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OPENSEQ.org
cIp_4_20_cIV_3_20
Genes: A B A+B
Length: 463 261 656
Sequences: 2145 2753 372
Seq/Len: 4.63 10.55 0.57
MirrorTree (Pazo et al. 2001) 0.57
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 0.01 0.00 0.05
20 0.02 0.00 0.08
100 0.03 0.00 0.15
∞ 0.09 0.01 0.51
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
155_V 131_L 1.72 0.75 0.01
412_V 254_V 1.68 0.73 0.01
106_V 84_I 1.38 0.50 0.01
295_G 194_G 1.29 0.44 0.01
435_L 258_W 1.26 0.41 0.00
339_Q 132_L 1.23 0.39 0.00
363_V 164_L 1.22 0.38 0.00
197_M 110_P 1.20 0.37 0.00
339_Q 123_P 1.13 0.32 0.00
453_T 28_T 1.13 0.32 0.00
304_K 80_R 1.13 0.32 0.00
188_T 110_P 1.10 0.30 0.00
444_L 161_Q 1.10 0.30 0.00
418_R 126_P 1.10 0.30 0.00
345_A 18_L 1.10 0.30 0.00
264_N 25_L 1.10 0.29 0.00
377_S 62_T 1.09 0.29 0.00
429_F 66_T 1.09 0.29 0.00
444_L 192_I 1.09 0.29 0.00
439_S 167_I 1.08 0.28 0.00
293_L 97_F 1.07 0.28 0.00
278_V 144_I 1.07 0.28 0.00
188_T 120_G 1.06 0.27 0.00
291_V 153_E 1.06 0.27 0.00
277_V 220_I 1.06 0.27 0.00
418_R 168_L 1.04 0.26 0.00
261_L 170_G 1.04 0.26 0.00
101_L 255_S 1.03 0.25 0.00
242_D 39_S 1.01 0.24 0.00
386_T 54_M 1.00 0.24 0.00
106_V 135_S 1.00 0.23 0.00
360_D 122_T 1.00 0.23 0.00
293_L 95_A 1.00 0.23 0.00
272_T 97_F 0.99 0.23 0.00
154_A 27_M 0.98 0.22 0.00
274_D 54_M 0.98 0.22 0.00
106_V 178_A 0.98 0.22 0.00
257_E 129_V 0.98 0.22 0.00
334_V 139_A 0.98 0.22 0.00
182_N 101_F 0.97 0.22 0.00
454_Q 226_H 0.97 0.22 0.00
317_D 18_L 0.97 0.22 0.00
425_K 105_S 0.97 0.22 0.00
386_T 144_I 0.96 0.21 0.00
315_E 136_V 0.96 0.21 0.00
444_L 5_S 0.95 0.21 0.00
152_S 222_Q 0.95 0.21 0.00
155_V 222_Q 0.95 0.21 0.00
339_Q 55_Y 0.94 0.20 0.00
386_T 206_L 0.94 0.20 0.00
217_V 88_T 0.94 0.20 0.00
339_Q 210_I 0.94 0.20 0.00
189_T 20_G 0.94 0.20 0.00
342_R 155_N 0.94 0.20 0.00
320_V 219_F 0.94 0.20 0.00
182_N 78_G 0.94 0.20 0.00
344_I 24_A 0.93 0.20 0.00
200_F 43_L 0.93 0.20 0.00
360_D 23_S 0.93 0.20 0.00
295_G 150_S 0.93 0.20 0.00
259_E 15_P 0.93 0.20 0.00
187_V 153_E 0.92 0.19 0.00
106_V 116_W 0.92 0.19 0.00
449_A 38_H 0.91 0.19 0.00
347_C 176_L 0.90 0.18 0.00
315_E 161_Q 0.90 0.18 0.00
351_M 21_A 0.90 0.18 0.00
370_E 176_L 0.90 0.18 0.00
348_L 136_V 0.90 0.18 0.00
110_D 219_F 0.90 0.18 0.00
339_Q 48_L 0.89 0.18 0.00
225_A 63_R 0.89 0.18 0.00
291_V 194_G 0.89 0.18 0.00
312_D 175_L 0.89 0.18 0.00
374_S 136_V 0.88 0.17 0.00
350_K 210_I 0.88 0.17 0.00
169_W 195_S 0.88 0.17 0.00
102_S 111_Q 0.87 0.17 0.00
173_L 152_M 0.87 0.17 0.00
348_L 132_L 0.86 0.17 0.00
348_L 189_S 0.86 0.17 0.00
272_T 7_A 0.86 0.17 0.00
101_L 194_G 0.86 0.17 0.00
353_P 222_Q 0.86 0.16 0.00
400_I 206_L 0.86 0.16 0.00
280_A 22_L 0.86 0.16 0.00
315_E 33_M 0.86 0.16 0.00
392_P 18_L 0.85 0.16 0.00
152_S 147_A 0.85 0.16 0.00
185_M 136_V 0.85 0.16 0.00
170_I 226_H 0.85 0.16 0.00
430_A 73_P 0.85 0.16 0.00
80_I 84_I 0.85 0.16 0.00
213_F 6_H 0.85 0.16 0.00
152_S 256_I 0.85 0.16 0.00
332_C 48_L 0.84 0.16 0.00
220_A 63_R 0.84 0.16 0.00
126_Y 43_L 0.84 0.16 0.00
160_N 25_L 0.84 0.16 0.00
188_T 81_Y 0.84 0.15 0.00
119_G 16_W 0.84 0.15 0.00
150_A 255_S 0.84 0.15 0.00
411_L 31_L 0.84 0.15 0.00
292_M 8_Y 0.84 0.15 0.00
437_K 147_A 0.84 0.15 0.00
341_L 172_Y 0.84 0.15 0.00
315_E 153_E 0.83 0.15 0.00
449_A 159_M 0.83 0.15 0.00
209_K 66_T 0.83 0.15 0.00
353_P 65_S 0.83 0.15 0.00
412_V 251_F 0.83 0.15 0.00
160_N 176_L 0.83 0.15 0.00
393_P 129_V 0.83 0.15 0.00
431_H 97_F 0.83 0.15 0.00
173_L 7_A 0.83 0.15 0.00
318_V 122_T 0.83 0.15 0.00
150_A 196_T 0.83 0.15 0.00
189_T 53_T 0.82 0.15 0.00
317_D 143_S 0.82 0.15 0.00
157_K 95_A 0.82 0.15 0.00
189_T 170_G 0.82 0.15 0.00
101_L 131_L 0.82 0.15 0.00
348_L 106_L 0.82 0.15 0.00
153_L 131_L 0.82 0.15 0.00
334_V 168_L 0.82 0.15 0.00
373_T 29_S 0.82 0.15 0.00
150_A 27_M 0.81 0.14 0.00
444_L 127_L 0.81 0.14 0.00
332_C 259_W 0.81 0.14 0.00
188_T 23_S 0.81 0.14 0.00
185_M 146_W 0.81 0.14 0.00
369_A 198_F 0.81 0.14 0.00
286_Y 32_T 0.81 0.14 0.00
452_G 130_P 0.81 0.14 0.00
443_M 233_F 0.81 0.14 0.00
257_E 155_N 0.80 0.14 0.00
259_E 63_R 0.80 0.14 0.00
186_A 188_I 0.80 0.14 0.00
157_K 47_L 0.80 0.14 0.00
82_L 29_S 0.80 0.14 0.00
393_P 31_L 0.80 0.14 0.00
144_M 198_F 0.80 0.14 0.00
106_V 158_Q 0.80 0.14 0.00
338_R 69_G 0.79 0.14 0.00
450_I 224_M 0.79 0.14 0.00
150_A 191_G 0.79 0.14 0.00
351_M 28_T 0.79 0.14 0.00
169_W 168_L 0.79 0.14 0.00
82_L 19_T 0.79 0.14 0.00
314_V 171_L 0.79 0.14 0.00
296_S 51_T 0.79 0.14 0.00
107_R 216_T 0.79 0.14 0.00
239_G 112_L 0.79 0.13 0.00
163_P 182_F 0.79 0.13 0.00
295_G 55_Y 0.78 0.13 0.00
304_K 183_E 0.78 0.13 0.00
257_E 223_L 0.78 0.13 0.00
449_A 190_D 0.78 0.13 0.00
174_F 50_N 0.78 0.13 0.00
151_Y 26_L 0.78 0.13 0.00
445_A 32_T 0.78 0.13 0.00
78_K 253_Y 0.78 0.13 0.00
82_L 152_M 0.78 0.13 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
4312 0.57 cIp_4_20_cIV_3_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4311 0.48 cIp_4_4_cIV_3_4 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4309 0.65 cIp_4_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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