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cytb_40_cIV_B_40_Hsal
Genes: A B A+B
Length: 270 255 434
Sequences: 1515 3468 761
Seq/Len: 5.61 13.6 1.75
MirrorTree (Pazo et al. 2001) 0.71
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.01 0.07
2 0.03 0.01 0.10
5 0.03 0.01 0.28
10 0.03 0.01 0.65
20 0.03 0.02 0.71
100 0.03 0.03 0.84
∞ 0.03 0.10 1.45
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
67_N 159_V 1.36 0.81 0.07
95_S 41_N 1.21 0.70 0.05
222_Q 178_S 1.19 0.68 0.04
178_V 213_T 1.18 0.67 0.04
91_V 84_T 1.13 0.62 0.04
175_I 130_T 1.11 0.60 0.04
140_L 153_A 1.09 0.58 0.03
91_V 172_L 1.06 0.55 0.03
189_T 149_S 1.05 0.53 0.03
167_E 83_I 1.04 0.53 0.03
95_S 224_Q 1.03 0.52 0.03
159_V 178_S 1.01 0.49 0.03
85_S 106_Q 1.00 0.49 0.03
251_T 87_V 1.00 0.48 0.03
180_L 45_L 0.97 0.46 0.02
252_T 164_M 0.97 0.45 0.02
166_K 182_I 0.96 0.44 0.02
189_T 245_V 0.95 0.43 0.02
106_S 245_V 0.95 0.43 0.02
240_L 241_Y 0.94 0.42 0.02
107_A 197_V 0.94 0.42 0.02
136_F 35_E 0.93 0.41 0.02
85_S 227_S 0.93 0.41 0.02
224_M 245_V 0.93 0.41 0.02
231_G 92_V 0.93 0.41 0.02
78_L 102_G 0.93 0.41 0.02
33_W 57_G 0.92 0.40 0.02
233_A 126_V 0.92 0.39 0.02
151_A 227_S 0.91 0.39 0.02
236_Q 54_L 0.91 0.39 0.02
87_L 128_V 0.91 0.39 0.02
231_G 164_M 0.89 0.37 0.02
231_G 77_E 0.89 0.37 0.02
32_V 170_T 0.88 0.36 0.02
179_L 96_V 0.88 0.36 0.02
227_G 198_P 0.88 0.35 0.02
108_A 84_T 0.87 0.34 0.02
122_C 241_Y 0.86 0.34 0.01
251_T 210_E 0.85 0.33 0.01
177_I 28_Q 0.85 0.33 0.01
250_V 164_M 0.85 0.33 0.01
43_Y 50_P 0.84 0.33 0.01
216_V 54_L 0.84 0.32 0.01
137_L 47_A 0.83 0.31 0.01
170_E 72_A 0.82 0.31 0.01
263_M 107_T 0.82 0.30 0.01
184_M 175_R 0.82 0.30 0.01
124_V 169_D 0.81 0.29 0.01
97_A 217_Y 0.81 0.29 0.01
213_I 45_L 0.81 0.29 0.01
228_F 204_L 0.81 0.29 0.01
236_Q 162_Q 0.81 0.29 0.01
189_T 233_I 0.80 0.28 0.01
189_T 153_A 0.79 0.28 0.01
34_L 128_V 0.79 0.28 0.01
40_I 91_V 0.79 0.27 0.01
168_P 77_E 0.79 0.27 0.01
46_L 87_V 0.79 0.27 0.01
106_S 30_Q 0.78 0.27 0.01
180_L 131_I 0.78 0.27 0.01
157_L 73_K 0.78 0.27 0.01
222_Q 95_F 0.78 0.27 0.01
181_S 126_V 0.78 0.26 0.01
179_L 242_E 0.78 0.26 0.01
36_R 130_T 0.77 0.26 0.01
179_L 126_V 0.77 0.26 0.01
223_L 225_G 0.77 0.26 0.01
222_Q 49_L 0.77 0.26 0.01
193_L 181_V 0.77 0.26 0.01
95_S 54_L 0.76 0.25 0.01
140_L 211_E 0.76 0.25 0.01
100_G 154_T 0.76 0.25 0.01
42_D 94_L 0.76 0.25 0.01
171_V 164_M 0.76 0.25 0.01
83_F 211_E 0.76 0.25 0.01
94_I 211_E 0.76 0.25 0.01
91_V 240_T 0.76 0.25 0.01
267_A 144_E 0.75 0.24 0.01
223_L 101_Y 0.75 0.24 0.01
132_N 31_S 0.75 0.24 0.01
48_E 90_A 0.75 0.24 0.01
241_L 164_M 0.74 0.24 0.01
172_N 185_F 0.74 0.24 0.01
107_A 239_D 0.74 0.23 0.01
150_A 221_F 0.74 0.23 0.01
44_L 187_A 0.74 0.23 0.01
104_S 237_D 0.73 0.23 0.01
91_V 166_V 0.73 0.23 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)
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