YDGD - ECOLI - GREMLIN Contacts

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YDGD - Uncharacterized serine protease YdgD

UniProt:	P76176	Sequences: MRTTIAVVLGAISLTSAFVFADKPDVARSANDEVSTLFFGHDDRVPVNDTTQSPWDAVGQLETASGNLCTATLIAPNLALTAGHCLLTPPKGKADKAVALRFVSNKGLWRYEIHDIEGRVDPTLGKRLKADGDGWIVPPAAAPWDFGLIVLRNPPSGITPLPLFEGDKAALTAALKAAGRKVTQAGYPEDHLDTLYSHQNCEVTGWAQTSVMSHQCDTLPGDSGSPLMLHTDDGWQLIGVQSSAPAAKDRWRADNRAISVTGFRDKLDQLSQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13925
Length:	273 (215)
Sequences:	15173 (10144)
Seq/√Len:	691.8

ECOLI - YDGD
BACSU - MPR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
175_L	229_L	3.415	1.00
69_C	85_C	2.805	1.00
125_G	150_V	2.585	1.00
78_L	150_V	2.517	1.00
72_T	237_L	2.433	1.00
47_V	189_E	2.407	1.00
123_T	152_R	2.405	1.00
78_L	148_L	2.401	1.00
86_L	147_G	2.373	1.00
52_Q	190_D	2.237	1.00
53_S	190_D	2.227	1.00
71_A	79_A	2.181	1.00
80_L	237_L	2.134	1.00
104_S	155_P	2.118	1.00
144_W	263_F	2.111	1.00
73_L	155_P	2.086	1.00
56_D	178_A	2.081	1.00
60_Q	67_N	2.067	1.00
76_P	154_P	2.063	1.00
77_N	150_V	2.001	1.00
77_N	154_P	1.985	1.00
201_C	214_H	1.979	1.00
128_L	270_L	1.977	1.00
146_F	263_F	1.970	1.00
47_V	187_Y	1.935	1.00
75_A	78_L	1.935	1.00
84_H	223_S	1.928	1.00
57_A	71_A	1.928	1.00
57_A	104_S	1.895	1.00
151_L	155_P	1.879	1.00
103_V	121_D	1.856	1.00
243_S	256_R	1.852	1.00
126_K	150_V	1.797	1.00
211_V	262_G	1.781	1.00
124_L	149_I	1.773	1.00
131_D	270_L	1.731	1.00
122_P	155_P	1.731	1.00
217_D	255_N	1.721	1.00
264_R	268_D	1.712	1.00
53_S	178_A	1.682	1.00
138_P	141_A	1.675	1.00
219_L	247_A	1.663	1.00
143_P	211_V	1.589	1.00
189_E	192_L	1.552	1.00
101_R	121_D	1.540	1.00
132_G	144_W	1.535	1.00
48_N	53_S	1.497	1.00
125_G	152_R	1.481	1.00
55_W	228_M	1.479	1.00
258_I	263_F	1.476	1.00
57_A	79_A	1.474	1.00
122_P	152_R	1.471	1.00
175_L	195_L	1.422	1.00
178_A	228_M	1.405	1.00
50_T	107_G	1.397	1.00
213_S	227_L	1.389	1.00
122_P	153_N	1.385	1.00
161_L	237_L	1.385	1.00
103_V	106_K	1.383	1.00
51_T	107_G	1.354	1.00
177_A	218_T	1.348	1.00
51_T	157_G	1.330	1.00
161_L	228_M	1.326	1.00
174_A	229_L	1.313	1.00
104_S	158_I	1.310	1.00
72_T	161_L	1.307	1.00
144_W	211_V	1.285	1.00
218_T	241_Q	1.284	1.00
245_P	253_A	1.281	1.00
130_A	144_W	1.279	1.00
259_S	262_G	1.274	1.00
86_L	129_K	1.271	1.00
183_T	189_E	1.269	1.00
81_T	86_L	1.265	1.00
72_T	240_V	1.260	1.00
229_L	238_I	1.252	1.00
49_D	52_Q	1.231	1.00
198_H	208_Q	1.209	1.00
227_L	257_A	1.202	1.00
196_Y	254_D	1.199	1.00
175_L	179_G	1.188	1.00
230_H	235_W	1.186	1.00
146_F	258_I	1.177	1.00
55_W	235_W	1.177	1.00
194_T	216_C	1.177	1.00
129_K	147_G	1.177	1.00
128_L	150_V	1.171	1.00
47_V	107_G	1.170	1.00
198_H	259_S	1.148	1.00
219_L	248_K	1.145	1.00
79_A	102_F	1.140	1.00
48_N	190_D	1.136	1.00
108_L	187_Y	1.130	1.00
174_A	192_L	1.102	1.00
241_Q	244_A	1.098	1.00
143_P	209_T	1.092	1.00
56_D	70_T	1.080	1.00
73_L	104_S	1.072	1.00
56_D	180_R	1.070	1.00
101_R	123_T	1.070	1.00
82_A	240_V	1.063	1.00
56_D	188_P	1.062	1.00
42_D	45_V	1.062	1.00
197_S	200_N	1.060	1.00
212_M	243_S	1.057	1.00
211_V	263_F	1.049	1.00
175_L	227_L	1.047	1.00
46_P	190_D	1.041	1.00
72_T	80_L	1.038	1.00
56_D	226_P	1.030	1.00
120_V	158_I	1.025	1.00
83_G	129_K	1.012	1.00
189_E	193_D	1.009	1.00
198_H	202_E	1.004	1.00
108_L	111_Y	0.997	1.00
130_A	133_D	0.996	1.00
102_F	124_L	0.991	1.00
78_L	128_L	0.990	1.00
68_L	100_L	0.984	1.00
55_W	162_P	0.984	1.00
127_R	149_I	0.983	1.00
70_T	225_S	0.978	1.00
218_T	255_N	0.978	1.00
185_A	249_D	0.976	1.00
176_K	192_L	0.972	1.00
164_F	264_R	0.958	1.00
78_L	270_L	0.957	1.00
84_H	145_D	0.944	1.00
73_L	79_A	0.941	1.00
215_Q	227_L	0.934	1.00
174_A	194_T	0.929	1.00
81_T	147_G	0.927	1.00
86_L	127_R	0.923	1.00
163_L	264_R	0.911	1.00
265_D	269_Q	0.911	1.00
75_A	160_P	0.910	1.00
177_A	191_H	0.904	1.00
86_L	149_I	0.902	1.00
107_G	187_Y	0.902	1.00
78_L	271_S	0.902	1.00
53_S	176_K	0.897	1.00
162_P	236_Q	0.894	1.00
177_A	241_Q	0.894	1.00
106_K	113_I	0.890	1.00
104_S	122_P	0.889	1.00
175_L	180_R	0.883	1.00
133_D	139_P	0.883	1.00
241_Q	257_A	0.875	1.00
102_F	149_I	0.874	1.00
168_K	171_L	0.870	1.00
73_L	160_P	0.868	1.00
155_P	158_I	0.864	1.00
200_N	203_V	0.861	1.00
120_V	156_S	0.860	1.00
168_K	236_Q	0.858	1.00
174_A	179_G	0.858	1.00
57_A	102_F	0.848	1.00
122_P	151_L	0.843	1.00
53_S	235_W	0.837	1.00
228_M	235_W	0.834	1.00
226_P	237_L	0.828	1.00
217_D	257_A	0.826	1.00
182_V	185_A	0.824	1.00
209_T	212_M	0.824	1.00
215_Q	257_A	0.823	1.00
106_K	112_E	0.816	1.00
225_S	241_Q	0.813	1.00
83_G	133_D	0.812	1.00
170_A	238_I	0.811	1.00
240_V	258_I	0.806	1.00
106_K	114_H	0.798	1.00
188_P	192_L	0.796	1.00
195_L	238_I	0.796	1.00
210_S	262_G	0.793	1.00
74_I	80_L	0.792	1.00
212_M	256_R	0.792	1.00
202_E	206_W	0.790	1.00
230_H	233_D	0.782	1.00
237_L	260_V	0.776	1.00
246_A	249_D	0.775	1.00
138_P	143_P	0.767	1.00
218_T	244_A	0.766	1.00
62_E	67_N	0.765	1.00
41_H	45_V	0.764	1.00
130_A	266_K	0.762	1.00
87_L	129_K	0.762	1.00
266_K	270_L	0.761	1.00
175_L	238_I	0.757	1.00
164_F	236_Q	0.752	1.00
172_T	175_L	0.751	1.00
268_D	271_S	0.749	1.00
128_L	148_L	0.749	1.00
143_P	212_M	0.741	1.00
55_W	178_A	0.731	1.00
231_T	234_G	0.729	1.00
115_D	157_G	0.728	1.00
175_L	178_A	0.728	1.00
193_D	215_Q	0.723	1.00
50_T	157_G	0.720	1.00
165_E	236_Q	0.711	1.00
75_A	271_S	0.704	1.00
259_S	263_F	0.704	1.00
48_N	107_G	0.701	1.00
127_R	147_G	0.701	1.00
177_A	193_D	0.701	1.00
56_D	228_M	0.700	1.00
148_L	266_K	0.697	1.00
106_K	111_Y	0.694	1.00
203_V	206_W	0.690	1.00
73_L	151_L	0.687	1.00
198_H	210_S	0.686	1.00
53_S	228_M	0.679	1.00
200_N	204_T	0.679	1.00
86_L	100_L	0.675	1.00
165_E	168_K	0.673	1.00
240_V	260_V	0.672	1.00
204_T	253_A	0.671	1.00
242_S	258_I	0.670	1.00
97_A	127_R	0.667	1.00
55_W	161_L	0.666	1.00
223_S	241_Q	0.664	1.00
82_A	85_C	0.663	1.00
196_Y	200_N	0.663	1.00
231_T	236_Q	0.662	1.00
162_P	234_G	0.660	1.00
104_S	120_V	0.659	1.00
199_Q	203_V	0.659	1.00
42_D	191_H	0.657	1.00
131_D	266_K	0.652	1.00
205_G	253_A	0.645	1.00
208_Q	211_V	0.642	1.00
123_T	153_N	0.641	1.00
263_F	266_K	0.640	1.00
217_D	244_A	0.640	1.00
64_A	99_A	0.640	1.00
77_N	125_G	0.640	1.00
182_V	220_P	0.638	1.00
178_A	190_D	0.637	1.00
63_T	66_G	0.636	1.00
102_F	105_N	0.634	1.00
105_N	158_I	0.632	1.00
165_E	268_D	0.632	1.00
120_V	155_P	0.630	1.00
146_F	240_V	0.628	1.00
80_L	260_V	0.624	1.00
72_T	260_V	0.622	1.00
79_A	151_L	0.622	1.00
102_F	151_L	0.622	1.00
100_L	124_L	0.620	1.00
167_D	261_T	0.620	1.00
145_D	223_S	0.618	1.00
80_L	146_F	0.618	1.00
205_G	245_P	0.617	1.00
56_D	225_S	0.615	1.00
71_A	102_F	0.615	1.00
54_P	159_T	0.613	1.00
70_T	82_A	0.613	1.00
60_Q	101_R	0.608	1.00
204_T	251_W	0.607	1.00
43_D	248_K	0.607	1.00
237_L	241_Q	0.606	1.00
148_L	270_L	0.606	1.00
122_P	154_P	0.602	1.00
193_D	257_A	0.602	1.00
162_P	235_W	0.601	1.00
176_K	179_G	0.600	1.00
140_A	143_P	0.596	1.00
72_T	226_P	0.590	1.00
48_N	52_Q	0.588	1.00
179_G	183_T	0.588	1.00
263_F	267_L	0.588	1.00
223_S	244_A	0.587	1.00
260_V	267_L	0.584	1.00
218_T	257_A	0.583	1.00
175_L	181_K	0.578	1.00
191_H	194_T	0.576	1.00
195_L	229_L	0.572	1.00
61_L	68_L	0.570	1.00
181_K	222_D	0.570	1.00
164_F	168_K	0.569	1.00
81_T	149_I	0.568	1.00
167_D	170_A	0.567	1.00
63_T	100_L	0.566	1.00
166_G	268_D	0.566	1.00
261_T	264_R	0.559	1.00
177_A	180_R	0.556	1.00
50_T	115_D	0.555	1.00
168_K	231_T	0.554	1.00
222_D	225_S	0.548	1.00
52_Q	107_G	0.546	1.00
146_F	266_K	0.545	1.00
111_Y	115_D	0.540	1.00
172_T	195_L	0.537	1.00
151_L	154_P	0.534	1.00
74_I	267_L	0.534	1.00
176_K	180_R	0.532	1.00
87_L	90_P	0.531	1.00
138_P	142_A	0.528	1.00
208_Q	212_M	0.526	1.00
72_T	228_M	0.524	1.00
262_G	265_D	0.522	1.00
206_W	253_A	0.520	1.00
50_T	113_I	0.520	1.00
173_A	229_L	0.517	0.99
248_K	255_N	0.514	0.99
220_P	223_S	0.514	0.99
167_D	259_S	0.514	0.99
49_D	107_G	0.512	0.99
159_T	162_P	0.511	0.99
83_G	130_A	0.511	0.99
182_V	186_G	0.510	0.99
53_S	56_D	0.509	0.99
239_G	257_A	0.508	0.99
106_K	109_W	0.505	0.99
97_A	100_L	0.504	0.99
87_L	133_D	0.504	0.99
62_E	101_R	0.503	0.99
80_L	267_L	0.502	0.99
178_A	226_P	0.501	0.99
105_N	120_V	0.501	0.99
181_K	184_Q	0.500	0.99
180_R	183_T	0.500	0.99

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
4nzqA	1	0.9487	100	0.186	Contact Map
3nxpA	1	0.9267	100	0.19	Contact Map
2bdyA	1	0.9231	100	0.202	Contact Map
2f83A	2	0.8974	100	0.205	Contact Map
4kkdA	1	0.967	100	0.207	Contact Map
2xxlA	1	0.9414	100	0.21	Contact Map
2b9lA	1	0.9487	100	0.216	Contact Map
4igdA	1	0.9451	100	0.224	Contact Map
2vntA	1	0.8498	100	0.228	Contact Map
3gylB	1	0.7949	100	0.228	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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