_A 436_C 1.01 0.27 0.00
191_Y 553_L 1.00 0.26 0.00
142_L 275_V 1.00 0.26 0.00
251_A 625_M 0.99 0.25 0.00
252_W 140_Q 0.99 0.25 0.00
4_K 381_I 0.98 0.25 0.00
210_Y 377_L 0.98 0.25 0.00
70_V 178_V 0.97 0.24 0.00
140_L 400_I 0.97 0.24 0.00
26_V 135_A 0.97 0.24 0.00
186_T 170_M 0.97 0.24 0.00
157_W 140_Q 0.96 0.24 0.00
229_V 64_V 0.96 0.23 0.00
108_F 160_Y 0.96 0.23 0.00
153_V 554_Y 0.96 0.23 0.00
183_V 477_V 0.95 0.23 0.00
25_F 135_A 0.95 0.23 0.00
169_K 68_F 0.95 0.23 0.00
155_V 291_F 0.94 0.23 0.00
88_Y 481_G 0.93 0.22 0.00
210_Y 381_I 0.92 0.21 0.00
98_V 188_F 0.92 0.21 0.00
158_A 529_L 0.92 0.21 0.00
126_V 551_P 0.92 0.21 0.00
169_K 529_L 0.92 0.21 0.00
262_L 204_R 0.92 0.21 0.00
69_V 503_D 0.91 0.21 0.00
114_Y 303_A 0.91 0.21 0.00
138_W 36_L 0.91 0.20 0.00
204_V 198_Q 0.91 0.20 0.00
103_A 371_M 0.90 0.20 0.00
229_V 89_T 0.90 0.20 0.00
121_P 357_G 0.89 0.20 0.00
35_M 181_F 0.89 0.19 0.00
62_M 190_I 0.89 0.19 0.00
63_F 41_L 0.89 0.19 0.00
157_W 273_F 0.89 0.19 0.00
21_A 542_L 0.88 0.19 0.00
232_I 18_L 0.88 0.19 0.00
180_I 420_A 0.88 0.19 0.00
4_K 275_V 0.88 0.19 0.00
134_T 74_I 0.87 0.19 0.00
265_F 364_A 0.87 0.18 0.00
31_A 615_S 0.87 0.18 0.00
265_F 567_Y 0.87 0.18 0.00
133_V 365_M 0.86 0.18 0.00
51_F 202_I 0.86 0.18 0.00
125_G 513_A 0.86 0.18 0.00
7_D 243_L 0.86 0.18 0.00
270_I 243_L 0.86 0.18 0.00
90_F 66_G 0.86 0.18 0.00
201_A 432_V 0.86 0.18 0.00
8_Y 448_L 0.86 0.18 0.00
245_V 187_I 0.85 0.18 0.00
222_I 182_G 0.85 0.18 0.00
182_G 141_M 0.85 0.17 0.00
215_F 319_Y 0.85 0.17 0.00
215_F 233_V 0.85 0.17 0.00
71_N 292_I 0.85 0.17 0.00
222_I 281_L 0.84 0.17 0.00
238_Q 512_H 0.84 0.17 0.00
210_Y 527_L 0.84 0.17 0.00
240_T 289_K 0.84 0.17 0.00
6_H 97_Y 0.83 0.17 0.00
169_K 87_V 0.83 0.17 0.00
210_Y 336_V 0.83 0.17 0.00
48_P 13_S 0.83 0.16 0.00
252_W 267_M 0.83 0.16 0.00
188_L 421_Y 0.82 0.16 0.00
199_G 36_L 0.82 0.16 0.00
18_F 476_G 0.82 0.16 0.00
109_I 91_S 0.82 0.16 0.00
217_G 62_W 0.82 0.16 0.00
116_M 483_V 0.82 0.16 0.00
88_Y 124_F 0.82 0.16 0.00
210_Y 230_L 0.82 0.16 0.00
197_A 18_L 0.81 0.16 0.00
135_F 434_A 0.81 0.16 0.00
24_A 297_A 0.81 0.16 0.00
135_F 305_T 0.81 0.16 0.00
90_F 417_I 0.81 0.16 0.00
88_Y 150_V 0.81 0.16 0.00
92_L 122_L 0.81 0.16 0.00
53_I 420_A 0.81 0.16 0.00
266_V 392_T 0.81 0.16 0.00
50_M 292_I 0.81 0.16 0.00
56_V 626_V 0.81 0.15 0.00
9_Q 363_H 0.81 0.15 0.00
90_F 177_R 0.81 0.15 0.00
114_Y 174_I 0.80 0.15 0.00
169_K 14_L 0.80 0.15 0.00
179_V 517_V 0.80 0.15 0.00
90_F 80_T 0.80 0.15 0.00
73_G 212_T 0.80 0.15 0.00
90_F 452_G 0.80 0.15 0.00
271_W 372_R 0.80 0.15 0.00
102_V 87_V 0.80 0.15 0.00
210_Y 386_W 0.80 0.15 0.00
187_G 69_H 0.80 0.15 0.00
108_F 408_A 0.80 0.15 0.00
123_K 366_H 0.80 0.15 0.00
222_I 371_M 0.79 0.15 0.00
146_L 471_M 0.79 0.15 0.00
102_V 615_S 0.79 0.15 0.00
232_I 449_T 0.79 0.15 0.00
173_N 571_F 0.79 0.15 0.00
34_W 307_G 0.79 0.15 0.00
182_G 143_F 0.79 0.15 0.00
135_F 135_A 0.79 0.15 0.00
68_D 411_L 0.79 0.15 0.00
12_P 303_A 0.79 0.15 0.00
166_G 553_L 0.79 0.15 0.00
47_G 315_R 0.78 0.14 0.00
36_K 315_R 0.78 0.14 0.00
62_M 373_N 0.78 0.14 0.00
228_F 285_A 0.78 0.14 0.00
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
3203 3.81 cIV_C_4_cI_Ld500_560_20_8_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.38 Done - Shared
3202 3.83 cIV_C_4_cI_Ld500_560_10_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
3198 0.66 cIV_C_4_cI_Ld500_560_10_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3197 0.66 cIV_C_4_cI_Ld500_560_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3196 0.65 cIV_C_4_cI_Ld500_560_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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