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OPENSEQ.org
cIp_4_20_cIV_C_40
Genes: A B A+B
Length: 412 274 666
Sequences: 2346 2529 320
Seq/Len: 5.69 9.23 0.48
MirrorTree (Pazo et al. 2001) 0.48
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 0.02
5 0.01 0.00 0.03
10 0.02 0.00 0.05
20 0.02 0.00 0.08
100 0.03 0.00 0.14
∞ 0.10 0.00 0.47
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
361_V 267_V 1.96 0.83 0.12
102_I 143_L 1.66 0.66 0.06
242_G 207_A 1.38 0.46 0.03
286_E 135_T 1.36 0.44 0.02
384_I 271_I 1.27 0.38 0.02
53_V 92_I 1.26 0.37 0.02
239_M 9_Y 1.26 0.37 0.02
129_N 105_W 1.25 0.36 0.02
208_L 183_G 1.25 0.36 0.02
323_D 148_I 1.18 0.32 0.01
147_P 52_F 1.18 0.31 0.01
134_V 166_E 1.17 0.31 0.01
53_V 126_G 1.16 0.30 0.01
225_V 156_V 1.16 0.30 0.01
388_S 180_V 1.15 0.30 0.01
402_T 29_L 1.15 0.30 0.01
53_V 168_D 1.15 0.30 0.01
29_I 165_L 1.14 0.29 0.01
240_V 105_W 1.12 0.28 0.01
211_E 26_F 1.09 0.26 0.01
98_W 109_F 1.09 0.26 0.01
53_V 147_L 1.09 0.26 0.01
144_L 118_G 1.07 0.25 0.01
219_L 105_W 1.06 0.24 0.01
392_M 246_V 1.06 0.24 0.01
242_G 162_A 1.05 0.23 0.01
298_L 127_V 1.05 0.23 0.01
393_L 205_V 1.04 0.23 0.01
133_G 201_L 1.03 0.23 0.01
102_I 166_E 1.02 0.22 0.01
286_E 223_I 1.02 0.22 0.01
136_T 183_G 1.02 0.22 0.01
53_V 191_A 1.02 0.22 0.01
222_I 32_A 1.01 0.22 0.01
29_I 30_T 1.01 0.22 0.01
262_D 148_I 0.99 0.21 0.01
135_T 89_Y 0.99 0.21 0.01
279_C 57_V 0.98 0.20 0.01
318_A 211_Y 0.98 0.20 0.01
279_C 243_K 0.98 0.20 0.01
309_R 24_G 0.97 0.19 0.01
386_W 159_A 0.96 0.19 0.01
374_R 113_A 0.96 0.19 0.01
303_A 74_G 0.96 0.19 0.01
243_S 60_L 0.95 0.18 0.01
174_F 84_R 0.95 0.18 0.01
327_L 88_Q 0.94 0.18 0.01
296_Q 242_Q 0.94 0.18 0.01
335_T 156_V 0.94 0.18 0.01
262_D 181_I 0.94 0.18 0.01
115_S 156_V 0.94 0.18 0.01
117_I 239_Q 0.94 0.18 0.01
349_V 236_L 0.93 0.18 0.01
383_S 28_M 0.93 0.18 0.01
393_L 139_W 0.93 0.18 0.01
55_R 104_A 0.93 0.18 0.01
27_F 92_I 0.93 0.17 0.01
79_N 222_I 0.93 0.17 0.01
294_A 155_A 0.92 0.17 0.01
211_E 172_T 0.92 0.17 0.01
120_L 219_A 0.92 0.17 0.01
157_L 77_G 0.92 0.17 0.01
127_I 237_K 0.91 0.17 0.01
317_R 19_F 0.91 0.17 0.01
308_A 223_I 0.91 0.17 0.01
224_I 233_I 0.90 0.17 0.01
99_C 269_I 0.90 0.17 0.01
132_M 148_I 0.90 0.16 0.01
294_A 179_A 0.90 0.16 0.01
28_N 71_V 0.90 0.16 0.01
107_G 189_L 0.89 0.16 0.01
270_N 232_L 0.89 0.16 0.01
262_D 206_Y 0.89 0.16 0.01
132_M 158_W 0.89 0.16 0.01
246_A 181_I 0.89 0.16 0.00
222_I 150_L 0.89 0.16 0.00
342_A 141_L 0.89 0.16 0.00
99_C 159_A 0.89 0.16 0.00
245_L 144_I 0.89 0.16 0.00
97_A 141_L 0.89 0.16 0.00
54_E 181_I 0.89 0.16 0.00
165_C 113_A 0.88 0.16 0.00
208_L 47_E 0.88 0.16 0.00
261_F 167_G 0.88 0.16 0.00
386_W 24_G 0.88 0.16 0.00
66_G 137_D 0.88 0.16 0.00
294_A 189_L 0.88 0.16 0.00
297_K 223_I 0.88 0.16 0.00
55_R 175_G 0.88 0.15 0.00
29_I 63_M 0.88 0.15 0.00
133_G 183_G 0.88 0.15 0.00
133_G 115_Y 0.88 0.15 0.00
232_D 24_G 0.87 0.15 0.00
295_V 127_V 0.87 0.15 0.00
136_T 62_V 0.86 0.15 0.00
135_T 118_G 0.86 0.15 0.00
194_W 209_A 0.86 0.15 0.00
136_T 21_G 0.86 0.15 0.00
141_V 219_A 0.86 0.15 0.00
169_L 207_A 0.86 0.15 0.00
176_P 105_W 0.86 0.15 0.00
238_V 166_E 0.86 0.15 0.00
403_L 183_G 0.86 0.15 0.00
205_L 87_L 0.85 0.14 0.00
403_L 239_Q 0.85 0.14 0.00
145_T 130_P 0.85 0.14 0.00
298_L 22_A 0.85 0.14 0.00
298_L 201_L 0.85 0.14 0.00
309_R 134_V 0.84 0.14 0.00
393_L 174_N 0.84 0.14 0.00
390_G 155_A 0.84 0.14 0.00
52_I 189_L 0.84 0.14 0.00
79_N 199_F 0.84 0.14 0.00
313_T 233_I 0.84 0.14 0.00
326_S 71_V 0.83 0.14 0.00
124_I 77_G 0.83 0.14 0.00
367_K 138_P 0.83 0.14 0.00
194_W 109_F 0.83 0.14 0.00
359_Y 91_F 0.83 0.14 0.00
196_E 235_L 0.82 0.13 0.00
53_V 24_G 0.82 0.13 0.00
262_D 168_D 0.82 0.13 0.00
71_M 199_F 0.82 0.13 0.00
401_A 16_I 0.82 0.13 0.00
120_L 65_G 0.82 0.13 0.00
113_R 101_F 0.82 0.13 0.00
110_I 54_I 0.81 0.13 0.00
99_C 235_L 0.81 0.13 0.00
172_A 72_N 0.81 0.13 0.00
296_Q 114_L 0.81 0.13 0.00
319_E 189_L 0.81 0.13 0.00
351_A 90_G 0.81 0.13 0.00
188_L 19_F 0.81 0.13 0.00
135_T 132_G 0.81 0.13 0.00
362_A 25_A 0.81 0.13 0.00
159_I 8_D 0.81 0.13 0.00
112_R 123_I 0.81 0.13 0.00
322_R 183_G 0.81 0.13 0.00
402_T 165_L 0.81 0.13 0.00
374_R 238_G 0.81 0.13 0.00
81_P 194_Y 0.81 0.13 0.00
265_I 192_Y 0.81 0.13 0.00
360_L 14_P 0.81 0.13 0.00
402_T 96_M 0.81 0.13 0.00
29_I 47_E 0.80 0.13 0.00
120_L 159_A 0.80 0.13 0.00
295_V 114_L 0.80 0.13 0.00
45_V 28_M 0.80 0.13 0.00
204_D 154_V 0.80 0.13 0.00
295_V 19_F 0.80 0.13 0.00
120_L 8_D 0.80 0.13 0.00
374_R 78_E 0.80 0.12 0.00
238_V 207_A 0.80 0.12 0.00
137_G 154_V 0.80 0.12 0.00
144_L 89_Y 0.79 0.12 0.00
169_L 85_I 0.79 0.12 0.00
160_F 7_H 0.79 0.12 0.00
201_L 90_G 0.79 0.12 0.00
400_I 103_V 0.79 0.12 0.00
279_C 272_W 0.79 0.12 0.00
183_L 9_Y 0.79 0.12 0.00
183_L 260_V 0.79 0.12 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
4000 0.41 cIp_4_20_cIV_C_60 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3999 0.53 cIp_4_20_cIV_C_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3998 0.52 cIp_4_10_cIV_C_40 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3997 0.48 cIp_4_20_cIV_C_40 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3996 0.47 cIp_4_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3995 0.62 cIp_4_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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