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OPENSEQ.org
cI_2_40_cI_9_40_tt
Genes: A B A+B
Length: 181 182 341
Sequences: 1903 683 764
Seq/Len: 10.51 3.75 2.24
MirrorTree (Pazo et al. 2001) 0.76
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 1.73
10 0.01 0.00 1.89
20 0.01 0.00 1.93
100 0.02 0.00 1.95
∞ 0.04 0.01 2.10
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
150_L 17_L 1.25 0.80 0.07
81_Q 112_A 1.16 0.73 0.05
25_A 67_A 1.10 0.66 0.04
41_I 152_R 1.08 0.65 0.04
82_V 32_A 1.05 0.61 0.04
21_E 134_E 1.04 0.60 0.04
27_I 134_E 1.00 0.56 0.03
24_R 153_T 0.99 0.54 0.03
96_L 2_T 0.98 0.54 0.03
110_E 22_V 0.98 0.54 0.03
77_K 7_A 0.98 0.53 0.03
59_E 60_A 0.96 0.51 0.03
119_V 10_L 0.96 0.51 0.03
62_G 157_V 0.95 0.50 0.03
122_V 112_A 0.94 0.49 0.03
75_T 37_F 0.94 0.48 0.03
105_G 152_R 0.90 0.45 0.02
78_Y 10_L 0.90 0.44 0.02
85_T 95_M 0.90 0.44 0.02
102_E 18_F 0.90 0.44 0.02
62_G 70_V 0.89 0.43 0.02
51_R 7_A 0.89 0.43 0.02
138_D 86_R 0.89 0.43 0.02
104_L 13_T 0.89 0.43 0.02
26_A 91_Y 0.89 0.43 0.02
59_E 94_N 0.88 0.42 0.02
112_T 62_A 0.87 0.41 0.02
26_A 58_L 0.86 0.40 0.02
92_G 10_L 0.86 0.40 0.02
119_V 13_T 0.86 0.40 0.02
55_T 103_L 0.85 0.39 0.02
72_F 154_G 0.84 0.38 0.02
79_H 100_F 0.84 0.38 0.02
70_Y 149_E 0.83 0.37 0.02
11_L 10_L 0.83 0.36 0.02
70_Y 132_G 0.83 0.36 0.02
153_L 146_Q 0.83 0.36 0.02
123_E 41_H 0.82 0.36 0.02
130_T 100_F 0.82 0.35 0.02
107_G 20_K 0.81 0.35 0.02
60_V 134_E 0.81 0.35 0.02
159_A 19_S 0.81 0.34 0.02
6_D 19_S 0.81 0.34 0.02
40_W 83_A 0.81 0.34 0.02
47_E 13_T 0.80 0.33 0.02
156_G 8_Q 0.80 0.33 0.01
60_V 67_A 0.79 0.32 0.01
57_P 150_A 0.79 0.32 0.01
101_T 21_P 0.78 0.32 0.01
130_T 97_R 0.78 0.31 0.01
91_A 66_Y 0.77 0.31 0.01
25_A 103_L 0.77 0.31 0.01
92_G 107_A 0.76 0.30 0.01
121_K 94_N 0.76 0.29 0.01
146_T 14_L 0.76 0.29 0.01
22_G 2_T 0.76 0.29 0.01
97_W 72_P 0.76 0.29 0.01
62_G 75_N 0.76 0.29 0.01
134_I 15_K 0.75 0.29 0.01
159_A 11_G 0.75 0.29 0.01
9_D 19_S 0.75 0.28 0.01
144_C 128_D 0.75 0.28 0.01
86_L 42_V 0.75 0.28 0.01
22_G 48_N 0.74 0.28 0.01
55_T 15_K 0.74 0.28 0.01
125_L 35_P 0.74 0.28 0.01
68_S 31_V 0.74 0.27 0.01
100_L 76_D 0.74 0.27 0.01
5_D 18_F 0.73 0.27 0.01
121_K 41_H 0.73 0.27 0.01
41_I 32_A 0.73 0.27 0.01
104_L 116_G 0.73 0.26 0.01
104_L 9_S 0.73 0.26 0.01
33_R 77_P 0.72 0.26 0.01
30_L 95_M 0.72 0.26 0.01
93_A 73_A 0.72 0.26 0.01
70_Y 65_A 0.72 0.26 0.01
20_P 134_E 0.71 0.25 0.01
84_A 9_S 0.71 0.25 0.01
63_V 11_G 0.71 0.25 0.01
21_E 72_P 0.70 0.24 0.01
51_R 127_S 0.70 0.24 0.01
18_Y 95_M 0.70 0.24 0.01
39_G 150_A 0.70 0.24 0.01
69_Y 111_G 0.70 0.24 0.01
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
4944 2.24 cI_2_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4943 2.36 cI_2_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
4938 2.49 cI_2_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
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