YDIS - BACSU - GREMLIN Contacts

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YDIS - Type-2 restriction enzyme BsuMI component YdiS

UniProt:	O34885	Sequences: MEISKQTSDLLLSLEKKKGTLPKFSVLRSIPRNRIIYGAPGTGKSNYLEREVGKIFGDNPYVFTRVTFFPGYTYGQFIGAYKPVPIYKKLSGEEEIFSSNFRDKMENFEPMIDYQFVPGPFIDVLIKALKNRYTNFILIIEEINRANAASVFGDIFQLLDRNKNGESDYPVTFGPDIMNYLARNGIKDEMIKLPSNFFIWATMNNADQGVLPLDTAFKRRWSFEYLELEKYRKAVDSWKLSLRYKGHNKVIMWNDFRDIINKRLKGKVPEDKLLGPFFLKESELWNQNVFKNKLLYYLKEDVFKHNPTIDFLNASTFSELIEKYDGSDNIFTFDIDDSSFVSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	343 (262)
Sequences:	838 (669)
Seq/√Len:	41.3

ECOLI - MCRB
BACSU - YDIS
SULSO - Q97YJ5

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_A	151_V	11.460	1.00
119_G	128_A	5.696	1.00
121_F	125_L	4.254	1.00
227_E	273_L	3.699	1.00
52_V	137_I	3.364	1.00
269_P	272_K	3.288	1.00
126_I	129_L	3.204	1.00
138_L	197_F	3.190	1.00
131_N	134_T	3.175	1.00
165_G	192_K	3.124	1.00
121_F	128_A	3.057	1.00
63_F	139_I	2.974	1.00
222_S	293_K	2.799	1.00
119_G	125_L	2.760	1.00
125_L	128_A	2.681	1.00
52_V	63_F	2.598	1.00
135_N	198_F	2.477	1.00
159_L	199_I	2.436	1.00
116_F	119_G	2.302	1.00
271_D	277_F	2.285	1.00
116_F	128_A	2.214	1.00
281_E	289_V	1.988	0.99
225_Y	270_E	1.972	0.99
118_P	128_A	1.919	0.99
121_F	193_L	1.916	0.99
192_K	210_V	1.902	0.99
210_V	303_F	1.898	0.99
62_V	134_T	1.889	0.99
162_N	169_Y	1.876	0.98
53_G	56_F	1.870	0.98
124_V	128_A	1.867	0.98
48_L	139_I	1.846	0.98
31_P	293_K	1.837	0.98
52_V	139_I	1.823	0.98
122_I	128_A	1.798	0.98
72_Y	150_S	1.782	0.98
67_T	157_Q	1.749	0.98
211_L	304_K	1.739	0.97
124_V	138_L	1.682	0.97
131_N	136_F	1.657	0.97
122_I	125_L	1.635	0.96
119_G	122_I	1.634	0.96
118_P	122_I	1.580	0.96
64_T	127_K	1.554	0.95
73_T	150_S	1.546	0.95
55_I	137_I	1.532	0.95
51_E	54_K	1.509	0.94
120_P	128_A	1.476	0.94
79_G	187_K	1.464	0.93
110_P	128_A	1.458	0.93
278_F	289_V	1.418	0.92
124_V	197_F	1.411	0.92
181_L	187_K	1.403	0.92
145_R	219_R	1.389	0.91
143_I	203_M	1.360	0.90
137_I	198_F	1.352	0.90
114_Y	128_A	1.350	0.90
56_F	62_V	1.341	0.90
53_G	57_G	1.340	0.90
165_G	170_P	1.329	0.89
181_L	186_I	1.329	0.89
140_I	199_I	1.317	0.89
172_T	190_M	1.298	0.88
210_V	304_K	1.295	0.88
229_E	232_R	1.287	0.88
68_F	77_F	1.281	0.87
214_D	219_R	1.260	0.87
125_L	193_L	1.251	0.86
223_F	296_Y	1.210	0.84
143_I	201_A	1.206	0.84
112_I	128_A	1.200	0.84
56_F	137_I	1.190	0.83
145_R	153_G	1.187	0.83
119_G	124_V	1.166	0.82
206_A	215_T	1.165	0.82
120_P	125_L	1.158	0.82
310_D	318_S	1.147	0.81
203_M	214_D	1.138	0.80
33_N	309_I	1.136	0.80
121_F	124_V	1.130	0.80
31_P	37_Y	1.129	0.80
31_P	222_S	1.123	0.79
68_F	140_I	1.120	0.79
33_N	159_L	1.116	0.79
79_G	186_I	1.104	0.78
250_V	254_N	1.103	0.78
73_T	76_Q	1.094	0.78
76_Q	268_V	1.093	0.78
70_P	78_I	1.090	0.77
110_P	119_G	1.089	0.77
33_N	70_P	1.082	0.77
75_G	276_P	1.081	0.77
311_F	314_A	1.079	0.77
153_G	219_R	1.078	0.77
120_P	124_V	1.076	0.76
144_N	203_M	1.072	0.76
47_Y	224_E	1.069	0.76
116_F	125_L	1.067	0.76
114_Y	124_V	1.065	0.76
125_L	197_F	1.064	0.76
60_P	63_F	1.063	0.76
193_L	197_F	1.051	0.75
222_S	292_N	1.043	0.74
180_Y	190_M	1.041	0.74
225_Y	299_K	1.037	0.74
34_R	224_E	1.033	0.73
124_V	127_K	1.033	0.73
274_L	294_L	1.033	0.73
48_L	52_V	1.032	0.73
314_A	317_F	1.030	0.73
112_I	122_I	1.021	0.73
66_V	72_Y	1.010	0.72
56_F	135_N	1.008	0.72
42_T	202_T	1.007	0.72
64_T	124_V	1.006	0.71
165_G	195_S	1.003	0.71
190_M	255_D	0.997	0.71
40_P	214_D	0.994	0.71
139_I	198_F	0.990	0.70
34_R	136_F	0.987	0.70
19_G	22_P	0.987	0.70
153_G	194_P	0.979	0.69
156_F	217_F	0.973	0.69
32_R	198_F	0.968	0.68
50_R	53_G	0.968	0.68
315_S	318_S	0.957	0.68
224_E	292_N	0.956	0.68
48_L	70_P	0.951	0.67
51_E	55_I	0.948	0.67
22_P	262_K	0.945	0.67
145_R	207_D	0.944	0.67
218_K	301_D	0.941	0.66
208_Q	301_D	0.934	0.66
51_E	66_V	0.929	0.65
52_V	55_I	0.928	0.65
35_I	223_F	0.927	0.65
157_Q	163_K	0.925	0.65
38_G	44_K	0.924	0.65
39_A	42_T	0.924	0.65
157_Q	202_T	0.919	0.64
65_R	141_E	0.918	0.64
48_L	137_I	0.914	0.64
236_D	254_N	0.911	0.64
147_N	205_N	0.910	0.64
18_K	21_L	0.909	0.64
25_S	29_S	0.906	0.63
80_A	296_Y	0.904	0.63
216_A	219_R	0.900	0.63
221_W	296_Y	0.899	0.63
64_T	138_L	0.894	0.62
80_A	209_G	0.893	0.62
172_T	192_K	0.892	0.62
49_E	53_G	0.891	0.62
116_F	122_I	0.891	0.62
62_V	136_F	0.889	0.62
277_F	297_Y	0.886	0.62
75_G	147_N	0.877	0.61
121_F	131_N	0.873	0.60
148_A	151_V	0.872	0.60
110_P	124_V	0.871	0.60
207_D	219_R	0.871	0.60
50_R	132_R	0.871	0.60
83_P	274_L	0.868	0.60
145_R	214_D	0.866	0.60
40_P	219_R	0.866	0.60
160_D	205_N	0.863	0.59
110_P	116_F	0.862	0.59
81_Y	251_I	0.862	0.59
84_V	139_I	0.857	0.59
167_S	195_S	0.851	0.58
272_K	302_V	0.847	0.58
153_G	214_D	0.842	0.58
45_S	221_W	0.840	0.57
181_L	257_R	0.835	0.57
157_Q	182_A	0.833	0.57
40_P	277_F	0.831	0.57
160_D	163_K	0.829	0.56
70_P	149_A	0.825	0.56
110_P	113_D	0.822	0.56
290_F	304_K	0.821	0.56
255_D	287_Q	0.819	0.55
74_Y	214_D	0.817	0.55
53_G	63_F	0.814	0.55
23_K	29_S	0.812	0.55
124_V	136_F	0.810	0.55
153_G	207_D	0.806	0.54
170_P	210_V	0.803	0.54
78_I	155_I	0.796	0.53
69_F	74_Y	0.795	0.53
286_N	289_V	0.793	0.53
299_K	306_N	0.791	0.53
128_A	133_Y	0.790	0.53
238_W	245_K	0.786	0.52
159_L	195_S	0.786	0.52
57_G	311_F	0.786	0.52
253_W	281_E	0.785	0.52
215_T	293_K	0.785	0.52
203_M	207_D	0.783	0.52
155_I	209_G	0.781	0.52
187_K	190_M	0.780	0.52
218_K	296_Y	0.780	0.52
216_A	220_R	0.771	0.51
45_S	160_D	0.770	0.51
114_Y	157_Q	0.770	0.51
45_S	157_Q	0.766	0.51
74_Y	194_P	0.762	0.50
148_A	213_L	0.760	0.50
232_R	282_S	0.756	0.50
35_I	143_I	0.755	0.50
263_R	305_H	0.754	0.49
230_K	258_D	0.753	0.49
78_I	306_N	0.752	0.49
254_N	258_D	0.749	0.49
76_Q	316_T	0.742	0.48
232_R	254_N	0.736	0.48
129_L	295_L	0.734	0.48
311_F	318_S	0.730	0.47
52_V	56_F	0.730	0.47
110_P	114_Y	0.728	0.47
40_P	216_A	0.727	0.47
261_N	264_L	0.727	0.47
145_R	194_P	0.725	0.47
215_T	268_V	0.723	0.47
231_Y	258_D	0.722	0.46
211_L	223_F	0.720	0.46
271_D	293_K	0.718	0.46
74_Y	153_G	0.717	0.46
37_Y	67_T	0.716	0.46
156_F	160_D	0.714	0.46
227_E	270_E	0.714	0.46
67_T	148_A	0.713	0.46
201_A	264_L	0.713	0.46
141_E	149_A	0.713	0.46
255_D	258_D	0.713	0.46
153_G	275_G	0.712	0.46
159_L	162_N	0.708	0.45
33_N	268_V	0.707	0.45
137_I	200_W	0.706	0.45
154_D	193_L	0.704	0.45
42_T	74_Y	0.702	0.45
65_R	155_I	0.701	0.45
269_P	302_V	0.696	0.44
77_F	154_D	0.695	0.44
117_V	127_K	0.694	0.44
77_F	214_D	0.693	0.44
285_W	288_N	0.692	0.44
57_G	316_T	0.692	0.44
259_I	262_K	0.690	0.44
163_K	297_Y	0.690	0.44
194_P	219_R	0.689	0.43
157_Q	217_F	0.687	0.43
40_P	145_R	0.685	0.43
142_E	204_N	0.684	0.43
76_Q	200_W	0.683	0.43
227_E	268_V	0.682	0.43
211_L	228_L	0.681	0.43
182_A	187_K	0.680	0.43
210_V	266_G	0.679	0.43
68_F	203_M	0.677	0.42
211_L	272_K	0.675	0.42
77_F	153_G	0.674	0.42
228_L	269_P	0.671	0.42
40_P	206_A	0.670	0.42
165_G	210_V	0.666	0.41
118_P	125_L	0.665	0.41
21_L	26_V	0.662	0.41
273_L	277_F	0.657	0.41
73_T	155_I	0.657	0.41
114_Y	125_L	0.657	0.41
42_T	70_P	0.656	0.40
60_P	133_Y	0.655	0.40
142_E	207_D	0.655	0.40
110_P	136_F	0.651	0.40
205_N	209_G	0.650	0.40
251_I	256_F	0.649	0.40
122_I	129_L	0.649	0.40
227_E	303_F	0.644	0.39
212_P	303_F	0.638	0.39
76_Q	150_S	0.632	0.38
228_L	296_Y	0.629	0.38
304_K	308_T	0.627	0.38
75_G	154_D	0.627	0.38
160_D	276_P	0.626	0.38
34_R	222_S	0.623	0.38
113_D	124_V	0.620	0.37
163_K	182_A	0.619	0.37
284_L	289_V	0.618	0.37
49_E	52_V	0.617	0.37
64_T	123_D	0.616	0.37
114_Y	119_G	0.615	0.37
47_Y	226_L	0.614	0.37
63_F	198_F	0.613	0.37
33_N	164_N	0.612	0.37
31_P	34_R	0.612	0.37
128_A	131_N	0.609	0.36
237_S	248_N	0.609	0.36
78_I	138_L	0.608	0.36
194_P	275_G	0.608	0.36
69_F	154_D	0.608	0.36
270_E	306_N	0.607	0.36
253_W	289_V	0.607	0.36
40_P	153_G	0.604	0.36
200_W	277_F	0.604	0.36
49_E	63_F	0.603	0.36
281_E	286_N	0.600	0.36
68_F	144_N	0.597	0.35
307_P	310_D	0.597	0.35
268_V	314_A	0.596	0.35
215_T	272_K	0.595	0.35
181_L	296_Y	0.594	0.35
141_E	191_I	0.593	0.35
46_N	201_A	0.592	0.35
206_A	300_E	0.591	0.35
144_N	204_N	0.590	0.35
118_P	121_F	0.588	0.35
67_T	272_K	0.587	0.34
75_G	223_F	0.587	0.34
80_A	191_I	0.584	0.34
274_L	297_Y	0.582	0.34
23_K	27_L	0.582	0.34
134_T	280_K	0.581	0.34
140_I	152_F	0.579	0.34
311_F	316_T	0.578	0.34
253_W	283_E	0.578	0.34
109_E	258_D	0.576	0.34
204_N	220_R	0.576	0.34
314_A	318_S	0.575	0.33
310_D	316_T	0.571	0.33
26_V	29_S	0.570	0.33
66_V	136_F	0.569	0.33
67_T	181_L	0.566	0.33
73_T	316_T	0.565	0.33
33_N	226_L	0.565	0.33
264_L	269_P	0.562	0.32
70_P	186_I	0.562	0.32
150_S	210_V	0.562	0.32
251_I	255_D	0.561	0.32
117_V	128_A	0.558	0.32
173_F	181_L	0.557	0.32
141_E	221_W	0.557	0.32
130_K	133_Y	0.555	0.32
86_I	115_Q	0.555	0.32
297_Y	301_D	0.554	0.32
35_I	77_F	0.554	0.32
277_F	292_N	0.554	0.32
170_P	192_K	0.553	0.32
283_E	287_Q	0.549	0.31
112_I	120_P	0.549	0.31
273_L	303_F	0.548	0.31
69_F	214_D	0.546	0.31
75_G	228_L	0.544	0.31
49_E	171_V	0.540	0.31
76_Q	303_F	0.540	0.31
75_G	80_A	0.539	0.31
49_E	55_I	0.538	0.30
24_F	224_E	0.538	0.30
113_D	287_Q	0.537	0.30
310_D	314_A	0.536	0.30
36_I	169_Y	0.534	0.30
110_P	118_P	0.534	0.30
232_R	279_L	0.533	0.30
62_V	137_I	0.531	0.30
39_A	205_N	0.530	0.30
19_G	25_S	0.527	0.30
285_W	307_P	0.524	0.29
39_A	263_R	0.524	0.29
24_F	288_N	0.521	0.29
168_D	236_D	0.521	0.29
286_N	307_P	0.519	0.29
150_S	215_T	0.519	0.29
50_R	54_K	0.518	0.29
208_Q	212_P	0.518	0.29
203_M	219_R	0.517	0.29
18_K	60_P	0.516	0.29
172_T	189_E	0.516	0.29
27_L	30_I	0.514	0.29
53_G	137_I	0.514	0.29
142_E	145_R	0.514	0.29
299_K	309_I	0.513	0.28
308_T	311_F	0.513	0.28
230_K	279_L	0.512	0.28
21_L	24_F	0.512	0.28
72_Y	165_G	0.512	0.28
48_L	198_F	0.511	0.28
273_L	291_K	0.511	0.28
282_S	286_N	0.510	0.28
206_A	223_F	0.509	0.28
157_Q	164_N	0.507	0.28
161_R	164_N	0.507	0.28
131_N	255_D	0.506	0.28
78_I	143_I	0.505	0.28
212_P	300_E	0.504	0.28
263_R	267_K	0.500	0.28

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4akgA	2	0.7872	99.9	0.761	Contact Map
3vkgA	2	0.8222	99.8	0.787	Contact Map
2r44A	1	0.7988	99.8	0.794	Contact Map
4rh7A	1	0.8222	99.7	0.8	Contact Map
4r7yA	3	0.7901	99.6	0.818	Contact Map
1g8pA	1	0.7638	99.6	0.823	Contact Map
3hwsA	3	0.7405	99.6	0.827	Contact Map
3ja83	1	0.758	99.6	0.828	Contact Map
1r6bX	1	0.7376	99.6	0.829	Contact Map
4qosA	1	0.6822	99.6	0.829	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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