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OPENSEQ.org
cIp_5_40_cIV_A_40
Genes: A B A+B
Length: 207 558 730
Sequences: 946 3242 431
Seq/Len: 4.57 5.81 0.59
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 0.00 0.00 0.01
2 0.00 0.00 0.02
5 0.00 0.01 0.04
10 0.00 0.01 0.05
20 0.00 0.02 0.08
100 0.00 0.03 0.13
∞ 0.00 0.06 0.56
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
124_F 421_V 1.35 0.49 0.00
137_I 219_L 1.18 0.36 0.00
124_F 371_T 1.09 0.30 0.00
126_I 86_L 1.07 0.28 0.00
109_V 97_L 1.05 0.27 0.00
51_R 348_A 1.03 0.26 0.00
109_V 512_F 1.01 0.24 0.00
109_V 497_F 0.95 0.21 0.00
137_I 426_A 0.92 0.20 0.00
170_V 488_I 0.92 0.20 0.00
25_V 188_V 0.91 0.19 0.00
109_V 188_V 0.91 0.19 0.00
160_V 188_V 0.91 0.19 0.00
162_W 372_P 0.91 0.19 0.00
35_T 232_L 0.90 0.18 0.00
170_V 445_G 0.89 0.18 0.00
85_M 349_V 0.89 0.18 0.00
59_S 394_S 0.88 0.18 0.00
130_G 141_G 0.88 0.18 0.00
67_V 238_L 0.88 0.18 0.00
49_F 458_L 0.88 0.18 0.00
22_E 143_A 0.87 0.17 0.00
110_F 439_Q 0.87 0.17 0.00
165_I 488_I 0.87 0.17 0.00
46_L 391_V 0.86 0.17 0.00
139_T 308_M 0.86 0.17 0.00
137_I 151_A 0.86 0.17 0.00
134_L 344_T 0.85 0.16 0.00
132_S 504_I 0.85 0.16 0.00
120_V 221_A 0.84 0.16 0.00
61_L 25_S 0.84 0.16 0.00
65_T 290_I 0.84 0.16 0.00
91_I 228_A 0.84 0.16 0.00
25_V 293_V 0.84 0.16 0.00
166_E 207_M 0.84 0.16 0.00
91_I 191_A 0.83 0.16 0.00
25_V 52_Y 0.83 0.16 0.00
94_K 188_V 0.83 0.15 0.00
166_E 214_L 0.83 0.15 0.00
46_L 33_I 0.82 0.15 0.00
157_Y 436_S 0.82 0.15 0.00
36_V 92_T 0.82 0.15 0.00
168_R 298_A 0.82 0.15 0.00
137_I 191_A 0.81 0.15 0.00
124_F 544_E 0.81 0.15 0.00
81_H 95_G 0.81 0.15 0.00
95_V 141_G 0.81 0.15 0.00
107_I 421_V 0.81 0.15 0.00
51_R 217_V 0.80 0.14 0.00
69_N 524_N 0.80 0.14 0.00
120_V 398_L 0.80 0.14 0.00
132_S 296_T 0.80 0.14 0.00
170_V 219_L 0.79 0.14 0.00
93_V 110_G 0.79 0.14 0.00
81_H 49_F 0.79 0.14 0.00
174_V 527_A 0.79 0.14 0.00
137_I 130_L 0.79 0.14 0.00
109_V 181_L 0.79 0.14 0.00
36_V 294_I 0.79 0.14 0.00
82_L 294_I 0.79 0.14 0.00
155_T 84_G 0.78 0.14 0.00
91_I 198_I 0.78 0.14 0.00
101_E 37_F 0.78 0.14 0.00
83_L 454_I 0.78 0.14 0.00
180_Y 353_I 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
3980 0.77 cIp_5_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3979 0.59 cIp_5_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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