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OPENSEQ.org
cIp_4_40_isp_2_human
Genes: A B A+B
Length: 463 275 628
Sequences: 2956 547 99
Seq/Len: 6.38 1.99 0.16
MirrorTree (Pazo et al. 2001) 0.33
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
∞ 0.05 0.00 0.13
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
295_G 119_T 1.52 0.28 0.00
332_C 258_N 1.45 0.26 0.00
281_E 273_I 1.31 0.20 0.00
197_M 212_V 1.30 0.20 0.00
344_I 115_S 1.29 0.19 0.00
232_V 217_V 1.27 0.18 0.00
213_F 67_A 1.26 0.18 0.00
255_L 183_K 1.23 0.17 0.00
108_K 127_A 1.23 0.17 0.00
218_S 184_E 1.21 0.16 0.00
268_W 97_V 1.19 0.16 0.00
434_G 127_A 1.18 0.16 0.00
163_P 273_I 1.17 0.15 0.00
335_E 273_I 1.16 0.15 0.00
126_Y 151_A 1.15 0.15 0.00
214_Y 166_M 1.15 0.15 0.00
162_R 82_T 1.13 0.14 0.00
330_Y 246_A 1.12 0.14 0.00
335_E 167_A 1.11 0.14 0.00
257_E 145_A 1.11 0.14 0.00
368_R 246_A 1.11 0.14 0.00
268_W 138_V 1.10 0.13 0.00
449_A 188_E 1.10 0.13 0.00
330_Y 192_E 1.09 0.13 0.00
436_D 94_R 1.09 0.13 0.00
451_I 174_P 1.09 0.13 0.00
331_L 148_L 1.06 0.12 0.00
436_D 117_L 1.04 0.12 0.00
101_L 82_T 1.04 0.12 0.00
438_M 64_P 1.03 0.12 0.00
241_M 100_S 1.03 0.12 0.00
153_L 197_R 1.03 0.12 0.00
186_A 167_A 1.03 0.12 0.00
373_T 212_V 1.03 0.12 0.00
276_G 196_L 1.02 0.12 0.00
63_P 217_V 1.02 0.11 0.00
344_I 166_M 1.02 0.11 0.00
232_V 145_A 1.01 0.11 0.00
205_E 184_E 1.01 0.11 0.00
213_F 202_D 1.01 0.11 0.00
169_W 89_F 1.01 0.11 0.00
65_P 217_V 1.00 0.11 0.00
400_I 127_A 1.00 0.11 0.00
402_A 127_A 1.00 0.11 0.00
111_P 256_P 0.99 0.11 0.00
339_Q 105_R 0.99 0.11 0.00
274_D 91_E 0.99 0.11 0.00
142_V 199_P 0.98 0.11 0.00
458_F 118_V 0.98 0.10 0.00
330_Y 225_P 0.98 0.10 0.00
76_I 208_K 0.98 0.10 0.00
292_M 105_R 0.98 0.10 0.00
233_H 112_K 0.98 0.10 0.00
187_V 100_S 0.97 0.10 0.00
263_T 119_T 0.97 0.10 0.00
264_N 105_R 0.97 0.10 0.00
347_C 94_R 0.97 0.10 0.00
344_I 111_R 0.97 0.10 0.00
351_M 244_Y 0.97 0.10 0.00
102_S 123_T 0.96 0.10 0.00
400_I 124_V 0.96 0.10 0.00
142_V 198_D 0.96 0.10 0.00
315_E 75_A 0.96 0.10 0.00
364_S 100_S 0.96 0.10 0.00
255_L 263_T 0.95 0.10 0.00
62_K 109_E 0.95 0.10 0.00
163_P 113_G 0.95 0.10 0.00
320_V 109_E 0.95 0.10 0.00
210_M 268_S 0.95 0.10 0.00
205_E 114_F 0.95 0.10 0.00
259_E 162_E 0.95 0.10 0.00
98_V 118_V 0.95 0.10 0.00
377_S 108_S 0.95 0.10 0.00
102_S 168_F 0.95 0.10 0.00
342_R 130_A 0.95 0.10 0.00
232_V 77_V 0.94 0.10 0.00
300_W 66_V 0.94 0.10 0.00
259_E 263_T 0.94 0.10 0.00
217_V 137_F 0.94 0.10 0.00
274_D 100_S 0.94 0.10 0.00
281_E 186_E 0.93 0.10 0.00
127_K 262_P 0.93 0.10 0.00
143_S 146_D 0.93 0.10 0.00
458_F 225_P 0.93 0.09 0.00
264_N 166_M 0.93 0.09 0.00
145_M 183_K 0.93 0.09 0.00
368_R 225_P 0.92 0.09 0.00
109_C 172_G 0.92 0.09 0.00
313_Q 87_P 0.92 0.09 0.00
409_V 102_K 0.92 0.09 0.00
430_A 235_Y 0.92 0.09 0.00
287_G 215_I 0.91 0.09 0.00
396_T 135_T 0.91 0.09 0.00
210_M 188_E 0.91 0.09 0.00
322_S 251_R 0.91 0.09 0.00
181_L 135_T 0.90 0.09 0.00
393_P 105_R 0.90 0.09 0.00
448_V 118_V 0.90 0.09 0.00
206_E 120_G 0.90 0.09 0.00
368_R 196_L 0.90 0.09 0.00
324_G 164_K 0.90 0.09 0.00
108_K 256_P 0.90 0.09 0.00
332_C 119_T 0.89 0.09 0.00
337_M 137_F 0.89 0.09 0.00
451_I 179_H 0.89 0.09 0.00
439_S 264_Y 0.89 0.09 0.00
81_T 249_R 0.89 0.09 0.00
128_T 273_I 0.89 0.09 0.00
431_H 241_G 0.88 0.09 0.00
258_L 273_I 0.88 0.09 0.00
342_R 67_A 0.88 0.09 0.00
315_E 120_G 0.88 0.09 0.00
236_L 132_N 0.88 0.09 0.00
368_R 235_Y 0.88 0.09 0.00
102_S 211_W 0.88 0.09 0.00
162_R 79_Y 0.88 0.09 0.00
453_T 244_Y 0.87 0.08 0.00
147_N 116_Y 0.87 0.08 0.00
330_Y 188_E 0.87 0.08 0.00
274_D 183_K 0.87 0.08 0.00
443_M 187_Q 0.87 0.08 0.00
292_M 64_P 0.87 0.08 0.00
212_E 116_Y 0.86 0.08 0.00
168_Q 273_I 0.86 0.08 0.00
364_S 231_D 0.86 0.08 0.00
358_V 217_V 0.86 0.08 0.00
306_Q 108_S 0.86 0.08 0.00
133_L 100_S 0.85 0.08 0.00
64_P 273_I 0.85 0.08 0.00
133_L 166_M 0.85 0.08 0.00
442_H 63_R 0.85 0.08 0.00
265_N 106_E 0.85 0.08 0.00
81_T 258_N 0.85 0.08 0.00
335_E 114_F 0.85 0.08 0.00
107_R 183_K 0.85 0.08 0.00
339_Q 127_A 0.84 0.08 0.00
252_S 123_T 0.84 0.08 0.00
277_V 114_F 0.84 0.08 0.00
248_S 135_T 0.84 0.08 0.00
82_L 109_E 0.84 0.08 0.00
127_K 227_A 0.84 0.08 0.00
111_P 171_R 0.84 0.08 0.00
198_T 219_T 0.84 0.08 0.00
458_F 139_S 0.84 0.08 0.00
323_R 268_S 0.84 0.08 0.00
448_V 65_L 0.84 0.08 0.00
344_I 76_S 0.83 0.08 0.00
253_L 70_G 0.83 0.08 0.00
313_Q 93_R 0.83 0.08 0.00
201_F 78_C 0.83 0.08 0.00
398_T 134_V 0.83 0.08 0.00
292_M 148_L 0.83 0.08 0.00
80_I 71_L 0.83 0.08 0.00
249_K 202_D 0.83 0.08 0.00
319_P 164_K 0.83 0.08 0.00
276_G 125_G 0.83 0.08 0.00
399_A 145_A 0.83 0.08 0.00
270_N 265_E 0.82 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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