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OPENSEQ.org
ParB SMC NTH
Genes: A B A+B
Length: 282 106 382
Sequences: 2845 1038 124
Seq/Len: 10.09 9.79 0.32
MirrorTree (Pazo et al. 2001) 0.58
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 0.00
100 0.13 0.02 0.01
∞ 0.13 0.03 0.32
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
126_A 101_F 1.80 0.64 0.00
110_L 86_V 1.61 0.51 0.00
140_Q 95_E 1.57 0.48 0.00
268_E 24_L 1.49 0.43 0.00
34_N 97_R 1.48 0.42 0.00
232_A 40_V 1.43 0.39 0.00
141_L 14_R 1.42 0.38 0.00
31_L 50_S 1.36 0.34 0.00
208_L 95_E 1.32 0.32 0.00
40_K 27_D 1.26 0.28 0.00
165_I 54_I 1.26 0.28 0.00
237_R 92_S 1.23 0.27 0.00
210_Q 38_V 1.23 0.27 0.00
264_F 77_A 1.23 0.27 0.00
136_L 80_I 1.21 0.26 0.00
113_L 24_L 1.21 0.26 0.00
31_L 16_N 1.21 0.26 0.00
63_L 77_A 1.20 0.25 0.00
126_A 45_Y 1.20 0.25 0.00
35_P 97_R 1.17 0.24 0.00
109_L 78_F 1.17 0.23 0.00
71_G 40_V 1.17 0.23 0.00
94_A 62_K 1.16 0.23 0.00
195_V 4_I 1.16 0.23 0.00
27_K 101_F 1.13 0.22 0.00
132_K 99_S 1.13 0.21 0.00
180_R 12_R 1.12 0.21 0.00
153_A 40_V 1.11 0.21 0.00
169_I 85_K 1.11 0.21 0.00
116_E 89_I 1.11 0.21 0.00
246_G 105_A 1.10 0.20 0.00
101_E 4_I 1.08 0.20 0.00
110_L 71_S 1.06 0.18 0.00
236_E 88_E 1.05 0.18 0.00
35_P 41_T 1.05 0.18 0.00
63_L 1_M 1.04 0.18 0.00
252_K 40_V 1.04 0.18 0.00
168_L 38_V 1.04 0.18 0.00
66_R 100_I 1.04 0.18 0.00
150_P 86_V 1.03 0.17 0.00
113_L 73_L 1.03 0.17 0.00
3_K 95_E 1.03 0.17 0.00
136_L 78_F 1.03 0.17 0.00
91_T 101_F 1.03 0.17 0.00
264_F 43_R 1.03 0.17 0.00
63_L 100_I 1.03 0.17 0.00
237_R 89_I 1.01 0.17 0.00
166_Q 2_E 1.01 0.17 0.00
59_I 89_I 1.00 0.16 0.00
238_E 81_I 1.00 0.16 0.00
49_E 72_G 1.00 0.16 0.00
208_L 7_A 0.99 0.16 0.00
187_N 40_V 0.99 0.16 0.00
129_S 28_D 0.98 0.16 0.00
269_D 97_R 0.98 0.16 0.00
182_L 4_I 0.96 0.15 0.00
174_L 52_F 0.96 0.15 0.00
95_I 100_I 0.96 0.15 0.00
207_Q 99_S 0.95 0.15 0.00
74_I 68_F 0.95 0.14 0.00
174_L 92_S 0.95 0.14 0.00
185_L 96_D 0.94 0.14 0.00
168_L 4_I 0.94 0.14 0.00
10_N 72_G 0.94 0.14 0.00
199_I 65_I 0.94 0.14 0.00
96_V 30_F 0.94 0.14 0.00
148_S 26_N 0.94 0.14 0.00
123_E 84_G 0.93 0.14 0.00
237_R 94_A 0.93 0.14 0.00
241_L 59_C 0.93 0.14 0.00
245_F 79_S 0.93 0.14 0.00
231_D 93_K 0.92 0.14 0.00
262_I 23_T 0.92 0.14 0.00
233_V 90_L 0.92 0.13 0.00
175_S 19_E 0.91 0.13 0.00
4_G 2_E 0.91 0.13 0.00
166_Q 77_A 0.91 0.13 0.00
113_L 26_N 0.90 0.13 0.00
26_I 62_K 0.90 0.13 0.00
261_E 72_G 0.90 0.13 0.00
246_G 18_A 0.90 0.13 0.00
74_I 50_S 0.90 0.13 0.00
127_Y 9_S 0.90 0.13 0.00
150_P 54_I 0.90 0.13 0.00
138_Q 43_R 0.89 0.13 0.00
92_V 100_I 0.89 0.12 0.00
92_V 79_S 0.89 0.12 0.00
243_N 17_L 0.88 0.12 0.00
165_I 17_L 0.88 0.12 0.00
269_D 45_Y 0.88 0.12 0.00
181_T 24_L 0.88 0.12 0.00
180_R 31_L 0.88 0.12 0.00
101_E 92_S 0.88 0.12 0.00
82_R 52_F 0.87 0.12 0.00
270_L 104_A 0.87 0.12 0.00
204_N 38_V 0.87 0.12 0.00
28_I 25_D 0.87 0.12 0.00
1_M 40_V 0.86 0.12 0.00
162_P 70_D 0.86 0.12 0.00
199_I 45_Y 0.86 0.12 0.00
130_L 14_R 0.86 0.12 0.00
59_I 80_I 0.86 0.12 0.00
108_A 86_V 0.86 0.12 0.00
248_T 41_T 0.86 0.12 0.00
253_R 86_V 0.85 0.12 0.00
51_K 85_K 0.85 0.12 0.00
113_L 53_L 0.85 0.12 0.00
127_Y 14_R 0.85 0.12 0.00
134_L 100_I 0.85 0.12 0.00
10_N 73_L 0.85 0.12 0.00
85_K 92_S 0.85 0.12 0.00
151_H 82_S 0.85 0.11 0.00
169_I 22_L 0.85 0.11 0.00
22_T 9_S 0.84 0.11 0.00
35_P 19_E 0.84 0.11 0.00
151_H 36_H 0.84 0.11 0.00
126_A 76_E 0.84 0.11 0.00
148_S 25_D 0.84 0.11 0.00
246_G 77_A 0.84 0.11 0.00
74_I 63_D 0.84 0.11 0.00
67_K 79_S 0.84 0.11 0.00
42_F 97_R 0.83 0.11 0.00
57_H 85_K 0.83 0.11 0.00
212_I 5_I 0.83 0.11 0.00
7_K 56_N 0.83 0.11 0.00
167_Q 37_E 0.83 0.11 0.00
169_I 11_S 0.82 0.11 0.00
64_I 101_F 0.82 0.11 0.00
181_T 12_R 0.82 0.11 0.00
186_K 4_I 0.82 0.11 0.00
81_F 64_I 0.82 0.11 0.00
246_G 79_S 0.81 0.10 0.00
145_L 70_D 0.81 0.10 0.00
52_E 22_L 0.81 0.10 0.00
22_T 57_Q 0.81 0.10 0.00
141_L 70_D 0.81 0.10 0.00
59_I 28_D 0.81 0.10 0.00
165_I 4_I 0.81 0.10 0.00
105_R 82_S 0.81 0.10 0.00
75_V 9_S 0.81 0.10 0.00
60_L 38_V 0.80 0.10 0.00
136_L 58_P 0.80 0.10 0.00
264_F 19_E 0.80 0.10 0.00
14_N 94_A 0.80 0.10 0.00
221_R 89_I 0.80 0.10 0.00
247_T 61_L 0.80 0.10 0.00
57_H 71_S 0.80 0.10 0.00
123_E 83_Q 0.80 0.10 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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