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OPENSEQ.org
S2SLF1_S3RNase_10JH
Genes: A B A+B
Length: 330 222 491
Sequences: 2800 1915 63
Seq/Len: 8.48 8.63 0.13
MirrorTree (Pazo et al. 2001) 0.16
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 0.21 0.01 0.05
2 0.24 0.01 0.06
5 0.27 0.01 0.06
10 0.28 0.01 0.06
20 0.28 0.01 0.08
100 0.32 0.01 0.11
∞ 0.36 0.01 0.24
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
314_L 44_I 1.95 0.45 0.00
197_P 87_L 1.88 0.42 0.00
287_D 24_F 1.51 0.24 0.00
144_W 118_C 1.50 0.24 0.00
61_A 140_D 1.49 0.24 0.00
72_N 91_W 1.41 0.21 0.00
186_M 136_K 1.40 0.20 0.00
181_I 132_A 1.33 0.18 0.00
58_G 112_Y 1.28 0.17 0.00
244_E 67_E 1.24 0.15 0.00
287_D 140_D 1.23 0.15 0.00
144_W 59_P 1.21 0.15 0.00
166_K 169_T 1.18 0.14 0.00
58_G 129_F 1.17 0.14 0.00
75_T 45_C 1.17 0.14 0.00
73_P 152_P 1.16 0.13 0.00
59_L 128_Y 1.16 0.13 0.00
166_K 89_R 1.15 0.13 0.00
73_P 188_L 1.15 0.13 0.00
251_W 108_W 1.15 0.13 0.00
251_W 115_H 1.15 0.13 0.00
251_W 178_C 1.15 0.13 0.00
251_W 194_C 1.15 0.13 0.00
314_L 54_I 1.14 0.13 0.00
62_L 54_I 1.13 0.12 0.00
142_D 111_E 1.12 0.12 0.00
257_I 160_E 1.11 0.12 0.00
142_D 18_S 1.10 0.12 0.00
58_G 108_W 1.10 0.12 0.00
58_G 115_H 1.10 0.12 0.00
58_G 178_C 1.10 0.12 0.00
58_G 194_C 1.10 0.12 0.00
58_G 145_L 1.10 0.12 0.00
184_F 190_E 1.09 0.12 0.00
113_V 169_T 1.09 0.12 0.00
72_N 57_L 1.08 0.12 0.00
191_F 152_P 1.07 0.11 0.00
94_R 30_V 1.07 0.11 0.00
143_S 87_L 1.05 0.11 0.00
314_L 129_F 1.05 0.11 0.00
185_D 152_P 1.05 0.11 0.00
69_I 111_E 1.05 0.11 0.00
73_P 108_W 1.05 0.11 0.00
73_P 115_H 1.05 0.11 0.00
73_P 178_C 1.05 0.11 0.00
73_P 194_C 1.05 0.11 0.00
306_S 192_G 1.04 0.11 0.00
251_W 87_L 1.04 0.10 0.00
309_V 111_E 1.04 0.10 0.00
144_W 108_W 1.03 0.10 0.00
144_W 115_H 1.03 0.10 0.00
144_W 178_C 1.03 0.10 0.00
144_W 194_C 1.03 0.10 0.00
310_Y 152_P 1.03 0.10 0.00
61_A 80_K 1.03 0.10 0.00
61_A 119_S 1.02 0.10 0.00
38_V 193_I 1.02 0.10 0.00
276_L 156_H 1.01 0.10 0.00
70_V 43_N 1.01 0.10 0.00
61_A 92_V 1.01 0.10 0.00
188_T 202_F 1.01 0.10 0.00
240_W 128_Y 1.00 0.10 0.00
251_W 56_G 1.00 0.10 0.00
163_M 138_K 0.99 0.10 0.00
211_L 191_V 0.99 0.10 0.00
181_I 204_D 0.99 0.10 0.00
186_M 191_V 0.99 0.10 0.00
209_Y 156_H 0.99 0.10 0.00
251_W 116_G 0.99 0.10 0.00
72_N 108_W 0.98 0.09 0.00
72_N 115_H 0.98 0.09 0.00
72_N 178_C 0.98 0.09 0.00
72_N 194_C 0.98 0.09 0.00
185_D 108_W 0.98 0.09 0.00
185_D 115_H 0.98 0.09 0.00
185_D 178_C 0.98 0.09 0.00
185_D 194_C 0.98 0.09 0.00
251_W 55_H 0.98 0.09 0.00
251_W 58_W 0.98 0.09 0.00
251_W 38_C 0.98 0.09 0.00
137_C 112_Y 0.98 0.09 0.00
114_R 190_E 0.98 0.09 0.00
59_L 54_I 0.97 0.09 0.00
286_Y 138_K 0.97 0.09 0.00
251_W 118_C 0.97 0.09 0.00
83_A 153_G 0.96 0.09 0.00
271_N 203_H 0.96 0.09 0.00
186_M 27_I 0.96 0.09 0.00
268_V 195_F 0.96 0.09 0.00
70_V 202_F 0.95 0.09 0.00
286_Y 159_G 0.95 0.09 0.00
165_Y 184_G 0.95 0.09 0.00
251_W 91_W 0.95 0.09 0.00
251_W 205_C 0.95 0.09 0.00
58_G 56_G 0.94 0.09 0.00
259_P 59_P 0.94 0.09 0.00
242_M 150_I 0.93 0.09 0.00
110_Y 169_T 0.93 0.09 0.00
93_H 81_D 0.93 0.09 0.00
85_P 176_L 0.93 0.09 0.00
58_G 116_G 0.93 0.09 0.00
139_L 119_S 0.93 0.08 0.00
58_G 55_H 0.93 0.08 0.00
58_G 58_W 0.93 0.08 0.00
265_P 48_I 0.92 0.08 0.00
58_G 38_C 0.92 0.08 0.00
74_A 67_E 0.92 0.08 0.00
147_L 28_Q 0.92 0.08 0.00
70_V 208_S 0.92 0.08 0.00
136_V 168_V 0.92 0.08 0.00
218_F 94_M 0.92 0.08 0.00
216_E 107_L 0.92 0.08 0.00
237_M 37_F 0.91 0.08 0.00
304_S 164_A 0.91 0.08 0.00
58_G 118_C 0.91 0.08 0.00
279_R 166_K 0.91 0.08 0.00
81_L 128_Y 0.91 0.08 0.00
104_D 116_G 0.90 0.08 0.00
75_T 114_K 0.90 0.08 0.00
102_G 145_L 0.90 0.08 0.00
184_F 74_F 0.90 0.08 0.00
185_D 114_K 0.90 0.08 0.00
58_G 205_C 0.90 0.08 0.00
71_L 67_E 0.90 0.08 0.00
254_K 190_E 0.90 0.08 0.00
73_P 128_Y 0.90 0.08 0.00
58_G 91_W 0.89 0.08 0.00
139_L 127_A 0.89 0.08 0.00
195_K 156_H 0.89 0.08 0.00
161_A 130_L 0.89 0.08 0.00
140_S 150_I 0.89 0.08 0.00
186_M 135_L 0.89 0.08 0.00
215_C 90_H 0.89 0.08 0.00
239_I 193_I 0.88 0.08 0.00
61_A 144_T 0.88 0.08 0.00
185_D 33_W 0.88 0.08 0.00
275_L 31_L 0.88 0.08 0.00
73_P 56_G 0.88 0.08 0.00
166_K 85_N 0.87 0.08 0.00
241_V 32_T 0.87 0.08 0.00
144_W 56_G 0.87 0.08 0.00
101_F 116_G 0.87 0.07 0.00
139_L 174_P 0.87 0.07 0.00
150_V 171_N 0.87 0.07 0.00
285_S 176_L 0.87 0.07 0.00
255_Y 89_R 0.87 0.07 0.00
259_P 167_T 0.87 0.07 0.00
101_F 174_P 0.86 0.07 0.00
163_M 121_N 0.86 0.07 0.00
262_I 69_C 0.86 0.07 0.00
191_F 27_I 0.86 0.07 0.00
182_L 163_K 0.86 0.07 0.00
144_W 116_G 0.86 0.07 0.00
314_L 34_P 0.85 0.07 0.00
279_R 141_L 0.85 0.07 0.00
183_C 144_T 0.85 0.07 0.00
315_T 191_V 0.85 0.07 0.00
77_N 190_E 0.85 0.07 0.00
144_W 55_H 0.85 0.07 0.00
144_W 58_W 0.85 0.07 0.00
57_D 53_T 0.85 0.07 0.00
105_T 201_S 0.85 0.07 0.00
73_P 116_G 0.85 0.07 0.00
144_W 38_C 0.85 0.07 0.00
52_L 94_M 0.85 0.07 0.00
112_V 31_L 0.85 0.07 0.00
74_A 68_F 0.85 0.07 0.00
171_W 144_T 0.85 0.07 0.00
73_P 55_H 0.85 0.07 0.00
73_P 58_W 0.85 0.07 0.00
158_V 106_P 0.84 0.07 0.00
73_P 38_C 0.84 0.07 0.00
189_E 134_R 0.84 0.07 0.00
251_W 59_P 0.84 0.07 0.00
275_L 163_K 0.84 0.07 0.00
218_F 65_R 0.84 0.07 0.00
111_K 112_Y 0.84 0.07 0.00
310_Y 188_L 0.84 0.07 0.00
256_T 132_A 0.84 0.07 0.00
73_P 118_C 0.84 0.07 0.00
251_W 52_F 0.84 0.07 0.00
54_G 93_Q 0.84 0.07 0.00
246_G 29_L 0.84 0.07 0.00
201_S 141_L 0.84 0.07 0.00
245_Y 88_E 0.83 0.07 0.00
111_K 108_W 0.83 0.07 0.00
111_K 115_H 0.83 0.07 0.00
111_K 178_C 0.83 0.07 0.00
111_K 194_C 0.83 0.07 0.00
107_S 86_D 0.83 0.07 0.00
106_I 171_N 0.83 0.07 0.00
167_E 140_D 0.83 0.07 0.00
251_W 107_L 0.82 0.07 0.00
144_W 205_C 0.82 0.07 0.00
82_P 164_A 0.82 0.07 0.00
73_P 91_W 0.82 0.07 0.00
144_W 91_W 0.82 0.07 0.00
58_G 54_I 0.82 0.07 0.00
251_W 112_Y 0.82 0.07 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
7846 0.13 S2SLF1_S3RNase_10JH Δgene:(1, 100) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7845 0.02 S2SLF1_S3RNase_10 Δgene:(1, 100) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
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