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OPENSEQ.org
Ecoli Cas1-Cas2
Genes: A B A+B
Length: 305 94 391
Sequences: 445 314 266
Seq/Len: 1.46 3.34 0.68
MirrorTree (Pazo et al. 2001) 0.83
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 0.00 0.66
2 0.01 0.00 0.67
5 0.01 0.00 0.67
10 0.01 0.00 0.67
20 0.01 0.00 0.67
100 0.01 0.01 0.67
∞ 0.02 0.02 0.67
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
30_G 14_R 1.72 0.80 0.04
60_V 41_E 1.56 0.70 0.03
38_T 90_S 1.40 0.58 0.02
96_S 11_V 1.37 0.55 0.01
114_K 41_E 1.36 0.54 0.01
69_A 18_R 1.36 0.54 0.01
48_S 35_V 1.35 0.54 0.01
201_A 8_T 1.34 0.53 0.01
53_M 58_M 1.29 0.49 0.01
62_H 30_V 1.27 0.47 0.01
137_L 38_K 1.27 0.47 0.01
231_K 86_L 1.25 0.45 0.01
16_S 65_E 1.23 0.44 0.01
273_A 41_E 1.23 0.44 0.01
300_A 4_L 1.23 0.43 0.01
116_V 20_A 1.17 0.38 0.01
96_S 51_A 1.16 0.38 0.01
39_G 54_G 1.15 0.38 0.01
207_V 82_D 1.15 0.37 0.01
30_G 31_Y 1.14 0.36 0.01
181_S 74_G 1.14 0.36 0.01
160_W 30_V 1.13 0.36 0.01
207_V 61_A 1.13 0.35 0.01
301_G 59_A 1.12 0.35 0.01
42_T 90_S 1.11 0.34 0.01
71_V 21_I 1.10 0.34 0.01
120_F 56_V 1.10 0.33 0.01
82_G 31_Y 1.09 0.32 0.01
225_F 84_D 1.08 0.32 0.01
203_A 20_A 1.08 0.32 0.01
51_C 28_A 1.07 0.32 0.01
84_R 40_R 1.07 0.31 0.01
146_R 32_V 1.06 0.30 0.01
261_L 69_E 1.06 0.30 0.01
66_R 35_V 1.06 0.30 0.01
181_S 58_M 1.05 0.30 0.01
268_I 31_Y 1.05 0.30 0.01
135_E 86_L 1.04 0.29 0.01
94_A 18_R 1.02 0.28 0.01
21_Q 8_T 1.02 0.27 0.01
146_R 13_P 1.01 0.27 0.01
248_R 65_E 1.01 0.27 0.01
276_E 47_I 1.00 0.26 0.01
31_A 70_F 1.00 0.26 0.01
49_V 5_V 0.99 0.26 0.01
44_I 10_N 0.99 0.26 0.01
194_A 74_G 0.98 0.25 0.00
89_G 30_V 0.98 0.25 0.00
162_G 26_V 0.98 0.25 0.00
61_S 5_V 0.98 0.25 0.00
77_W 30_V 0.97 0.25 0.00
95_R 60_W 0.97 0.24 0.00
151_L 45_E 0.97 0.24 0.00
121_E 52_E 0.96 0.24 0.00
303_R 39_I 0.96 0.24 0.00
241_G 42_M 0.96 0.24 0.00
28_I 10_N 0.96 0.24 0.00
18_I 41_E 0.95 0.24 0.00
103_A 33_G 0.95 0.24 0.00
104_K 63_N 0.95 0.23 0.00
93_G 52_E 0.95 0.23 0.00
18_I 36_S 0.95 0.23 0.00
247_V 41_E 0.95 0.23 0.00
28_I 66_T 0.95 0.23 0.00
272_L 47_I 0.95 0.23 0.00
203_A 84_D 0.95 0.23 0.00
203_A 60_W 0.95 0.23 0.00
254_I 45_E 0.95 0.23 0.00
50_A 4_L 0.94 0.23 0.00
207_V 63_N 0.94 0.23 0.00
9_I 74_G 0.94 0.23 0.00
53_M 6_V 0.94 0.23 0.00
276_E 71_Q 0.94 0.23 0.00
104_K 90_S 0.94 0.22 0.00
207_V 45_E 0.94 0.22 0.00
16_S 58_M 0.94 0.22 0.00
248_R 44_W 0.94 0.22 0.00
190_V 28_A 0.93 0.22 0.00
193_A 80_P 0.92 0.21 0.00
296_S 37_A 0.92 0.21 0.00
69_A 21_I 0.92 0.21 0.00
219_I 27_R 0.91 0.21 0.00
214_S 29_G 0.91 0.21 0.00
126_E 81_V 0.90 0.21 0.00
88_S 53_E 0.90 0.21 0.00
185_S 74_G 0.90 0.21 0.00
170_W 78_R 0.90 0.20 0.00
44_I 89_V 0.90 0.20 0.00
142_G 44_W 0.90 0.20 0.00
171_E 62_T 0.90 0.20 0.00
123_R 22_W 0.90 0.20 0.00
223_I 8_T 0.89 0.20 0.00
284_E 26_V 0.89 0.20 0.00
120_F 6_V 0.89 0.20 0.00
156_Y 41_E 0.89 0.20 0.00
276_E 59_A 0.89 0.20 0.00
22_Y 80_P 0.89 0.20 0.00
23_G 21_I 0.89 0.20 0.00
29_D 84_D 0.89 0.20 0.00
156_Y 82_D 0.88 0.20 0.00
19_F 64_T 0.88 0.19 0.00
207_V 65_E 0.88 0.19 0.00
42_T 83_L 0.88 0.19 0.00
162_G 21_I 0.88 0.19 0.00
192_E 55_N 0.87 0.19 0.00
201_A 66_T 0.87 0.19 0.00
228_V 51_A 0.87 0.19 0.00
195_I 38_K 0.87 0.19 0.00
230_P 44_W 0.87 0.19 0.00
23_G 84_D 0.87 0.19 0.00
251_C 9_E 0.87 0.19 0.00
68_A 31_Y 0.87 0.19 0.00
196_L 20_A 0.86 0.18 0.00
146_R 73_F 0.85 0.18 0.00
296_S 39_I 0.85 0.18 0.00
186_C 26_V 0.85 0.18 0.00
131_R 86_L 0.85 0.18 0.00
271_V 75_L 0.85 0.18 0.00
53_M 72_T 0.85 0.18 0.00
173_G 34_D 0.85 0.18 0.00
85_V 78_R 0.85 0.18 0.00
159_T 84_D 0.85 0.18 0.00
212_P 80_P 0.85 0.18 0.00
263_K 41_E 0.85 0.18 0.00
80_E 30_V 0.84 0.18 0.00
154_K 26_V 0.84 0.17 0.00
276_E 79_T 0.84 0.17 0.00
231_K 59_A 0.84 0.17 0.00
156_Y 75_L 0.84 0.17 0.00
212_P 74_G 0.84 0.17 0.00
135_E 65_E 0.84 0.17 0.00
231_K 23_L 0.84 0.17 0.00
248_R 33_G 0.84 0.17 0.00
200_Y 27_R 0.83 0.17 0.00
49_V 4_L 0.83 0.17 0.00
14_R 56_V 0.83 0.17 0.00
108_D 57_V 0.83 0.17 0.00
87_A 22_W 0.83 0.17 0.00
213_L 23_L 0.83 0.17 0.00
144_R 22_W 0.83 0.17 0.00
215_F 16_R 0.83 0.17 0.00
87_A 83_L 0.83 0.17 0.00
25_I 86_L 0.83 0.17 0.00
71_V 68_F 0.82 0.17 0.00
162_G 9_E 0.82 0.17 0.00
125_G 49_G 0.82 0.17 0.00
130_A 45_E 0.82 0.17 0.00
247_V 89_V 0.82 0.17 0.00
113_L 31_Y 0.82 0.16 0.00
204_I 44_W 0.82 0.16 0.00
303_R 23_L 0.82 0.16 0.00
194_A 78_R 0.82 0.16 0.00
49_V 69_E 0.82 0.16 0.00
240_P 49_G 0.82 0.16 0.00
300_A 6_V 0.82 0.16 0.00
65_V 74_G 0.82 0.16 0.00
104_K 60_W 0.82 0.16 0.00
265_I 52_E 0.82 0.16 0.00
116_V 9_E 0.81 0.16 0.00
134_V 20_A 0.81 0.16 0.00
9_I 23_L 0.81 0.16 0.00
178_Q 8_T 0.81 0.16 0.00
185_S 21_I 0.81 0.16 0.00
161_N 59_A 0.81 0.16 0.00
226_D 45_E 0.80 0.16 0.00
112_R 15_L 0.80 0.16 0.00
230_P 33_G 0.80 0.16 0.00
130_A 81_V 0.80 0.15 0.00
4_L 4_L 0.80 0.15 0.00
297_L 75_L 0.80 0.15 0.00
259_K 45_E 0.80 0.15 0.00
255_F 14_R 0.80 0.15 0.00
11_L 64_T 0.80 0.15 0.00
255_F 28_A 0.80 0.15 0.00
176_I 47_I 0.80 0.15 0.00
13_D 56_V 0.80 0.15 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
10206 0.68 cas1, cas2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
4599 0.68 Ecoli Cas1-Cas2 Δgene:(1, 2) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.04 Done
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