YDDR - BACSU - GREMLIN Contacts

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YDDR - UPF0173 protein YddR

UniProt:	P96655	Sequences: MNITQIRNATIVVKYANKKFLIDPMLAEKGTYATFPETIRQDLFNPLVSLPTSIDNILDGVDAVIVTHLHLDHFDDVAKNVLPKNIKMFVQNEADAKEVKASGFKNVEVLHQDTVFEGIQLVKTKGEHGRGEELLNLMGDVCGLVFKHPSEKVLYVAGDTVWYDAIEDEIHTHQPEIIVVNGGDNQRLDLGSLIMGKEDIYEVHKAAPHAKIISVHMEAVNHWTLSREELKNFSKEKGFSSNILVPEDGESYTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (235)
Sequences:	4777 (3391)
Seq/√Len:	221.2

ECOLI - ULAG
BACSU - YDDR YTKL
HALSA - Q9HR59 Y1038 Q9HR33
SULSO - Y099 Q97W37

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
123_K	142_C	3.662	1.00
11_I	215_V	3.536	1.00
147_K	153_V	3.283	1.00
124_T	145_V	3.149	1.00
120_Q	147_K	3.086	1.00
14_K	19_K	3.079	1.00
204_H	212_I	2.950	1.00
67_T	156_V	2.896	1.00
178_I	209_H	2.880	1.00
162_W	206_A	2.646	1.00
88_M	108_E	2.557	1.00
20_F	63_A	2.504	1.00
247_E	250_E	2.387	1.00
167_E	171_H	2.370	1.00
4_T	251_S	2.360	1.00
115_V	120_Q	2.311	1.00
176_E	210_A	2.295	1.00
195_M	203_V	2.291	1.00
122_V	147_K	2.274	1.00
154_L	179_V	2.185	1.00
145_V	173_H	2.177	1.00
179_V	213_I	2.168	1.00
96_A	109_V	2.125	1.00
124_T	143_G	2.124	1.00
18_K	117_E	2.073	1.00
184_D	196_G	2.062	1.00
198_E	233_F	2.028	1.00
122_V	173_H	2.022	1.00
22_I	67_T	2.016	1.00
157_A	181_N	1.970	1.00
49_S	52_T	1.951	1.00
96_A	100_K	1.942	1.00
12_V	19_K	1.922	1.00
167_E	206_A	1.890	1.00
65_I	146_F	1.885	1.00
11_I	179_V	1.883	1.00
65_I	144_L	1.842	1.00
129_G	193_L	1.838	1.00
157_A	180_V	1.765	1.00
233_F	236_E	1.755	1.00
211_K	244_L	1.748	1.00
202_E	205_K	1.748	1.00
204_H	209_H	1.722	1.00
202_E	206_A	1.709	1.00
3_I	177_I	1.681	1.00
27_A	75_D	1.679	1.00
179_V	215_V	1.638	1.00
22_I	156_V	1.587	1.00
228_E	232_N	1.553	1.00
177_I	213_I	1.542	1.00
170_I	208_P	1.515	1.00
233_F	237_K	1.515	1.00
205_K	237_K	1.503	1.00
108_E	111_H	1.463	1.00
93_E	111_H	1.411	1.00
156_V	215_V	1.407	1.00
15_Y	148_H	1.403	1.00
168_D	172_T	1.354	1.00
3_I	11_I	1.347	1.00
110_L	123_K	1.344	1.00
123_K	144_L	1.309	1.00
191_G	199_D	1.308	1.00
42_D	45_N	1.301	1.00
76_D	80_N	1.292	1.00
63_A	88_M	1.280	1.00
186_Q	189_D	1.280	1.00
115_V	122_V	1.277	1.00
182_G	200_I	1.271	1.00
69_L	98_E	1.263	1.00
196_G	199_D	1.260	1.00
121_L	144_L	1.252	1.00
18_K	119_I	1.251	1.00
4_T	14_K	1.242	1.00
157_A	178_I	1.235	1.00
168_D	171_H	1.216	1.00
64_V	89_F	1.211	1.00
229_E	232_N	1.201	1.00
113_D	125_K	1.188	1.00
107_V	110_L	1.185	1.00
13_V	154_L	1.179	1.00
6_I	10_T	1.168	1.00
26_L	50_L	1.148	1.00
232_N	236_E	1.148	1.00
13_V	22_I	1.145	1.00
162_W	202_E	1.143	1.00
25_M	30_G	1.139	1.00
230_L	234_S	1.133	1.00
65_I	121_L	1.129	1.00
200_I	212_I	1.117	1.00
229_E	233_F	1.116	1.00
22_I	146_F	1.106	1.00
180_V	203_V	1.104	1.00
63_A	90_V	1.093	1.00
91_Q	95_D	1.091	1.00
90_V	144_L	1.082	1.00
68_H	159_D	1.075	1.00
143_G	157_A	1.073	1.00
84_K	87_K	1.065	1.00
166_I	203_V	1.063	1.00
234_S	243_I	1.059	1.00
18_K	62_D	1.058	1.00
20_F	119_I	1.058	1.00
12_V	61_V	1.057	1.00
42_D	46_P	1.051	1.00
135_L	138_M	1.045	1.00
177_I	211_K	1.044	1.00
230_L	233_F	1.040	1.00
146_F	154_L	1.029	1.00
6_I	26_L	1.022	1.00
22_I	65_I	1.013	1.00
29_K	38_T	1.003	1.00
225_L	229_E	0.995	1.00
211_K	242_N	0.991	1.00
21_L	61_V	0.988	1.00
10_T	22_I	0.988	1.00
145_V	169_E	0.980	1.00
180_V	207_A	0.977	1.00
178_I	207_A	0.970	1.00
51_P	81_V	0.970	1.00
6_I	12_V	0.966	1.00
19_K	60_G	0.964	1.00
124_T	155_Y	0.961	1.00
99_V	102_S	0.957	1.00
127_E	163_Y	0.952	1.00
6_I	47_L	0.944	1.00
213_I	244_L	0.935	1.00
113_D	120_Q	0.932	1.00
145_V	175_P	0.921	0.99
185_N	222_H	0.920	0.99
95_D	139_G	0.919	0.99
68_H	216_H	0.913	0.99
78_A	82_L	0.912	0.99
126_G	160_T	0.910	0.99
178_I	204_H	0.909	0.99
164_D	168_D	0.896	0.99
157_A	160_T	0.895	0.99
148_H	151_E	0.895	0.99
227_R	230_L	0.892	0.99
153_V	174_Q	0.892	0.99
63_A	121_L	0.892	0.99
10_T	26_L	0.889	0.99
19_K	61_V	0.887	0.99
90_V	121_L	0.887	0.99
46_P	50_L	0.886	0.99
197_K	225_L	0.885	0.99
15_Y	20_F	0.880	0.99
18_K	63_A	0.877	0.99
235_K	240_S	0.876	0.99
58_L	61_V	0.875	0.99
108_E	116_F	0.869	0.99
106_N	111_H	0.865	0.99
90_V	116_F	0.861	0.99
113_D	172_T	0.856	0.99
212_I	243_I	0.855	0.99
226_S	229_E	0.855	0.99
3_I	179_V	0.852	0.99
113_D	173_H	0.851	0.99
111_H	129_G	0.850	0.99
5_Q	215_V	0.848	0.99
75_D	78_A	0.846	0.99
20_F	121_L	0.841	0.99
97_K	100_K	0.835	0.99
65_I	142_C	0.830	0.99
121_L	146_F	0.826	0.99
153_V	175_P	0.826	0.99
204_H	234_S	0.821	0.99
110_L	114_T	0.820	0.99
19_K	62_D	0.820	0.99
107_V	111_H	0.819	0.99
93_E	97_K	0.816	0.99
70_H	159_D	0.808	0.99
211_K	214_S	0.805	0.99
26_L	78_A	0.792	0.98
108_E	185_N	0.790	0.98
155_Y	203_V	0.789	0.98
12_V	21_L	0.789	0.98
170_I	178_I	0.789	0.98
180_V	195_M	0.786	0.98
129_G	136_N	0.786	0.98
164_D	167_E	0.785	0.98
152_K	176_E	0.785	0.98
89_F	104_F	0.785	0.98
11_I	213_I	0.784	0.98
16_A	151_E	0.781	0.98
246_P	251_S	0.777	0.98
159_D	216_H	0.776	0.98
182_G	217_M	0.774	0.98
186_Q	196_G	0.765	0.98
238_G	241_S	0.764	0.98
184_D	225_L	0.763	0.98
47_L	51_P	0.760	0.98
196_G	200_I	0.760	0.98
230_L	239_F	0.755	0.98
199_D	202_E	0.752	0.98
153_V	176_E	0.751	0.98
3_I	213_I	0.751	0.98
201_Y	237_K	0.749	0.98
197_K	229_E	0.746	0.98
156_V	179_V	0.746	0.98
110_L	116_F	0.745	0.98
134_L	137_L	0.744	0.98
92_N	142_C	0.741	0.98
155_Y	207_A	0.737	0.98
133_E	137_L	0.732	0.97
6_I	46_P	0.731	0.97
223_W	230_L	0.729	0.97
231_K	245_V	0.728	0.97
99_V	104_F	0.725	0.97
231_K	235_K	0.723	0.97
4_T	12_V	0.722	0.97
233_F	238_G	0.715	0.97
133_E	136_N	0.713	0.97
217_M	231_K	0.712	0.97
80_N	83_P	0.709	0.97
10_T	75_D	0.706	0.97
9_A	181_N	0.704	0.97
230_L	238_G	0.704	0.97
66_V	74_F	0.701	0.97
69_L	139_G	0.700	0.97
106_N	109_V	0.699	0.97
79_K	82_L	0.695	0.96
214_S	217_M	0.685	0.96
198_E	229_E	0.684	0.96
112_Q	115_V	0.683	0.96
147_K	173_H	0.681	0.96
186_Q	190_L	0.679	0.96
201_Y	233_F	0.676	0.96
131_G	136_N	0.675	0.96
131_G	137_L	0.674	0.96
234_S	238_G	0.669	0.96
128_H	159_D	0.668	0.96
148_H	152_K	0.667	0.96
88_M	91_Q	0.666	0.95
122_V	145_V	0.664	0.95
126_G	143_G	0.663	0.95
48_V	52_T	0.663	0.95
90_V	93_E	0.662	0.95
223_W	226_S	0.661	0.95
235_K	238_G	0.660	0.95
5_Q	218_E	0.658	0.95
228_E	231_K	0.656	0.95
223_W	227_R	0.654	0.95
232_N	235_K	0.654	0.95
134_L	138_M	0.653	0.95
16_A	148_H	0.653	0.95
85_N	88_M	0.651	0.95
9_A	215_V	0.649	0.95
13_V	20_F	0.648	0.95
181_N	200_I	0.647	0.95
41_Q	45_N	0.646	0.95
197_K	201_Y	0.641	0.94
74_F	79_K	0.640	0.94
10_T	46_P	0.638	0.94
148_H	154_L	0.636	0.94
153_V	173_H	0.631	0.94
15_Y	119_I	0.628	0.94
68_H	72_D	0.628	0.94
154_L	177_I	0.627	0.94
98_E	102_S	0.627	0.94
44_F	248_D	0.625	0.94
46_P	49_S	0.624	0.94
43_L	221_N	0.624	0.94
83_P	86_I	0.623	0.94
127_E	161_V	0.621	0.93
50_L	81_V	0.620	0.93
162_W	166_I	0.620	0.93
130_R	139_G	0.617	0.93
111_H	114_T	0.616	0.93
86_I	90_V	0.614	0.93
170_I	175_P	0.608	0.93
18_K	118_G	0.607	0.93
3_I	13_V	0.607	0.93
106_N	110_L	0.606	0.93
38_T	41_Q	0.606	0.93
166_I	206_A	0.602	0.92
186_Q	191_G	0.601	0.92
47_L	50_L	0.601	0.92
180_V	204_H	0.600	0.92
5_Q	217_M	0.599	0.92
182_G	214_S	0.597	0.92
87_K	92_N	0.594	0.92
69_L	138_M	0.594	0.92
160_T	195_M	0.593	0.92
42_D	47_L	0.590	0.92
28_E	41_Q	0.590	0.92
14_K	17_N	0.587	0.91
209_H	212_I	0.586	0.91
42_D	219_A	0.585	0.91
41_Q	44_F	0.585	0.91
214_S	245_V	0.584	0.91
184_D	222_H	0.583	0.91
10_T	25_M	0.582	0.91
16_A	152_K	0.580	0.91
225_L	230_L	0.580	0.91
160_T	166_I	0.580	0.91
104_F	107_V	0.575	0.91
28_E	45_N	0.574	0.91
5_Q	248_D	0.572	0.90
125_K	140_D	0.570	0.90
88_M	106_N	0.569	0.90
79_K	104_F	0.568	0.90
68_H	73_H	0.567	0.90
96_A	103_G	0.567	0.90
94_A	99_V	0.567	0.90
28_E	75_D	0.564	0.90
92_N	144_L	0.564	0.90
203_V	207_A	0.561	0.90
223_W	229_E	0.561	0.90
98_E	101_A	0.558	0.89
80_N	84_K	0.557	0.89
77_V	81_V	0.556	0.89
90_V	123_K	0.555	0.89
28_E	31_T	0.554	0.89
91_Q	96_A	0.548	0.88
76_D	79_K	0.548	0.88
161_V	199_D	0.547	0.88
68_H	128_H	0.546	0.88
91_Q	144_L	0.544	0.88
165_A	168_D	0.541	0.88
61_V	64_V	0.541	0.88
86_I	104_F	0.541	0.88
124_T	169_E	0.540	0.88
163_Y	169_E	0.538	0.88
52_T	59_D	0.537	0.87
143_G	155_Y	0.536	0.87
15_Y	152_K	0.532	0.87
88_M	92_N	0.530	0.87
146_F	156_V	0.529	0.87
74_F	132_E	0.528	0.87
66_V	99_V	0.528	0.87
69_L	95_D	0.528	0.87
96_A	107_V	0.527	0.86
185_N	194_I	0.527	0.86
124_T	172_T	0.526	0.86
12_V	59_D	0.525	0.86
156_V	181_N	0.522	0.86
192_S	196_G	0.521	0.86
82_L	86_I	0.521	0.86
201_Y	205_K	0.521	0.86
15_Y	146_F	0.520	0.86
74_F	95_D	0.520	0.86
170_I	206_A	0.518	0.86
66_V	95_D	0.516	0.85
175_P	208_P	0.515	0.85
202_E	237_K	0.514	0.85
201_Y	238_G	0.513	0.85
157_A	166_I	0.511	0.85
129_G	185_N	0.511	0.85
180_V	212_I	0.509	0.85
76_D	102_S	0.506	0.84
212_I	230_L	0.506	0.84
163_Y	170_I	0.500	0.83

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
4qn9A	2	0.9685	100	0.338	Contact Map
3rpcA	2	0.9764	100	0.378	Contact Map
3bv6A	5	0.9685	100	0.485	Contact Map
2wylA	5	0.9252	100	0.502	Contact Map
4jo0A	2	0.9134	100	0.536	Contact Map
3kl7A	1	0.7953	100	0.575	Contact Map
3zwfA	2	0.8071	100	0.611	Contact Map
1zkpA	2	0.8543	100	0.613	Contact Map
2cbnA	2	0.8701	99.9	0.623	Contact Map
1y44A	2	0.8701	99.9	0.626	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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