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OPENSEQ.org
cIp_4_4_isp_2_human
Genes: A B A+B
Length: 463 275 619
Sequences: 3882 547 111
Seq/Len: 8.38 1.99 0.18
MirrorTree (Pazo et al. 2001) 0.11
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.01 0.00 0.01
∞ 0.07 0.00 0.15
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
436_D 94_R 1.46 0.28 0.00
264_N 79_Y 1.34 0.23 0.00
232_V 217_V 1.34 0.23 0.00
332_C 258_N 1.34 0.23 0.00
344_I 115_S 1.25 0.19 0.00
154_A 248_G 1.23 0.18 0.00
393_P 96_E 1.22 0.18 0.00
264_N 166_M 1.20 0.17 0.00
335_E 167_A 1.20 0.17 0.00
281_E 66_V 1.19 0.17 0.00
242_D 80_S 1.19 0.17 0.00
241_M 100_S 1.19 0.17 0.00
168_Q 273_I 1.17 0.17 0.00
213_F 67_A 1.16 0.16 0.00
443_M 125_G 1.15 0.16 0.00
259_E 162_E 1.12 0.15 0.00
107_R 266_F 1.12 0.15 0.00
368_R 246_A 1.11 0.15 0.00
218_S 184_E 1.10 0.14 0.00
264_N 129_A 1.09 0.14 0.00
111_P 256_P 1.07 0.14 0.00
434_G 179_H 1.06 0.13 0.00
335_E 273_I 1.06 0.13 0.00
205_E 114_F 1.06 0.13 0.00
197_M 212_V 1.03 0.12 0.00
331_L 148_L 1.02 0.12 0.00
108_K 127_A 1.02 0.12 0.00
127_K 262_P 1.01 0.12 0.00
142_V 199_P 1.00 0.12 0.00
369_A 264_Y 1.00 0.12 0.00
402_A 174_P 1.00 0.12 0.00
153_L 197_R 1.00 0.12 0.00
367_K 213_I 0.99 0.12 0.00
344_I 111_R 0.99 0.12 0.00
414_D 97_V 0.99 0.12 0.00
322_S 251_R 0.99 0.11 0.00
255_L 183_K 0.99 0.11 0.00
162_R 82_T 0.98 0.11 0.00
274_D 91_E 0.98 0.11 0.00
436_D 264_Y 0.98 0.11 0.00
397_Y 117_L 0.98 0.11 0.00
330_Y 246_A 0.97 0.11 0.00
255_L 263_T 0.97 0.11 0.00
106_V 268_S 0.97 0.11 0.00
162_R 117_L 0.96 0.11 0.00
344_I 166_M 0.96 0.11 0.00
347_C 100_S 0.96 0.11 0.00
212_E 116_Y 0.95 0.10 0.00
126_Y 151_A 0.93 0.10 0.00
181_L 135_T 0.93 0.10 0.00
157_K 115_S 0.93 0.10 0.00
127_K 227_A 0.93 0.10 0.00
205_E 130_A 0.92 0.10 0.00
169_W 89_F 0.92 0.10 0.00
210_M 109_E 0.92 0.10 0.00
268_W 97_V 0.92 0.10 0.00
187_V 137_F 0.92 0.10 0.00
268_W 138_V 0.92 0.10 0.00
69_V 273_I 0.91 0.10 0.00
287_G 215_I 0.91 0.10 0.00
236_L 269_D 0.91 0.10 0.00
394_G 114_F 0.90 0.10 0.00
262_L 67_A 0.90 0.09 0.00
173_L 84_I 0.90 0.09 0.00
155_V 99_D 0.90 0.09 0.00
163_P 79_Y 0.90 0.09 0.00
431_H 241_G 0.90 0.09 0.00
246_Q 80_S 0.90 0.09 0.00
253_L 70_G 0.89 0.09 0.00
264_N 105_R 0.89 0.09 0.00
344_I 84_I 0.89 0.09 0.00
173_L 231_D 0.89 0.09 0.00
351_M 244_Y 0.88 0.09 0.00
154_A 242_S 0.88 0.09 0.00
154_A 253_G 0.88 0.09 0.00
154_A 254_P 0.88 0.09 0.00
154_A 255_A 0.88 0.09 0.00
326_C 94_R 0.88 0.09 0.00
396_T 135_T 0.88 0.09 0.00
330_Y 192_E 0.88 0.09 0.00
431_H 230_G 0.87 0.09 0.00
217_V 109_E 0.87 0.09 0.00
330_Y 225_P 0.87 0.09 0.00
434_G 127_A 0.87 0.09 0.00
127_K 261_V 0.87 0.09 0.00
358_V 70_G 0.87 0.09 0.00
246_Q 147_V 0.87 0.09 0.00
402_A 127_A 0.87 0.09 0.00
427_P 238_P 0.87 0.09 0.00
427_P 259_L 0.87 0.09 0.00
368_R 235_Y 0.86 0.09 0.00
186_A 167_A 0.86 0.09 0.00
276_G 125_G 0.86 0.09 0.00
109_C 63_R 0.86 0.09 0.00
201_F 106_E 0.86 0.09 0.00
121_E 218_C 0.86 0.09 0.00
121_E 220_H 0.86 0.09 0.00
121_E 223_C 0.86 0.09 0.00
121_E 237_C 0.86 0.09 0.00
121_E 239_C 0.86 0.09 0.00
121_E 240_H 0.86 0.09 0.00
138_R 218_C 0.86 0.09 0.00
138_R 220_H 0.86 0.09 0.00
138_R 223_C 0.86 0.09 0.00
138_R 237_C 0.86 0.09 0.00
138_R 239_C 0.86 0.09 0.00
138_R 240_H 0.86 0.09 0.00
171_R 218_C 0.86 0.09 0.00
171_R 220_H 0.86 0.09 0.00
171_R 223_C 0.86 0.09 0.00
171_R 237_C 0.86 0.09 0.00
171_R 239_C 0.86 0.09 0.00
171_R 240_H 0.86 0.09 0.00
219_G 218_C 0.86 0.09 0.00
219_G 220_H 0.86 0.09 0.00
219_G 223_C 0.86 0.09 0.00
219_G 237_C 0.86 0.09 0.00
219_G 239_C 0.86 0.09 0.00
219_G 240_H 0.86 0.09 0.00
230_G 218_C 0.86 0.09 0.00
230_G 220_H 0.86 0.09 0.00
230_G 223_C 0.86 0.09 0.00
230_G 237_C 0.86 0.09 0.00
230_G 239_C 0.86 0.09 0.00
230_G 240_H 0.86 0.09 0.00
401_E 218_C 0.86 0.09 0.00
401_E 220_H 0.86 0.09 0.00
401_E 223_C 0.86 0.09 0.00
401_E 237_C 0.86 0.09 0.00
401_E 239_C 0.86 0.09 0.00
401_E 240_H 0.86 0.09 0.00
405_G 218_C 0.86 0.09 0.00
405_G 220_H 0.86 0.09 0.00
405_G 223_C 0.86 0.09 0.00
405_G 237_C 0.86 0.09 0.00
405_G 239_C 0.86 0.09 0.00
405_G 240_H 0.86 0.09 0.00
105_M 121_V 0.85 0.09 0.00
255_L 107_S 0.85 0.09 0.00
173_L 137_F 0.85 0.08 0.00
232_V 145_A 0.85 0.08 0.00
127_K 244_Y 0.84 0.08 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
5883 0.18 cIp_4_4_isp_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5882 0.16 cIp_4_40_isp_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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