YBEM - ECOLI - GREMLIN Contacts

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YBEM - Putative hydrolase YbeM

UniProt:	P39874	Sequences: MLVAAGQFAVTSVWEKNAEICASLMAQAAENDASLFALPEALLARDDHDADLSVKSAQLLEGEFLGRLRRESKRNMMTTILTIHVPSTPGRAWNMLVALQAGNIVARYAKLHLYDAFAIQESRRVDAGNEIAPLLEVEGMKVGLMTCYDLRFPELALAQALQGAEILVLPAAWVRGPLKEHHWSTLLAARALDTTCYMVAAGECGNKNIGQSRIIDPFGVTIAAASEMPALIMAEVTPERVRQVRAQLPVLNNRRFAPPQLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13162
Length:	262 (243)
Sequences:	14791 (10204)
Seq/√Len:	654.6

ECOLI - YBEM YAFV YOBB LNT
BACSU - MTNU YHCX
HALSA - Q9HQZ3
SULSO - Q97ZZ7 Q97WN8 Q981B6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_E	141_K	3.100	1.00
2_L	235_E	3.019	1.00
13_V	16_K	2.657	1.00
190_R	193_D	2.428	1.00
214_I	234_A	2.426	1.00
85_V	109_A	2.407	1.00
216_D	220_V	2.399	1.00
20_I	229_P	2.366	1.00
83_I	97_V	2.334	1.00
21_C	42_L	2.325	1.00
95_M	109_A	2.268	1.00
226_S	230_A	2.253	1.00
4_A	233_M	2.206	1.00
184_S	224_A	2.183	1.00
145_M	156_A	2.140	1.00
4_A	33_A	2.133	1.00
143_G	159_Q	2.103	1.00
5_A	199_V	2.037	1.00
22_A	71_E	1.995	1.00
22_A	67_R	1.992	1.00
26_A	74_R	1.985	1.00
78_T	100_Q	1.973	1.00
225_A	230_A	1.966	1.00
37_A	168_V	1.945	1.00
5_A	201_A	1.921	1.00
26_A	75_N	1.919	1.00
72_S	79_T	1.913	1.00
137_V	140_M	1.860	1.00
36_F	77_M	1.853	1.00
93_W	109_A	1.851	1.00
31_N	233_M	1.813	1.00
20_I	23_S	1.786	1.00
165_E	242_R	1.780	1.00
22_A	26_A	1.779	1.00
225_A	232_I	1.771	1.00
3_V	199_V	1.751	1.00
185_T	188_A	1.747	1.00
69_R	99_L	1.746	1.00
34_S	138_E	1.731	1.00
197_Y	217_P	1.716	1.00
91_R	126_D	1.715	1.00
27_Q	31_N	1.661	1.00
78_T	98_A	1.637	1.00
95_M	107_R	1.625	1.00
100_Q	138_E	1.617	1.00
167_L	196_C	1.613	1.00
96_L	144_L	1.583	1.00
141_K	165_E	1.581	1.00
142_V	166_I	1.579	1.00
33_A	233_M	1.554	1.00
23_S	27_Q	1.551	1.00
98_A	144_L	1.544	1.00
6_G	36_F	1.529	1.00
68_L	81_L	1.525	1.00
26_A	71_E	1.522	1.00
70_R	74_R	1.508	1.00
215_I	221_T	1.484	1.00
35_L	168_V	1.468	1.00
25_M	36_F	1.464	1.00
223_A	232_I	1.448	1.00
78_T	105_V	1.441	1.00
37_A	201_A	1.440	1.00
96_L	170_P	1.440	1.00
80_I	98_A	1.436	1.00
184_S	188_A	1.431	1.00
80_I	96_L	1.421	1.00
240_R	243_Q	1.408	1.00
18_A	67_R	1.399	1.00
187_L	200_A	1.395	1.00
80_I	168_V	1.394	1.00
21_C	38_L	1.387	1.00
19_E	23_S	1.383	1.00
11_T	16_K	1.378	1.00
156_A	167_L	1.375	1.00
145_M	169_L	1.370	1.00
199_V	214_I	1.365	1.00
78_T	137_V	1.359	1.00
115_D	122_S	1.345	1.00
65_L	97_V	1.343	1.00
24_L	27_Q	1.335	1.00
99_L	104_I	1.314	1.00
25_M	79_T	1.300	1.00
197_Y	222_I	1.296	1.00
120_Q	123_R	1.283	1.00
15_E	19_E	1.277	1.00
85_V	95_M	1.269	1.00
145_M	155_L	1.262	1.00
16_K	19_E	1.243	1.00
25_M	71_E	1.243	1.00
6_G	38_L	1.238	1.00
80_I	144_L	1.232	1.00
185_T	192_L	1.224	1.00
6_G	231_L	1.219	1.00
83_I	107_R	1.210	1.00
71_E	75_N	1.210	1.00
216_D	222_I	1.202	1.00
191_A	198_M	1.192	1.00
28_A	231_L	1.189	1.00
142_V	168_V	1.183	1.00
19_E	67_R	1.183	1.00
61_E	65_L	1.172	1.00
34_S	100_Q	1.171	1.00
148_Y	152_F	1.166	1.00
203_E	207_K	1.149	1.00
156_A	169_L	1.148	1.00
66_G	69_R	1.148	1.00
243_Q	247_Q	1.148	1.00
154_E	157_L	1.146	1.00
16_K	20_I	1.127	1.00
43_L	64_F	1.124	1.00
66_G	70_R	1.121	1.00
216_D	240_R	1.115	1.00
166_I	199_V	1.114	1.00
211_Q	224_A	1.113	1.00
65_L	99_L	1.106	1.00
158_A	162_Q	1.097	1.00
93_W	126_D	1.088	1.00
187_L	198_M	1.079	1.00
57_A	60_L	1.068	1.00
164_A	167_L	1.061	1.00
33_A	36_F	1.059	1.00
97_V	107_R	1.057	1.00
18_A	22_A	1.047	1.00
20_I	24_L	1.045	1.00
160_A	196_C	1.041	1.00
22_A	74_R	1.040	1.00
52_L	55_K	1.040	1.00
8_F	24_L	1.039	1.00
25_M	77_M	1.039	1.00
58_Q	62_G	1.030	1.00
70_R	73_K	1.015	1.00
143_G	164_A	1.007	1.00
24_L	231_L	1.003	1.00
184_S	213_R	0.991	1.00
8_F	21_C	0.973	1.00
242_R	246_A	0.971	1.00
61_E	66_G	0.967	1.00
134_L	141_K	0.966	1.00
67_R	70_R	0.962	1.00
78_T	138_E	0.961	1.00
157_L	194_T	0.960	1.00
67_R	71_E	0.958	1.00
6_G	24_L	0.958	1.00
98_A	135_L	0.954	1.00
191_A	215_I	0.950	1.00
134_L	164_A	0.949	1.00
68_L	79_T	0.944	1.00
81_L	99_L	0.941	1.00
26_A	30_E	0.938	1.00
187_L	215_I	0.936	1.00
22_A	70_R	0.931	1.00
108_Y	132_A	0.930	1.00
5_A	214_I	0.930	1.00
58_Q	64_F	0.928	1.00
137_V	142_V	0.926	1.00
106_A	135_L	0.925	1.00
140_M	166_I	0.917	1.00
76_M	100_Q	0.915	1.00
187_L	213_R	0.915	1.00
27_Q	30_E	0.915	1.00
29_A	77_M	0.913	1.00
140_M	165_E	0.910	1.00
185_T	189_A	0.908	1.00
183_W	200_A	0.904	1.00
41_A	125_V	0.904	1.00
110_K	147_C	0.904	1.00
18_A	68_L	0.899	1.00
21_C	68_L	0.891	1.00
5_A	232_I	0.888	1.00
71_E	74_R	0.877	1.00
237_T	240_R	0.877	1.00
222_I	234_A	0.871	1.00
65_L	104_I	0.867	1.00
15_E	63_E	0.853	1.00
223_A	234_A	0.852	1.00
59_L	86_P	0.849	1.00
112_H	149_D	0.839	1.00
204_C	228_M	0.837	1.00
44_A	61_E	0.831	1.00
239_E	242_R	0.831	1.00
221_T	224_A	0.827	1.00
28_A	33_A	0.825	1.00
2_L	233_M	0.820	1.00
136_E	139_G	0.817	1.00
62_G	66_G	0.815	1.00
69_R	103_N	0.814	1.00
5_A	212_S	0.813	1.00
25_M	75_N	0.808	1.00
52_L	57_A	0.806	1.00
108_Y	149_D	0.805	1.00
85_V	107_R	0.804	1.00
197_Y	236_V	0.803	1.00
197_Y	241_V	0.800	1.00
38_L	42_L	0.800	1.00
239_E	243_Q	0.794	1.00
41_A	46_D	0.794	1.00
106_A	132_A	0.791	1.00
23_S	26_A	0.790	1.00
135_L	142_V	0.789	1.00
29_A	75_N	0.788	1.00
62_G	65_L	0.788	1.00
169_L	198_M	0.785	1.00
4_A	231_L	0.785	1.00
111_L	131_I	0.782	1.00
157_L	161_L	0.778	1.00
15_E	67_R	0.778	1.00
111_L	155_L	0.773	1.00
94_N	110_K	0.772	1.00
14_W	18_A	0.771	1.00
7_Q	212_S	0.771	1.00
172_A	203_E	0.770	1.00
165_E	238_P	0.769	1.00
25_M	38_L	0.768	1.00
145_M	159_Q	0.761	1.00
9_A	204_C	0.753	1.00
4_A	36_F	0.746	1.00
35_L	139_G	0.745	1.00
3_V	236_V	0.744	1.00
241_V	245_R	0.744	1.00
88_T	91_R	0.743	1.00
4_A	28_A	0.742	1.00
197_Y	240_R	0.738	1.00
10_V	203_E	0.736	1.00
150_L	169_L	0.735	1.00
7_Q	210_G	0.729	1.00
13_V	17_N	0.727	1.00
115_D	120_Q	0.723	1.00
8_F	42_L	0.723	1.00
19_E	22_A	0.722	1.00
37_A	80_I	0.719	1.00
150_L	187_L	0.716	1.00
2_L	31_N	0.714	1.00
21_C	25_M	0.713	1.00
35_L	80_I	0.708	1.00
14_W	64_F	0.707	1.00
218_F	244_V	0.703	1.00
159_Q	164_A	0.703	1.00
69_R	104_I	0.699	1.00
140_M	238_P	0.698	1.00
174_V	179_K	0.697	1.00
240_R	244_V	0.696	1.00
97_V	104_I	0.693	1.00
31_N	231_L	0.684	1.00
21_C	81_L	0.681	1.00
57_A	62_G	0.679	1.00
94_N	147_C	0.678	1.00
35_L	78_T	0.678	1.00
9_A	229_P	0.671	1.00
65_L	69_R	0.668	1.00
30_E	75_N	0.668	1.00
213_R	221_T	0.663	1.00
72_S	75_N	0.658	1.00
41_A	84_H	0.653	1.00
61_E	83_I	0.650	1.00
42_L	81_L	0.648	1.00
69_R	72_S	0.647	1.00
53_S	56_S	0.645	1.00
160_A	251_L	0.645	1.00
65_L	81_L	0.643	1.00
173_W	179_K	0.643	1.00
56_S	59_L	0.640	1.00
51_D	55_K	0.640	1.00
18_A	71_E	0.638	1.00
104_I	107_R	0.637	1.00
167_L	198_M	0.633	1.00
37_A	199_V	0.631	1.00
114_Y	148_Y	0.630	1.00
98_A	142_V	0.627	1.00
238_P	242_R	0.626	1.00
204_C	229_P	0.626	1.00
84_H	125_V	0.625	1.00
180_E	211_Q	0.623	1.00
33_A	77_M	0.622	1.00
121_E	124_R	0.619	1.00
202_G	212_S	0.618	1.00
175_R	180_E	0.617	1.00
160_A	194_T	0.614	1.00
181_H	184_S	0.612	1.00
220_V	240_R	0.612	1.00
78_T	139_G	0.611	1.00
14_W	58_Q	0.609	1.00
112_H	152_F	0.603	1.00
151_R	173_W	0.603	1.00
18_A	64_F	0.599	1.00
58_Q	61_E	0.599	1.00
213_R	224_A	0.597	1.00
88_T	109_A	0.597	1.00
8_F	20_I	0.596	1.00
85_V	93_W	0.596	1.00
155_L	159_Q	0.595	1.00
151_R	186_L	0.594	1.00
94_N	146_T	0.592	1.00
111_L	158_A	0.590	1.00
64_F	67_R	0.585	1.00
181_H	188_A	0.584	1.00
51_D	54_V	0.584	1.00
63_E	66_G	0.582	1.00
82_T	94_N	0.577	1.00
22_A	75_N	0.574	1.00
28_A	32_D	0.574	1.00
48_H	52_L	0.573	1.00
27_Q	231_L	0.570	1.00
136_E	140_M	0.569	1.00
57_A	61_E	0.568	1.00
158_A	161_L	0.566	1.00
114_Y	151_R	0.565	1.00
190_R	194_T	0.564	1.00
40_E	147_C	0.563	1.00
85_V	97_V	0.563	1.00
28_A	77_M	0.560	1.00
173_W	183_W	0.560	1.00
60_L	65_L	0.560	1.00
148_Y	151_R	0.559	1.00
9_A	203_E	0.558	1.00
96_L	146_T	0.558	1.00
78_T	142_V	0.558	1.00
46_D	147_C	0.557	1.00
26_A	29_A	0.557	1.00
28_A	36_F	0.555	1.00
11_T	20_I	0.554	1.00
34_S	139_G	0.553	1.00
114_Y	174_V	0.553	1.00
184_S	211_Q	0.551	1.00
86_P	92_A	0.551	1.00
186_L	189_A	0.549	1.00
52_L	56_S	0.547	1.00
184_S	221_T	0.543	1.00
175_R	209_I	0.542	1.00
156_A	190_R	0.537	1.00
173_W	200_A	0.536	1.00
189_A	192_L	0.535	1.00
46_D	125_V	0.535	1.00
131_I	155_L	0.534	1.00
114_Y	147_C	0.534	1.00
188_A	221_T	0.530	0.99
72_S	99_L	0.530	0.99
134_L	162_Q	0.527	0.99
108_Y	128_G	0.526	0.99
241_V	244_V	0.526	0.99
141_K	162_Q	0.525	0.99
114_Y	173_W	0.524	0.99
15_E	18_A	0.522	0.99
14_W	17_N	0.522	0.99
21_C	24_L	0.519	0.99
29_A	76_M	0.518	0.99
76_M	101_A	0.517	0.99
195_T	244_V	0.515	0.99
34_S	76_M	0.515	0.99
157_L	251_L	0.514	0.99
165_E	241_V	0.514	0.99
24_L	229_P	0.514	0.99
29_A	32_D	0.513	0.99
121_E	125_V	0.512	0.99
119_I	123_R	0.509	0.99
144_L	170_P	0.507	0.99
191_A	219_G	0.506	0.99
159_Q	167_L	0.506	0.99
101_A	105_V	0.505	0.99
60_L	97_V	0.504	0.99
238_P	241_V	0.503	0.99
171_A	183_W	0.502	0.99
151_R	183_W	0.501	0.99
143_G	167_L	0.500	0.99
131_I	159_Q	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
2vhhA	5	0.9962	100	0.142	Contact Map
4izuA	2	0.9389	100	0.151	Contact Map
2w1vA	2	0.9809	100	0.161	Contact Map
3p8kA	2	0.9695	100	0.164	Contact Map
1emsA	3	0.9885	100	0.171	Contact Map
3ivzA	2	0.9542	100	0.171	Contact Map
1uf5A	4	0.9962	100	0.18	Contact Map
3wuyA	2	0.9313	100	0.18	Contact Map
1f89A	2	0.9427	100	0.185	Contact Map
2dyuA	5	0.9733	100	0.187	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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