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OPENSEQ.org
ParB_SMCCTH gremlin
Genes: A B A+B
Length: 282 155 419
Sequences: 2845 2381 785
Seq/Len: 10.09 15.36 1.87
MirrorTree (Pazo et al. 2001) 0.65
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 0.01 0.01 0.00
2 0.11 0.01 0.00
5 0.12 0.01 0.00
10 0.12 0.01 0.00
20 0.13 0.02 0.01
100 0.13 0.03 0.05
∞ 0.13 0.05 1.80
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
142_A 94_E 1.16 0.67 0.01
151_H 63_R 1.15 0.66 0.01
42_F 13_F 1.14 0.65 0.01
180_R 145_V 1.12 0.63 0.01
126_A 74_I 1.09 0.60 0.01
180_R 70_L 1.09 0.60 0.01
237_R 11_S 1.05 0.56 0.01
160_T 51_K 1.01 0.51 0.01
27_K 106_K 1.01 0.51 0.01
7_K 42_E 1.00 0.50 0.01
2_A 41_V 0.99 0.50 0.01
258_G 83_C 0.98 0.48 0.01
264_F 97_V 0.98 0.48 0.01
113_L 19_S 0.97 0.47 0.01
55_L 11_S 0.97 0.47 0.01
116_E 140_S 0.96 0.46 0.01
261_E 116_I 0.94 0.43 0.00
272_R 71_L 0.94 0.43 0.00
96_V 64_A 0.91 0.40 0.00
139_E 127_D 0.90 0.39 0.00
35_P 77_V 0.90 0.39 0.00
264_F 88_V 0.89 0.39 0.00
92_V 43_I 0.89 0.38 0.00
273_I 46_Q 0.89 0.38 0.00
26_I 106_K 0.89 0.38 0.00
145_L 119_R 0.89 0.38 0.00
65_V 6_F 0.88 0.38 0.00
95_I 116_I 0.88 0.38 0.00
34_N 71_L 0.88 0.38 0.00
279_E 132_V 0.88 0.37 0.00
75_V 45_A 0.88 0.37 0.00
123_E 89_E 0.88 0.37 0.00
28_I 144_S 0.87 0.37 0.00
135_D 41_V 0.87 0.37 0.00
67_K 142_V 0.87 0.37 0.00
139_E 114_I 0.87 0.37 0.00
13_F 80_V 0.87 0.36 0.00
63_L 127_D 0.87 0.36 0.00
34_N 91_A 0.86 0.36 0.00
64_I 46_Q 0.86 0.35 0.00
31_L 130_Y 0.86 0.35 0.00
261_E 13_F 0.85 0.35 0.00
107_I 32_D 0.85 0.35 0.00
269_D 78_R 0.85 0.34 0.00
74_I 116_I 0.85 0.34 0.00
265_F 88_V 0.84 0.34 0.00
32_R 58_L 0.84 0.33 0.00
66_R 120_K 0.84 0.33 0.00
123_E 57_L 0.84 0.33 0.00
241_L 95_A 0.84 0.33 0.00
150_P 29_R 0.83 0.33 0.00
123_E 23_G 0.83 0.33 0.00
75_V 20_L 0.83 0.33 0.00
185_L 112_Q 0.83 0.32 0.00
251_I 83_C 0.83 0.32 0.00
134_L 75_L 0.83 0.32 0.00
42_F 122_T 0.82 0.32 0.00
225_K 14_D 0.82 0.31 0.00
114_Q 26_A 0.81 0.30 0.00
266_S 68_I 0.81 0.30 0.00
40_K 142_V 0.81 0.30 0.00
19_S 9_I 0.81 0.30 0.00
113_L 63_R 0.80 0.30 0.00
20_E 149_E 0.80 0.29 0.00
148_S 63_R 0.79 0.29 0.00
176_M 80_V 0.79 0.29 0.00
36_Y 5_T 0.79 0.29 0.00
97_R 135_Q 0.79 0.29 0.00
194_L 69_A 0.79 0.28 0.00
129_S 91_A 0.78 0.28 0.00
142_A 8_Q 0.78 0.28 0.00
199_I 84_V 0.78 0.28 0.00
13_F 119_R 0.78 0.28 0.00
205_V 67_A 0.78 0.28 0.00
248_T 88_V 0.77 0.27 0.00
181_T 45_A 0.77 0.27 0.00
260_I 71_L 0.76 0.26 0.00
252_K 117_T 0.76 0.26 0.00
137_T 65_L 0.76 0.26 0.00
259_K 89_E 0.76 0.26 0.00
183_L 116_I 0.76 0.26 0.00
183_L 126_A 0.76 0.26 0.00
276_L 84_V 0.76 0.26 0.00
64_I 120_K 0.76 0.26 0.00
21_E 42_E 0.76 0.26 0.00
104_M 88_V 0.75 0.25 0.00
207_Q 111_T 0.75 0.25 0.00
10_N 69_A 0.75 0.25 0.00
266_S 100_F 0.74 0.24 0.00
106_E 52_L 0.74 0.24 0.00
260_I 16_V 0.74 0.24 0.00
202_Q 106_K 0.74 0.24 0.00
153_A 105_K 0.74 0.24 0.00
148_S 101_A 0.74 0.24 0.00
63_L 46_Q 0.74 0.24 0.00
212_I 58_L 0.74 0.24 0.00
185_L 10_R 0.73 0.24 0.00
262_I 9_I 0.73 0.23 0.00
94_A 84_V 0.73 0.23 0.00
25_E 144_S 0.73 0.23 0.00
184_G 73_S 0.72 0.23 0.00
116_E 6_F 0.72 0.23 0.00
151_H 55_L 0.72 0.23 0.00
60_L 141_K 0.72 0.23 0.00
127_Y 30_L 0.72 0.23 0.00
211_L 13_F 0.72 0.23 0.00
60_L 107_Y 0.72 0.23 0.00
105_R 76_K 0.72 0.23 0.00
198_V 102_Q 0.72 0.23 0.00
65_V 84_V 0.72 0.23 0.00
195_V 119_R 0.72 0.23 0.00
204_N 26_A 0.72 0.23 0.00
146_G 55_L 0.72 0.23 0.00
138_Q 43_I 0.72 0.23 0.00
126_A 111_T 0.72 0.23 0.00
201_E 122_T 0.72 0.23 0.00
41_H 94_E 0.71 0.23 0.00
155_H 80_V 0.71 0.23 0.00
120_P 30_L 0.71 0.23 0.00
33_P 30_L 0.71 0.22 0.00
95_I 144_S 0.71 0.22 0.00
26_I 34_N 0.71 0.22 0.00
42_F 117_T 0.71 0.22 0.00
123_E 37_L 0.71 0.22 0.00
233_V 26_A 0.70 0.22 0.00
171_E 124_E 0.70 0.22 0.00
162_P 100_F 0.70 0.22 0.00
13_F 89_E 0.70 0.22 0.00
194_L 64_A 0.70 0.21 0.00
37_Q 52_L 0.70 0.21 0.00
247_T 63_R 0.70 0.21 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)
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