YDDH - BACSU - GREMLIN Contacts

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YDDH - Probable endopeptidase YddH

UniProt:	P96645	Sequences: MISKKVVLPLVFSAPFIFFFVLCIVVVMTISRENQVGDDFIGGGDGEYETVGIAPEVERFRAVFEKYARQEGVFDQVNIIMALTMQESGGRSLDIMQSSESIGLPPNSITDPERSIEVGIKHFKKVFKQAGGDVRLTLQAYNFGSGFIDYVKKNGGKYTKKLALDFSRLQAFKMGWKSYGDPSYVDHVMRYVKGSDKNVKPVKGSMDFYETVMKEALKYEGQPYAWGGSNPETGFDCSGLVQWSFAKAGITLPRTAQEQHGATKKISEKEATAGDLVFFGGTYEGKAITHVGIYVGNGRMFNSNDSGIQYSDLKSGYWRDHLVSFGRIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	329 (290)
Sequences:	2574 (2170)
Seq/√Len:	127.4

ECOLI - MEPH YAFL MEPS NLPC
BACSU - YDDH CWLO LYTE LYTF YKFC CWLS PGDS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
219_Y	222_Q	3.989	1.00
295_V	310_Y	3.844	1.00
217_L	301_F	3.577	1.00
228_G	234_G	3.382	1.00
213_M	295_V	3.054	1.00
220_E	301_F	3.047	1.00
241_V	293_I	2.991	1.00
271_A	325_F	2.910	1.00
322_L	325_F	2.890	1.00
267_S	270_E	2.827	1.00
229_S	254_R	2.671	1.00
230_N	234_G	2.588	1.00
223_P	234_G	2.454	1.00
235_F	243_W	2.438	1.00
242_Q	254_R	2.438	1.00
241_V	276_L	2.417	1.00
217_L	310_Y	2.407	1.00
253_P	262_A	2.359	1.00
210_E	214_K	2.337	1.00
215_E	243_W	2.326	1.00
222_Q	230_N	2.298	1.00
255_T	258_E	2.245	1.00
241_V	259_Q	2.230	1.00
279_F	292_G	2.199	1.00
280_G	289_T	2.168	1.00
279_F	300_M	2.150	1.00
265_K	326_G	2.132	1.00
215_E	247_K	2.063	1.00
241_V	252_L	1.930	1.00
215_E	235_F	1.893	1.00
268_E	271_A	1.878	1.00
304_N	309_Q	1.873	1.00
278_F	291_V	1.854	1.00
256_A	260_H	1.853	1.00
162_L	165_D	1.807	1.00
155_G	159_T	1.751	1.00
243_W	247_K	1.749	1.00
222_Q	234_G	1.740	1.00
260_H	288_I	1.738	1.00
157_K	161_K	1.732	1.00
215_E	218_K	1.730	1.00
279_F	322_L	1.668	1.00
276_L	291_V	1.660	1.00
242_Q	246_A	1.654	1.00
222_Q	235_F	1.650	1.00
292_G	300_M	1.642	1.00
154_N	158_Y	1.636	1.00
280_G	321_H	1.630	1.00
82_A	86_Q	1.630	1.00
268_E	314_K	1.595	1.00
161_K	165_D	1.586	1.00
158_Y	161_K	1.585	1.00
209_Y	213_M	1.569	1.00
253_P	256_A	1.557	1.00
145_S	149_D	1.546	1.00
240_L	244_S	1.544	1.00
263_T	326_G	1.536	1.00
189_M	192_V	1.506	1.00
215_E	219_Y	1.493	1.00
164_L	168_R	1.485	1.00
148_I	152_K	1.484	1.00
268_E	322_L	1.476	1.00
106_P	110_T	1.466	1.00
231_P	235_F	1.461	1.00
137_T	140_A	1.458	1.00
292_G	302_N	1.456	1.00
188_V	191_Y	1.454	1.00
260_H	324_S	1.453	1.00
222_Q	228_G	1.448	1.00
159_T	163_A	1.447	1.00
300_M	313_L	1.447	1.00
181_D	184_Y	1.418	1.00
165_D	169_L	1.414	1.00
256_A	288_I	1.398	1.00
302_N	311_S	1.387	1.00
154_N	157_K	1.382	1.00
216_A	301_F	1.366	1.00
253_P	258_E	1.355	1.00
148_I	151_V	1.332	1.00
59_R	63_V	1.325	1.00
162_L	166_F	1.315	1.00
229_S	242_Q	1.307	1.00
280_G	287_A	1.297	1.00
159_T	162_L	1.291	1.00
298_G	313_L	1.290	1.00
124_K	128_K	1.287	1.00
171_A	174_M	1.280	1.00
220_E	310_Y	1.264	1.00
134_V	138_L	1.260	1.00
260_H	263_T	1.241	1.00
304_N	308_I	1.240	1.00
166_F	170_Q	1.238	1.00
138_L	142_N	1.229	1.00
180_G	184_Y	1.229	1.00
219_Y	230_N	1.220	0.99
214_K	217_L	1.214	0.99
299_R	310_Y	1.208	0.99
210_E	273_A	1.201	0.99
242_Q	259_Q	1.194	0.99
165_D	168_R	1.180	0.99
169_L	173_K	1.180	0.99
271_A	277_V	1.179	0.99
242_Q	255_T	1.173	0.99
273_A	295_V	1.166	0.99
217_L	295_V	1.166	0.99
213_M	301_F	1.161	0.99
271_A	313_L	1.157	0.99
87_E	91_R	1.157	0.99
183_S	187_H	1.133	0.99
230_N	235_F	1.122	0.99
24_I	27_V	1.119	0.99
147_F	150_Y	1.116	0.99
158_Y	162_L	1.110	0.99
279_F	289_T	1.103	0.99
260_H	278_F	1.102	0.99
31_S	35_Q	1.099	0.99
286_K	289_T	1.099	0.99
254_R	257_Q	1.093	0.99
254_R	258_E	1.091	0.99
152_K	155_G	1.089	0.99
147_F	151_V	1.086	0.99
72_G	75_D	1.081	0.99
175_G	179_Y	1.080	0.99
277_V	292_G	1.080	0.99
260_H	323_V	1.076	0.99
113_E	117_E	1.067	0.99
182_P	186_D	1.058	0.99
141_Y	145_S	1.056	0.98
257_Q	288_I	1.053	0.98
225_A	234_G	1.052	0.98
225_A	306_S	1.037	0.98
68_A	72_G	1.033	0.98
189_M	193_K	1.028	0.98
217_L	220_E	1.027	0.98
89_G	92_S	1.027	0.98
195_S	199_V	1.026	0.98
299_R	312_D	1.025	0.98
188_V	192_V	1.020	0.98
215_E	248_A	1.016	0.98
103_G	106_P	1.013	0.98
32_R	35_Q	1.007	0.98
211_T	248_A	0.999	0.98
160_K	164_L	0.998	0.98
156_G	160_K	0.992	0.98
268_E	325_F	0.985	0.98
41_I	44_G	0.985	0.98
25_V	28_M	0.985	0.98
215_E	244_S	0.985	0.98
161_K	164_L	0.984	0.98
73_V	77_V	0.983	0.98
266_I	270_E	0.981	0.98
82_A	85_M	0.979	0.98
143_F	147_F	0.977	0.97
29_T	32_R	0.975	0.97
102_I	106_P	0.970	0.97
53_I	56_E	0.968	0.97
192_V	196_D	0.964	0.97
139_Q	143_F	0.958	0.97
179_Y	183_S	0.958	0.97
213_M	217_L	0.953	0.97
225_A	228_G	0.952	0.97
258_E	261_G	0.950	0.97
302_N	309_Q	0.947	0.97
279_F	314_K	0.944	0.97
302_N	314_K	0.943	0.97
196_D	199_V	0.941	0.97
24_I	28_M	0.940	0.97
42_G	46_G	0.939	0.97
208_F	211_T	0.936	0.97
229_S	255_T	0.930	0.97
195_S	198_N	0.930	0.97
107_N	111_D	0.924	0.96
219_Y	244_S	0.924	0.96
212_V	248_A	0.922	0.96
120_I	124_K	0.918	0.96
184_Y	187_H	0.916	0.96
78_N	85_M	0.916	0.96
165_D	172_F	0.908	0.96
162_L	173_K	0.907	0.96
185_V	189_M	0.903	0.96
103_G	107_N	0.898	0.96
168_R	171_A	0.888	0.96
183_S	188_V	0.884	0.95
121_K	125_K	0.882	0.95
183_S	186_D	0.881	0.95
133_D	137_T	0.880	0.95
86_Q	89_G	0.878	0.95
170_Q	174_M	0.876	0.95
34_N	38_D	0.874	0.95
288_I	323_V	0.874	0.95
58_E	62_A	0.871	0.95
259_Q	291_V	0.865	0.95
185_V	190_R	0.861	0.95
295_V	301_F	0.857	0.95
157_K	160_K	0.856	0.95
257_Q	260_H	0.855	0.95
106_P	111_D	0.854	0.95
278_F	288_I	0.849	0.94
23_C	27_V	0.841	0.94
256_A	291_V	0.839	0.94
222_Q	232_E	0.835	0.94
181_D	189_M	0.833	0.94
35_Q	38_D	0.830	0.94
180_G	183_S	0.830	0.94
149_D	152_K	0.826	0.94
46_G	49_E	0.825	0.93
179_Y	182_P	0.824	0.93
226_W	234_G	0.823	0.93
92_S	95_I	0.823	0.93
181_D	185_V	0.822	0.93
240_L	248_A	0.819	0.93
116_I	119_G	0.817	0.93
211_T	214_K	0.817	0.93
74_F	77_V	0.815	0.93
240_L	304_N	0.813	0.93
85_M	92_S	0.809	0.93
187_H	190_R	0.809	0.93
163_A	167_S	0.808	0.93
126_V	129_Q	0.808	0.93
137_T	151_V	0.808	0.93
212_V	245_F	0.807	0.93
268_E	277_V	0.807	0.93
62_A	65_E	0.804	0.93
186_D	192_V	0.804	0.93
241_V	245_F	0.803	0.93
93_L	96_M	0.803	0.93
289_T	321_H	0.803	0.93
244_S	248_A	0.803	0.93
242_Q	252_L	0.802	0.93
116_I	120_I	0.800	0.92
209_Y	273_A	0.799	0.92
229_S	235_F	0.799	0.92
182_P	187_H	0.798	0.92
289_T	306_S	0.796	0.92
218_K	222_Q	0.796	0.92
166_F	169_L	0.795	0.92
191_Y	196_D	0.794	0.92
181_D	188_V	0.788	0.92
45_D	49_E	0.785	0.92
293_I	301_F	0.783	0.92
219_Y	240_L	0.781	0.91
235_F	308_I	0.777	0.91
186_D	190_R	0.776	0.91
260_H	325_F	0.774	0.91
26_V	30_I	0.774	0.91
36_V	40_F	0.774	0.91
300_M	321_H	0.774	0.91
182_P	185_V	0.770	0.91
181_D	186_D	0.769	0.91
181_D	187_H	0.768	0.91
162_L	172_F	0.766	0.91
78_N	81_M	0.762	0.90
41_I	45_D	0.761	0.90
90_G	97_Q	0.761	0.90
186_D	189_M	0.759	0.90
106_P	109_I	0.756	0.90
246_A	251_T	0.755	0.90
43_G	50_T	0.754	0.90
170_Q	173_K	0.749	0.90
245_F	248_A	0.748	0.90
98_S	101_S	0.748	0.90
79_I	82_A	0.748	0.90
187_H	193_K	0.742	0.89
219_Y	232_E	0.742	0.89
188_V	194_G	0.742	0.89
192_V	198_N	0.738	0.89
219_Y	248_A	0.735	0.89
301_F	310_Y	0.735	0.89
226_W	239_G	0.735	0.89
132_G	136_L	0.734	0.89
264_K	270_E	0.733	0.89
110_T	113_E	0.731	0.89
241_V	291_V	0.730	0.89
295_V	299_R	0.726	0.88
180_G	185_V	0.726	0.88
144_G	148_I	0.726	0.88
256_A	278_F	0.725	0.88
184_Y	189_M	0.724	0.88
134_V	141_Y	0.722	0.88
222_Q	308_I	0.716	0.88
23_C	26_V	0.716	0.88
131_G	134_V	0.713	0.87
119_G	122_H	0.712	0.87
27_V	30_I	0.709	0.87
257_Q	289_T	0.709	0.87
190_R	193_K	0.707	0.87
218_K	243_W	0.701	0.86
219_Y	243_W	0.701	0.86
229_S	246_A	0.700	0.86
54_A	58_E	0.699	0.86
243_W	246_A	0.695	0.86
305_D	308_I	0.695	0.86
190_R	196_D	0.695	0.86
245_F	250_I	0.693	0.86
151_V	155_G	0.688	0.85
67_Y	74_F	0.687	0.85
184_Y	188_V	0.685	0.85
102_I	110_T	0.684	0.85
109_I	113_E	0.684	0.85
163_A	166_F	0.682	0.85
219_Y	234_G	0.680	0.85
79_I	83_L	0.680	0.85
106_P	113_E	0.680	0.85
153_K	157_K	0.679	0.85
220_E	309_Q	0.679	0.85
146_G	150_Y	0.675	0.84
273_A	294_Y	0.671	0.84
143_F	146_G	0.671	0.84
254_R	262_A	0.670	0.84
294_Y	298_G	0.667	0.84
277_V	313_L	0.661	0.83
219_Y	235_F	0.660	0.83
137_T	144_G	0.657	0.83
61_R	65_E	0.657	0.83
192_V	195_S	0.656	0.83
37_G	40_F	0.653	0.82
225_A	229_S	0.653	0.82
240_L	303_S	0.649	0.82
252_L	263_T	0.648	0.82
261_G	265_K	0.647	0.82
117_E	120_I	0.645	0.82
135_R	139_Q	0.643	0.81
90_G	93_L	0.642	0.81
209_Y	303_S	0.642	0.81
40_F	44_G	0.642	0.81
271_A	322_L	0.641	0.81
47_E	51_V	0.638	0.81
154_N	161_K	0.632	0.80
151_V	154_N	0.630	0.80
212_V	244_S	0.629	0.80
279_F	313_L	0.622	0.79
81_M	85_M	0.621	0.79
116_I	130_A	0.621	0.79
54_A	61_R	0.621	0.79
164_L	167_S	0.617	0.79
144_G	147_F	0.617	0.79
153_K	160_K	0.616	0.78
179_Y	184_Y	0.614	0.78
212_V	252_L	0.614	0.78
241_V	247_K	0.607	0.77
276_L	293_I	0.605	0.77
103_G	110_T	0.604	0.77
226_W	255_T	0.603	0.77
222_Q	231_P	0.603	0.77
160_K	168_R	0.602	0.77
253_P	261_G	0.601	0.77
189_M	195_S	0.601	0.77
78_N	82_A	0.600	0.77
208_F	248_A	0.600	0.77
136_L	140_A	0.599	0.77
193_K	199_V	0.597	0.76
28_M	32_R	0.597	0.76
26_V	29_T	0.593	0.76
102_I	105_P	0.590	0.75
194_G	198_N	0.589	0.75
181_D	190_R	0.586	0.75
189_M	196_D	0.586	0.75
106_P	127_F	0.582	0.75
279_F	288_I	0.581	0.74
127_F	131_G	0.579	0.74
280_G	288_I	0.579	0.74
92_S	96_M	0.579	0.74
167_S	171_A	0.576	0.74
149_D	153_K	0.576	0.74
85_M	89_G	0.576	0.74
187_H	195_S	0.575	0.74
131_G	135_R	0.573	0.73
230_N	243_W	0.573	0.73
69_R	72_G	0.573	0.73
169_L	172_F	0.572	0.73
294_Y	299_R	0.570	0.73
252_L	259_Q	0.566	0.72
234_G	239_G	0.563	0.72
209_Y	212_V	0.562	0.72
138_L	141_Y	0.561	0.72
248_A	276_L	0.561	0.72
125_K	129_Q	0.559	0.72
245_F	293_I	0.559	0.72
65_E	68_A	0.559	0.72
229_S	239_G	0.558	0.71
232_E	235_F	0.557	0.71
265_K	324_S	0.553	0.71
271_A	279_F	0.553	0.71
171_A	175_G	0.553	0.71
75_D	79_I	0.552	0.71
39_D	42_G	0.552	0.71
67_Y	70_Q	0.551	0.70
193_K	197_K	0.548	0.70
119_G	126_V	0.547	0.70
256_A	263_T	0.547	0.70
194_G	197_K	0.547	0.70
280_G	304_N	0.545	0.70
134_V	137_T	0.544	0.69
140_A	143_F	0.541	0.69
230_N	303_S	0.540	0.69
27_V	31_S	0.540	0.69
152_K	156_G	0.539	0.69
31_S	34_N	0.538	0.69
254_R	288_I	0.538	0.69
260_H	265_K	0.537	0.69
244_S	247_K	0.536	0.68
58_E	61_R	0.535	0.68
92_S	97_Q	0.534	0.68
268_E	279_F	0.533	0.68
294_Y	297_N	0.528	0.67
105_P	116_I	0.528	0.67
229_S	243_W	0.527	0.67
271_A	295_V	0.526	0.67
313_L	322_L	0.525	0.67
56_E	59_R	0.520	0.66
103_G	113_E	0.519	0.66
197_K	200_K	0.519	0.66
259_Q	276_L	0.519	0.66
223_P	304_N	0.518	0.66
242_Q	256_A	0.518	0.66
88_S	95_I	0.518	0.66
183_S	189_M	0.517	0.66
179_Y	187_H	0.517	0.66
185_V	188_V	0.514	0.65
118_V	122_H	0.514	0.65
195_S	201_P	0.513	0.65
33_E	40_F	0.512	0.65
229_S	258_E	0.510	0.65
213_M	293_I	0.508	0.64
301_F	308_I	0.508	0.64
133_D	148_I	0.506	0.64
260_H	326_G	0.506	0.64
42_G	45_D	0.505	0.64
105_P	109_I	0.505	0.64
155_G	163_A	0.503	0.64
260_H	280_G	0.502	0.63
88_S	96_M	0.501	0.63
280_G	300_M	0.501	0.63
123_F	127_F	0.500	0.63
180_G	187_H	0.500	0.63

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
4q4gX	1	0.4012	100	0.331	Contact Map
4hpeA	1	0.8267	100	0.496	Contact Map
2k1gA	1	0.3708	100	0.498	Contact Map
4fdyA	1	0.8267	100	0.505	Contact Map
4xcmA	2	0.6687	100	0.52	Contact Map
3pbiA	1	0.5532	100	0.523	Contact Map
3npfA	2	0.8116	100	0.527	Contact Map
4lj1A	1	0.3495	100	0.527	Contact Map
2hbwA	1	0.5988	100	0.535	Contact Map
3h41A	1	0.8815	100	0.535	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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