YDBC - ECOLI - GREMLIN Contacts

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YDBC - Putative oxidoreductase YdbC

UniProt:	P25906	Sequences: MSSNTFTLGTKSVNRLGYGAMQLAGPGVFGPPRDRHVAITVLREALALGVNHIDTSDFYGPHVTNQIIREALYPYSDDLTIVTKIGARRGEDASWLPAFSPAELQKAVHDNLRNLGLDVLDVVNLRVMMGDGHGPAEGSIEASLTVLAEMQQQGLVKHIGLSNVTPTQVAEARKIAEIVCVQNEYNIAHRADDAMIDALAHDGIAYVPFFPLGGFTPLQSSTLSDVAASLGATPMQVALAWLLQRSPNILLIPGTSSVAHLRENMAAEKLHLSEEVLSTLDGISRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11309
Length:	286 (252)
Sequences:	32491 (20716)
Seq/√Len:	1305.0

ECOLI - YDBC YDJG YAJO YDHF TAS GPR YEAE DKGA DKGB
BACSU - YCSN YCCK GS69 IOLS YRPG YQKF YTBE GR
HALSA - Q9HPH9 Q9HQU7 Q9HNN3 Q9HSE6 Q9HS02 Q9HQT1
SULSO - Q97UG6 Q97ZZ1 Q97UV9 Q97UJ7 Q97V56 Q97U17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_E	262_R	3.072	1.00
109_H	155_L	2.871	1.00
73_Y	116_G	2.743	1.00
35_R	70_E	2.698	1.00
230_L	276_V	2.593	1.00
7_T	12_S	2.468	1.00
273_S	276_V	2.436	1.00
39_I	74_P	2.369	1.00
108_V	150_M	2.366	1.00
105_Q	149_E	2.343	1.00
105_Q	153_Q	2.289	1.00
44_E	48_L	2.270	1.00
229_S	279_T	2.089	1.00
39_I	70_E	2.007	1.00
148_A	152_Q	1.999	1.00
6_F	15_R	1.991	1.00
224_S	228_A	1.954	1.00
198_A	202_D	1.928	1.00
119_V	157_K	1.927	1.00
110_D	114_N	1.925	1.00
229_S	276_V	1.915	1.00
244_Q	277_L	1.911	1.00
149_E	153_Q	1.909	1.00
258_V	262_R	1.852	1.00
274_E	278_S	1.850	1.00
225_D	279_T	1.814	1.00
199_L	206_Y	1.810	1.00
101_P	149_E	1.780	1.00
44_E	258_V	1.774	1.00
17_G	52_H	1.761	1.00
232_A	270_L	1.738	1.00
48_L	262_R	1.709	1.00
124_N	180_C	1.703	1.00
245_R	281_D	1.692	1.00
81_I	117_L	1.675	1.00
5_T	12_S	1.673	1.00
170_A	174_K	1.667	1.00
149_E	152_Q	1.632	1.00
45_A	50_V	1.615	1.00
170_A	198_A	1.608	1.00
48_L	265_M	1.601	1.00
66_Q	114_N	1.596	1.00
39_I	71_A	1.594	1.00
240_A	270_L	1.589	1.00
83_T	120_L	1.583	1.00
101_P	105_Q	1.581	1.00
83_T	111_N	1.577	1.00
43_R	74_P	1.567	1.00
85_I	123_V	1.559	1.00
39_I	43_R	1.548	1.00
222_T	225_D	1.547	1.00
44_E	47_A	1.542	1.00
205_A	250_L	1.541	1.00
34_D	37_V	1.541	1.00
11_K	158_H	1.538	1.00
266_A	269_K	1.536	1.00
105_Q	109_H	1.529	1.00
108_V	123_V	1.526	1.00
146_V	149_E	1.520	1.00
233_T	263_E	1.520	1.00
85_I	104_L	1.515	1.00
82_V	124_N	1.477	1.00
20_A	53_I	1.472	1.00
278_S	282_G	1.469	1.00
35_R	39_I	1.429	1.00
43_R	75_Y	1.416	1.00
46_L	79_L	1.414	1.00
106_K	110_D	1.409	1.00
57_D	107_A	1.409	1.00
37_V	40_T	1.376	1.00
197_D	201_H	1.372	1.00
120_L	156_V	1.367	1.00
194_A	197_D	1.366	1.00
124_N	207_V	1.352	1.00
232_A	236_Q	1.344	1.00
109_H	113_R	1.339	1.00
42_L	71_A	1.336	1.00
200_A	246_S	1.320	1.00
158_H	179_V	1.317	1.00
173_R	202_D	1.316	1.00
11_K	80_T	1.302	1.00
262_R	266_A	1.300	1.00
240_A	244_Q	1.295	1.00
183_N	206_Y	1.288	1.00
165_T	168_Q	1.287	1.00
101_P	145_T	1.282	1.00
255_T	260_H	1.268	1.00
43_R	47_A	1.263	1.00
76_S	117_L	1.254	1.00
232_A	237_V	1.249	1.00
105_Q	146_V	1.248	1.00
279_T	282_G	1.247	1.00
173_R	198_A	1.245	1.00
156_V	159_I	1.236	1.00
40_T	44_E	1.233	1.00
141_E	175_I	1.231	1.00
110_D	113_R	1.225	1.00
150_M	156_V	1.223	1.00
69_R	116_G	1.222	1.00
101_P	146_V	1.215	1.00
80_T	122_V	1.212	1.00
255_T	261_L	1.207	1.00
225_D	229_S	1.189	1.00
222_T	279_T	1.188	1.00
115_L	120_L	1.177	1.00
53_I	68_I	1.174	1.00
65_N	111_N	1.168	1.00
166_P	198_A	1.166	1.00
233_T	236_Q	1.164	1.00
185_Y	245_R	1.157	1.00
148_A	151_Q	1.155	1.00
151_Q	179_V	1.154	1.00
224_S	234_P	1.129	1.00
188_A	220_S	1.128	1.00
142_A	145_T	1.122	1.00
122_V	180_C	1.120	1.00
76_S	119_V	1.118	1.00
70_E	116_G	1.115	1.00
170_A	201_H	1.112	1.00
103_E	106_K	1.108	1.00
259_A	262_R	1.107	1.00
196_I	200_A	1.106	1.00
36_H	40_T	1.101	1.00
66_Q	70_E	1.096	1.00
102_A	106_K	1.096	1.00
108_V	120_L	1.075	1.00
226_V	237_V	1.074	1.00
170_A	202_D	1.074	1.00
35_R	67_I	1.073	1.00
9_G	179_V	1.072	1.00
52_H	207_V	1.071	1.00
242_L	251_L	1.061	1.00
100_S	103_E	1.061	1.00
147_L	159_I	1.060	1.00
52_H	82_V	1.059	1.00
41_V	261_L	1.048	1.00
187_I	280_L	1.048	1.00
7_T	10_T	1.046	1.00
109_H	153_Q	1.040	1.00
40_T	258_V	1.035	1.00
43_R	71_A	1.034	1.00
171_E	175_I	1.030	1.00
225_D	228_A	1.020	1.00
125_L	147_L	1.019	1.00
150_M	155_L	1.018	1.00
221_S	224_S	1.014	1.00
221_S	225_D	1.013	1.00
223_L	234_P	1.006	1.00
166_P	170_A	0.999	1.00
51_N	80_T	0.995	1.00
184_E	189_H	0.995	1.00
20_A	68_I	0.993	1.00
236_Q	266_A	0.974	1.00
243_L	267_A	0.971	1.00
161_L	178_I	0.969	1.00
101_P	142_A	0.963	1.00
193_D	197_D	0.955	1.00
65_N	114_N	0.954	1.00
14_N	51_N	0.945	1.00
148_A	176_A	0.945	1.00
180_C	207_V	0.943	1.00
141_E	171_E	0.937	1.00
121_D	157_K	0.934	1.00
130_G	168_Q	0.933	1.00
15_R	243_L	0.929	1.00
187_I	238_A	0.929	1.00
70_E	74_P	0.927	1.00
261_L	265_M	0.924	1.00
150_M	153_Q	0.920	1.00
207_V	250_L	0.917	1.00
200_A	248_N	0.916	1.00
145_T	149_E	0.912	1.00
197_D	200_A	0.911	1.00
236_Q	263_E	0.907	1.00
57_D	89_R	0.904	1.00
66_Q	113_R	0.900	1.00
72_L	79_L	0.899	1.00
105_Q	108_V	0.894	1.00
57_D	103_E	0.892	1.00
14_N	50_V	0.891	1.00
263_E	266_A	0.887	1.00
146_V	150_M	0.887	1.00
15_R	268_E	0.875	1.00
82_V	207_V	0.868	1.00
259_A	263_E	0.866	1.00
40_T	43_R	0.866	1.00
42_L	53_I	0.866	1.00
257_S	260_H	0.863	1.00
278_S	281_D	0.862	1.00
106_K	109_H	0.860	1.00
145_T	148_A	0.859	1.00
226_V	230_L	0.853	1.00
171_E	174_K	0.846	1.00
198_A	201_H	0.844	1.00
244_Q	271_H	0.841	1.00
161_L	169_V	0.840	1.00
275_E	279_T	0.835	1.00
181_V	199_L	0.833	1.00
20_A	64_T	0.821	1.00
148_A	159_I	0.819	1.00
82_V	122_V	0.819	1.00
57_D	114_N	0.819	1.00
275_E	278_S	0.816	1.00
229_S	273_S	0.814	1.00
230_L	273_S	0.809	1.00
169_V	204_I	0.807	1.00
105_Q	150_M	0.805	1.00
239_L	267_A	0.799	1.00
245_R	277_L	0.798	1.00
159_I	178_I	0.798	1.00
190_R	281_D	0.797	1.00
211_P	253_P	0.797	1.00
238_A	242_L	0.785	1.00
18_Y	45_A	0.778	1.00
112_L	155_L	0.778	1.00
44_E	261_L	0.773	1.00
185_Y	196_I	0.773	1.00
151_Q	158_H	0.772	1.00
240_A	267_A	0.761	1.00
166_P	195_M	0.748	1.00
244_Q	274_E	0.747	1.00
163_N	209_F	0.746	1.00
196_I	206_Y	0.744	1.00
57_D	110_D	0.743	1.00
112_L	117_L	0.743	1.00
46_L	75_Y	0.734	1.00
232_A	269_K	0.734	1.00
83_T	123_V	0.734	1.00
127_V	163_N	0.731	1.00
6_F	205_A	0.731	1.00
256_S	260_H	0.729	1.00
173_R	177_E	0.724	1.00
190_R	193_D	0.723	1.00
208_P	211_P	0.722	1.00
48_L	266_A	0.721	1.00
55_T	68_I	0.718	1.00
75_Y	78_D	0.714	1.00
41_V	258_V	0.712	1.00
208_P	251_L	0.704	1.00
17_G	253_P	0.703	1.00
38_A	67_I	0.702	1.00
230_L	237_V	0.700	1.00
104_L	143_S	0.700	1.00
195_M	199_L	0.698	1.00
46_L	53_I	0.698	1.00
144_L	176_A	0.697	1.00
144_L	178_I	0.696	1.00
50_V	265_M	0.696	1.00
108_V	155_L	0.696	1.00
36_H	39_I	0.695	1.00
18_Y	23_L	0.692	1.00
144_L	172_A	0.691	1.00
196_I	245_R	0.688	1.00
5_T	51_N	0.686	1.00
87_A	90_G	0.686	1.00
232_A	266_A	0.685	1.00
166_P	194_A	0.684	1.00
199_L	204_I	0.683	1.00
241_W	281_D	0.680	1.00
144_L	159_I	0.678	1.00
16_L	243_L	0.676	1.00
77_D	119_V	0.674	1.00
205_A	249_I	0.672	1.00
161_L	181_V	0.669	1.00
161_L	164_V	0.667	1.00
192_D	197_D	0.665	1.00
220_S	224_S	0.665	1.00
143_S	146_V	0.663	1.00
107_A	110_D	0.663	1.00
11_K	157_K	0.661	1.00
235_M	263_E	0.658	1.00
111_N	123_V	0.657	1.00
226_V	276_V	0.653	1.00
42_L	46_L	0.649	1.00
124_N	160_G	0.648	1.00
13_V	250_L	0.646	1.00
228_A	231_G	0.644	1.00
58_F	86_G	0.644	1.00
46_L	51_N	0.644	1.00
222_T	283_I	0.644	1.00
227_A	237_V	0.642	1.00
104_L	150_M	0.642	1.00
242_L	249_I	0.642	1.00
51_N	78_D	0.641	1.00
147_L	151_Q	0.640	1.00
272_L	277_L	0.640	1.00
223_L	280_L	0.638	1.00
260_H	263_E	0.634	1.00
21_M	210_F	0.633	1.00
140_I	143_S	0.630	1.00
141_E	145_T	0.630	1.00
48_L	261_L	0.630	1.00
140_I	175_I	0.628	1.00
104_L	146_V	0.624	1.00
173_R	176_A	0.623	1.00
237_V	272_L	0.620	1.00
211_P	242_L	0.620	1.00
37_V	258_V	0.617	1.00
120_L	123_V	0.614	1.00
108_V	112_L	0.612	1.00
276_V	279_T	0.610	1.00
185_Y	242_L	0.610	1.00
161_L	172_A	0.605	1.00
5_T	14_N	0.604	1.00
47_A	258_V	0.600	1.00
23_L	38_A	0.598	1.00
223_L	238_A	0.598	1.00
232_A	240_A	0.597	1.00
89_R	103_E	0.595	1.00
237_V	270_L	0.590	1.00
17_G	250_L	0.586	1.00
170_A	173_R	0.585	1.00
41_V	255_T	0.584	1.00
112_L	120_L	0.581	1.00
54_D	182_Q	0.580	1.00
226_V	279_T	0.578	1.00
151_Q	156_V	0.578	1.00
185_Y	206_Y	0.577	1.00
272_L	276_V	0.574	1.00
227_A	234_P	0.573	1.00
112_L	119_V	0.571	1.00
100_S	143_S	0.568	1.00
17_G	252_I	0.567	1.00
168_Q	171_E	0.566	1.00
236_Q	270_L	0.564	1.00
105_Q	155_L	0.564	1.00
223_L	227_A	0.564	1.00
237_V	276_V	0.562	1.00
227_A	230_L	0.562	1.00
8_L	205_A	0.558	1.00
215_F	220_S	0.555	1.00
112_L	118_D	0.555	1.00
245_R	249_I	0.554	1.00
131_D	134_G	0.553	1.00
123_V	156_V	0.550	1.00
46_L	78_D	0.549	1.00
185_Y	249_I	0.549	1.00
123_V	147_L	0.547	1.00
24_A	64_T	0.547	1.00
13_V	52_H	0.545	1.00
188_A	215_F	0.545	1.00
45_A	53_I	0.545	1.00
167_T	170_A	0.544	1.00
55_T	64_T	0.544	1.00
16_L	268_E	0.544	1.00
185_Y	190_R	0.543	1.00
255_T	264_N	0.542	1.00
87_A	127_V	0.542	1.00
72_L	75_Y	0.536	1.00
46_L	71_A	0.536	1.00
237_V	280_L	0.533	1.00
23_L	41_V	0.531	1.00
42_L	68_I	0.530	1.00
57_D	86_G	0.529	1.00
187_I	241_W	0.529	1.00
85_I	107_A	0.528	1.00
258_V	261_L	0.527	1.00
173_R	204_I	0.526	1.00
226_V	283_I	0.522	1.00
140_I	171_E	0.522	1.00
125_L	143_S	0.519	1.00
208_P	248_N	0.518	1.00
18_Y	41_V	0.518	1.00
140_I	168_Q	0.518	1.00
65_N	83_T	0.517	1.00
70_E	73_Y	0.515	1.00
108_V	146_V	0.514	1.00
230_L	270_L	0.513	1.00
226_V	229_S	0.512	1.00
240_A	271_H	0.512	1.00
52_H	80_T	0.508	1.00
68_I	71_A	0.508	1.00
243_L	251_L	0.507	1.00
56_S	59_Y	0.505	1.00
6_F	13_V	0.504	1.00
124_N	162_S	0.501	1.00
277_L	281_D	0.500	1.00
90_G	125_L	0.500	1.00

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
3n2tA	1	0.9685	100	0.115	Contact Map
1pyfA	1	0.9615	100	0.116	Contact Map
3v0sA	1	0.9126	100	0.116	Contact Map
1pz1A	1	0.9615	100	0.12	Contact Map
3eauA	3	0.9545	100	0.128	Contact Map
4xk2A	5	0.9336	100	0.128	Contact Map
4r9oA	5	0.958	100	0.134	Contact Map
3lutA	3	0.951	100	0.14	Contact Map
3erpA	6	0.9545	100	0.142	Contact Map
1ynpA	1	0.9406	100	0.143	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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