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OPENSEQ.org
cIp_3_40_cIV_C_40
Genes: A B A+B
Length: 674 274 928
Sequences: 1916 2529 357
Seq/Len: 2.84 9.23 0.38
MirrorTree (Pazo et al. 2001) 0.30
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 0.01 0.00 0.01
10 0.01 0.00 0.02
20 0.01 0.00 0.02
100 0.03 0.00 0.06
∞ 0.09 0.00 0.38
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
9_I 271_I 1.45 0.44 0.00
233_I 36_M 1.35 0.38 0.00
241_S 62_V 1.28 0.33 0.00
84_I 32_A 1.24 0.31 0.00
403_V 192_Y 1.23 0.30 0.00
177_M 205_V 1.19 0.28 0.00
171_V 15_S 1.11 0.23 0.00
634_S 20_F 1.09 0.23 0.00
470_N 208_G 1.09 0.22 0.00
252_V 205_V 1.08 0.22 0.00
88_S 269_I 1.06 0.21 0.00
612_A 56_L 1.05 0.20 0.00
324_V 103_V 1.04 0.20 0.00
588_L 71_V 1.04 0.20 0.00
22_L 28_M 1.03 0.20 0.00
147_L 21_G 1.00 0.18 0.00
599_G 247_G 0.98 0.17 0.00
445_V 269_I 0.98 0.17 0.00
402_K 26_F 0.98 0.17 0.00
428_S 22_A 0.98 0.17 0.00
292_N 195_S 0.98 0.17 0.00
195_T 250_A 0.96 0.17 0.00
580_I 187_T 0.96 0.16 0.00
30_G 212_M 0.95 0.16 0.00
298_A 51_M 0.95 0.16 0.00
8_K 211_Y 0.95 0.16 0.00
439_K 241_T 0.94 0.16 0.00
533_R 52_F 0.94 0.16 0.00
248_K 72_N 0.94 0.15 0.00
224_P 168_D 0.93 0.15 0.00
135_Y 19_F 0.93 0.15 0.00
151_V 233_I 0.93 0.15 0.00
551_S 180_V 0.93 0.15 0.00
14_I 27_V 0.92 0.15 0.00
78_E 236_L 0.92 0.15 0.00
431_S 20_F 0.92 0.15 0.00
53_V 45_P 0.91 0.15 0.00
233_I 51_M 0.91 0.15 0.00
580_I 223_I 0.91 0.15 0.00
269_S 252_A 0.90 0.14 0.00
286_R 159_A 0.90 0.14 0.00
378_I 20_F 0.90 0.14 0.00
591_T 178_V 0.89 0.14 0.00
128_Y 204_T 0.89 0.14 0.00
232_S 189_L 0.89 0.14 0.00
546_C 32_A 0.89 0.14 0.00
71_K 208_G 0.89 0.14 0.00
4_L 202_A 0.89 0.14 0.00
9_I 267_V 0.88 0.14 0.00
602_R 226_I 0.88 0.14 0.00
84_I 35_W 0.88 0.14 0.00
82_S 105_W 0.88 0.13 0.00
376_Q 58_G 0.87 0.13 0.00
604_L 180_V 0.87 0.13 0.00
171_V 141_L 0.86 0.13 0.00
23_I 219_A 0.86 0.13 0.00
330_F 172_T 0.86 0.13 0.00
417_A 211_Y 0.86 0.13 0.00
467_L 219_A 0.85 0.13 0.00
611_L 5_K 0.85 0.12 0.00
189_T 89_Y 0.85 0.12 0.00
316_I 267_V 0.84 0.12 0.00
195_T 244_Q 0.84 0.12 0.00
426_L 11_I 0.84 0.12 0.00
23_I 223_I 0.84 0.12 0.00
243_I 175_G 0.83 0.12 0.00
250_R 33_V 0.83 0.12 0.00
439_K 191_A 0.83 0.12 0.00
298_A 28_M 0.82 0.12 0.00
70_V 233_I 0.82 0.12 0.00
307_A 23_I 0.82 0.12 0.00
62_P 31_G 0.82 0.12 0.00
525_I 223_I 0.82 0.12 0.00
567_A 173_I 0.82 0.12 0.00
72_D 141_L 0.82 0.12 0.00
233_I 212_M 0.82 0.12 0.00
340_G 96_M 0.82 0.12 0.00
292_N 229_F 0.82 0.12 0.00
299_S 136_F 0.81 0.12 0.00
97_G 175_G 0.81 0.12 0.00
308_A 113_A 0.81 0.12 0.00
375_I 141_L 0.81 0.11 0.00
181_G 24_G 0.81 0.11 0.00
233_I 34_A 0.81 0.11 0.00
316_I 208_G 0.81 0.11 0.00
635_F 109_F 0.81 0.11 0.00
312_K 184_V 0.81 0.11 0.00
429_L 175_G 0.81 0.11 0.00
190_S 147_L 0.81 0.11 0.00
289_I 196_H 0.81 0.11 0.00
575_K 209_A 0.80 0.11 0.00
240_G 159_A 0.80 0.11 0.00
193_N 13_P 0.80 0.11 0.00
425_A 153_G 0.80 0.11 0.00
399_K 144_I 0.80 0.11 0.00
575_K 153_G 0.80 0.11 0.00
289_I 167_G 0.80 0.11 0.00
575_K 230_V 0.80 0.11 0.00
289_I 26_F 0.80 0.11 0.00
188_I 24_G 0.80 0.11 0.00
89_P 166_E 0.80 0.11 0.00
366_I 144_I 0.80 0.11 0.00
432_R 72_N 0.80 0.11 0.00
393_I 154_V 0.80 0.11 0.00
439_K 32_A 0.80 0.11 0.00
387_P 204_T 0.80 0.11 0.00
25_A 26_F 0.80 0.11 0.00
431_S 138_P 0.80 0.11 0.00
170_E 108_A 0.79 0.11 0.00
13_I 197_A 0.79 0.11 0.00
309_R 162_A 0.79 0.11 0.00
132_F 60_L 0.79 0.11 0.00
586_A 138_P 0.79 0.11 0.00
89_P 27_V 0.79 0.11 0.00
649_A 105_W 0.79 0.11 0.00
83_E 48_G 0.79 0.11 0.00
9_I 21_G 0.79 0.11 0.00
378_I 229_F 0.79 0.11 0.00
398_S 189_L 0.79 0.11 0.00
55_V 56_L 0.79 0.11 0.00
316_I 39_I 0.79 0.11 0.00
274_F 24_G 0.79 0.11 0.00
18_P 70_V 0.78 0.11 0.00
156_T 19_F 0.78 0.11 0.00
500_A 191_A 0.78 0.11 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
4015 0.46 cIp_3_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4013 0.38 cIp_3_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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