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OPENSEQ.org
cIV_C_4_cI_M_40_1_Pdenitr
Genes: A B A+B
Length: 273 513 749
Sequences: 2888 3566 1405
Seq/Len: 10.58 6.95 1.88
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 0.04
2 0.00 0.01 0.10
5 0.00 0.01 1.17
10 0.00 0.01 1.31
20 0.00 0.01 1.37
100 0.00 0.02 1.42
∞ 0.01 0.03 1.79
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
262_L 113_Y 1.30 0.79 0.05
206_A 393_N 1.28 0.78 0.05
241_Q 132_D 1.17 0.68 0.04
58_V 473_L 1.13 0.64 0.03
32_V 260_V 1.13 0.64 0.03
76_G 393_N 1.10 0.61 0.03
222_I 313_I 1.08 0.59 0.03
251_A 396_L 1.06 0.57 0.03
27_M 411_G 1.06 0.57 0.03
162_F 429_L 1.06 0.57 0.03
121_P 303_A 1.05 0.56 0.02
50_M 117_F 1.04 0.55 0.02
174_G 472_T 1.00 0.51 0.02
167_D 434_A 1.00 0.51 0.02
224_T 394_V 1.00 0.51 0.02
136_D 282_G 0.99 0.49 0.02
161_A 348_F 0.98 0.48 0.02
228_F 421_L 0.98 0.48 0.02
210_Y 17_I 0.98 0.48 0.02
27_M 366_T 0.98 0.48 0.02
136_D 287_Y 0.97 0.48 0.02
229_V 382_Y 0.97 0.47 0.02
154_A 124_M 0.97 0.47 0.02
222_I 18_I 0.96 0.47 0.02
125_G 113_Y 0.95 0.45 0.02
107_A 248_Q 0.95 0.45 0.02
201_A 352_A 0.95 0.45 0.02
99_M 300_S 0.95 0.45 0.02
182_G 343_M 0.94 0.44 0.02
210_Y 14_V 0.94 0.44 0.02
210_Y 21_L 0.94 0.43 0.02
166_G 117_F 0.93 0.43 0.02
73_G 272_F 0.93 0.43 0.02
201_A 236_W 0.93 0.43 0.02
158_A 189_G 0.93 0.43 0.02
182_G 247_V 0.93 0.42 0.02
110_K 273_S 0.92 0.42 0.02
135_F 117_F 0.92 0.42 0.02
247_F 324_V 0.91 0.41 0.02
8_Y 135_L 0.91 0.41 0.01
57_G 230_A 0.91 0.40 0.01
66_W 265_G 0.91 0.40 0.01
203_T 447_I 0.90 0.40 0.01
69_V 296_I 0.90 0.40 0.01
229_V 466_I 0.90 0.39 0.01
23_G 226_F 0.90 0.39 0.01
210_Y 330_A 0.90 0.39 0.01
187_G 428_I 0.89 0.39 0.01
22_I 187_M 0.89 0.39 0.01
225_I 83_G 0.89 0.39 0.01
180_I 422_V 0.89 0.38 0.01
121_P 342_Q 0.89 0.38 0.01
53_I 466_I 0.88 0.38 0.01
166_G 288_V 0.88 0.38 0.01
104_W 265_G 0.88 0.37 0.01
137_P 270_L 0.88 0.37 0.01
155_V 335_G 0.87 0.37 0.01
70_V 84_I 0.87 0.37 0.01
203_T 326_M 0.87 0.36 0.01
23_G 369_I 0.87 0.36 0.01
154_A 322_G 0.86 0.36 0.01
57_G 119_V 0.86 0.36 0.01
182_G 161_Y 0.86 0.36 0.01
250_A 160_I 0.86 0.35 0.01
125_G 110_V 0.86 0.35 0.01
235_L 421_L 0.86 0.35 0.01
25_F 175_V 0.86 0.35 0.01
266_V 110_V 0.85 0.35 0.01
4_K 319_A 0.85 0.35 0.01
122_I 477_V 0.85 0.35 0.01
188_L 17_I 0.85 0.35 0.01
21_A 220_L 0.85 0.35 0.01
195_H 318_V 0.85 0.35 0.01
171_T 400_S 0.85 0.34 0.01
204_V 340_I 0.85 0.34 0.01
21_A 411_G 0.85 0.34 0.01
57_G 301_L 0.85 0.34 0.01
140_L 190_T 0.84 0.34 0.01
250_A 159_R 0.84 0.34 0.01
139_H 229_F 0.84 0.34 0.01
201_A 230_A 0.84 0.34 0.01
62_M 335_G 0.83 0.33 0.01
108_F 305_A 0.83 0.32 0.01
24_A 318_V 0.83 0.32 0.01
57_G 422_V 0.83 0.32 0.01
207_G 101_L 0.82 0.32 0.01
174_G 418_W 0.82 0.32 0.01
176_I 392_A 0.82 0.31 0.01
165_E 90_L 0.81 0.31 0.01
63_F 196_L 0.81 0.31 0.01
51_F 251_T 0.81 0.31 0.01
63_F 81_V 0.81 0.30 0.01
167_D 101_L 0.81 0.30 0.01
265_F 420_A 0.81 0.30 0.01
232_I 67_E 0.81 0.30 0.01
182_G 447_I 0.80 0.30 0.01
228_F 327_G 0.80 0.30 0.01
142_L 365_H 0.80 0.30 0.01
225_I 352_A 0.80 0.30 0.01
171_T 231_V 0.80 0.30 0.01
176_I 282_G 0.80 0.30 0.01
69_V 50_L 0.80 0.30 0.01
83_R 408_T 0.80 0.29 0.01
267_V 342_Q 0.79 0.29 0.01
90_F 435_L 0.79 0.29 0.01
21_A 428_I 0.79 0.29 0.01
251_A 113_Y 0.79 0.28 0.01
225_I 345_S 0.78 0.28 0.01
62_M 297_V 0.78 0.28 0.01
53_I 470_A 0.78 0.28 0.01
123_K 100_I 0.78 0.28 0.01
99_M 251_T 0.78 0.28 0.01
71_N 295_A 0.78 0.28 0.01
229_V 288_V 0.78 0.28 0.01
18_F 37_L 0.78 0.28 0.01
111_N 137_Y 0.78 0.28 0.01
103_A 185_Y 0.78 0.28 0.01
152_G 313_I 0.78 0.28 0.01
73_G 107_Q 0.78 0.28 0.01
204_V 92_T 0.78 0.28 0.01
23_G 111_K 0.78 0.28 0.01
218_A 163_S 0.78 0.28 0.01
91_I 119_V 0.78 0.28 0.01
232_I 407_L 0.78 0.28 0.01
8_Y 188_A 0.77 0.27 0.01
242_K 113_Y 0.77 0.27 0.01
221_I 384_A 0.77 0.27 0.01
121_P 281_S 0.77 0.27 0.01
135_F 180_A 0.77 0.27 0.01
215_F 154_W 0.77 0.27 0.01
170_T 387_M 0.77 0.27 0.01
171_T 318_V 0.77 0.27 0.01
154_A 365_H 0.77 0.27 0.01
111_N 84_I 0.77 0.27 0.01
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
4052 3.95 cIV_C_6_cI_M_80_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
3192 2.03 cIV_C_4_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3191 1.88 cIV_C_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3190 0.82 cIV_C_4_cI_M_60_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3189 3.94 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
3188 4.24 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3187 4.42 cIV_C_4_cI_M_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
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