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OPENSEQ.org
cIp_9_40_cIV_B_40
Genes: A B A+B
Length: 163 298 430
Sequences: 644 2549 456
Seq/Len: 3.95 8.55 1.06
MirrorTree (Pazo et al. 2001) 0.54
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 0.01
5 0.00 0.00 0.01
10 0.00 0.01 0.01
20 0.00 0.01 0.02
100 0.00 0.02 0.07
∞ 0.01 0.06 0.99
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
117_A 60_Q 1.22 0.56 0.00
9_T 90_N 1.16 0.50 0.00
73_V 260_V 1.16 0.50 0.00
43_P 268_Y 1.07 0.42 0.00
16_D 124_F 1.06 0.41 0.00
41_K 143_I 1.05 0.40 0.00
90_S 69_Y 1.01 0.36 0.00
18_I 73_A 1.01 0.36 0.00
127_A 168_L 0.97 0.32 0.00
26_R 88_R 0.96 0.32 0.00
31_P 203_V 0.95 0.31 0.00
21_F 284_S 0.94 0.30 0.00
155_N 143_I 0.94 0.30 0.00
160_A 113_V 0.93 0.29 0.00
5_F 175_D 0.92 0.29 0.00
84_E 261_K 0.91 0.28 0.00
21_F 276_K 0.90 0.27 0.00
11_Y 90_N 0.89 0.27 0.00
140_K 77_F 0.89 0.26 0.00
22_G 84_I 0.89 0.26 0.00
24_G 90_N 0.88 0.26 0.00
7_R 145_A 0.88 0.26 0.00
16_D 100_F 0.88 0.26 0.00
121_G 89_F 0.87 0.25 0.00
39_H 89_F 0.87 0.25 0.00
82_D 55_P 0.87 0.25 0.00
44_L 80_L 0.86 0.24 0.00
146_E 266_E 0.86 0.24 0.00
28_F 48_N 0.85 0.23 0.00
26_R 267_K 0.84 0.23 0.00
39_H 265_Q 0.84 0.23 0.00
5_F 87_V 0.82 0.22 0.00
21_F 120_A 0.81 0.21 0.00
139_Q 176_A 0.81 0.21 0.00
25_M 69_Y 0.81 0.21 0.00
43_P 209_I 0.80 0.21 0.00
118_I 271_W 0.80 0.20 0.00
17_F 116_L 0.79 0.20 0.00
141_L 81_L 0.79 0.20 0.00
37_Y 177_G 0.78 0.19 0.00
26_R 113_V 0.78 0.19 0.00
101_T 69_Y 0.78 0.19 0.00
136_Y 254_A 0.78 0.19 0.00
28_F 199_V 0.77 0.19 0.00
18_I 70_I 0.76 0.18 0.00
22_G 91_R 0.76 0.18 0.00
72_A 244_Q 0.76 0.18 0.00
20_G 162_A 0.76 0.18 0.00
21_F 197_K 0.76 0.18 0.00
127_A 267_K 0.76 0.18 0.00
129_E 271_W 0.76 0.18 0.00
18_I 87_V 0.75 0.18 0.00
30_S 53_S 0.75 0.17 0.00
77_Q 49_F 0.74 0.17 0.00
138_K 226_G 0.74 0.17 0.00
83_A 72_T 0.74 0.17 0.00
23_L 121_I 0.73 0.17 0.00
159_D 248_L 0.73 0.17 0.00
26_R 59_D 0.73 0.17 0.00
73_V 31_D 0.73 0.17 0.00
152_I 217_F 0.73 0.16 0.00
47_R 239_G 0.73 0.16 0.00
108_F 74_V 0.72 0.16 0.00
49_R 122_G 0.72 0.16 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
3685 2.1 cIp_9_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3682 1.06 cIp_9_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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