NUDE - ECOLI - GREMLIN Contacts

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NUDE - ADP compounds hydrolase NudE

UniProt:	P45799	Sequences: MSKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGRV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12926
Length:	186 (169)
Sequences:	5914 (4214)
Seq/√Len:	324.2

ECOLI - NUDE ADPP NUDK
BACSU - ADPP
HALSA - Q9HNS9 Q9HME6
SULSO - Q97WP3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_T	30_E	2.962	1.00
51_M	77_F	2.789	1.00
89_Y	93_N	2.472	1.00
14_E	26_S	2.394	1.00
106_D	130_Q	2.358	1.00
18_R	23_T	2.344	1.00
56_V	59_H	2.318	1.00
97_K	103_G	2.303	1.00
155_M	173_L	2.201	1.00
59_H	151_P	2.190	1.00
156_M	177_R	2.186	1.00
59_H	149_R	2.183	1.00
12_N	28_D	2.150	1.00
75_L	148_V	2.127	1.00
13_V	25_E	2.071	1.00
15_T	18_R	2.039	1.00
87_S	90_E	2.000	1.00
109_F	125_N	1.994	1.00
157_D	161_D	1.993	1.00
26_S	38_V	1.976	1.00
108_T	130_Q	1.973	1.00
28_D	36_R	1.971	1.00
61_I	149_R	1.968	1.00
112_K	123_K	1.939	1.00
56_V	149_R	1.936	1.00
64_R	146_P	1.903	1.00
105_N	131_D	1.798	1.00
43_R	121_S	1.797	1.00
25_E	43_R	1.797	1.00
105_N	133_Y	1.788	1.00
82_I	91_A	1.758	1.00
158_L	163_D	1.731	1.00
109_F	112_K	1.719	1.00
86_E	94_R	1.708	1.00
93_N	107_L	1.701	1.00
64_R	148_V	1.695	1.00
13_V	27_V	1.690	1.00
30_E	36_R	1.677	1.00
65_E	76_G	1.647	1.00
88_V	125_N	1.646	1.00
52_I	92_A	1.610	1.00
150_W	158_L	1.603	1.00
19_S	40_E	1.547	1.00
151_P	154_H	1.539	1.00
112_K	125_N	1.537	1.00
174_F	178_E	1.529	1.00
11_L	30_E	1.507	1.00
27_V	68_V	1.495	1.00
96_L	104_A	1.482	1.00
103_G	133_Y	1.474	1.00
10_I	68_V	1.457	1.00
28_D	38_V	1.448	1.00
53_V	172_A	1.436	1.00
90_E	93_N	1.413	1.00
154_H	157_D	1.411	1.00
77_F	172_A	1.403	1.00
114_S	165_N	1.367	1.00
89_Y	107_L	1.361	1.00
72_S	165_N	1.322	1.00
106_D	131_D	1.322	1.00
61_I	102_F	1.318	1.00
82_I	88_V	1.314	1.00
26_S	40_E	1.293	1.00
91_A	94_R	1.271	1.00
11_L	36_R	1.234	1.00
53_V	176_V	1.212	1.00
15_T	25_E	1.208	1.00
113_L	171_S	1.187	1.00
97_K	138_E	1.187	1.00
93_N	97_K	1.171	1.00
15_T	23_T	1.139	1.00
88_V	127_V	1.138	1.00
97_K	135_E	1.137	1.00
78_S	100_V	1.131	1.00
70_T	74_E	1.119	1.00
150_W	155_M	1.116	1.00
14_E	28_D	1.114	1.00
102_F	134_P	1.095	1.00
70_T	114_S	1.084	1.00
113_L	126_I	1.082	1.00
61_I	147_Q	1.079	1.00
156_M	160_E	1.066	1.00
116_A	122_S	1.066	1.00
54_P	96_L	1.064	1.00
154_H	158_L	1.048	1.00
160_E	178_E	1.047	1.00
68_V	71_E	1.046	1.00
109_F	127_V	1.046	1.00
157_D	160_E	1.019	1.00
48_E	82_I	0.982	1.00
86_E	91_A	0.979	1.00
64_R	73_Y	0.971	1.00
32_S	144_P	0.960	1.00
126_I	172_A	0.960	1.00
110_L	128_V	0.955	1.00
159_L	170_V	0.955	1.00
138_E	143_E	0.942	1.00
66_Y	71_E	0.927	1.00
50_V	92_A	0.927	1.00
171_S	174_F	0.912	1.00
49_A	124_M	0.893	1.00
16_V	24_V	0.886	1.00
107_L	129_A	0.870	1.00
74_E	117_P	0.865	1.00
89_Y	109_F	0.857	1.00
27_V	41_R	0.854	1.00
67_A	76_G	0.848	1.00
55_I	128_V	0.847	1.00
166_E	169_N	0.847	1.00
58_D	152_L	0.847	1.00
16_V	26_S	0.847	1.00
48_E	123_K	0.843	1.00
10_I	27_V	0.842	1.00
92_A	107_L	0.838	1.00
56_V	102_F	0.832	1.00
53_V	60_L	0.832	1.00
44_P	122_S	0.829	1.00
156_M	173_L	0.828	1.00
57_D	131_D	0.828	1.00
107_L	127_V	0.820	1.00
22_F	42_M	0.820	1.00
104_A	107_L	0.819	1.00
77_F	173_L	0.816	1.00
60_L	173_L	0.815	1.00
53_V	77_F	0.807	1.00
52_I	129_A	0.804	1.00
51_M	126_I	0.797	1.00
62_L	150_W	0.788	1.00
60_L	77_F	0.783	1.00
139_G	145_L	0.778	1.00
115_M	119_Y	0.764	1.00
17_A	24_V	0.754	0.99
42_M	119_Y	0.753	0.99
55_I	152_L	0.752	0.99
139_G	143_E	0.752	0.99
51_M	124_M	0.749	0.99
114_S	123_K	0.744	0.99
62_L	75_L	0.737	0.99
10_I	71_E	0.732	0.99
97_K	136_S	0.730	0.99
93_N	103_G	0.723	0.99
48_E	125_N	0.721	0.99
62_L	148_V	0.719	0.99
57_D	130_Q	0.718	0.99
113_L	167_A	0.706	0.99
124_M	168_R	0.705	0.99
64_R	75_L	0.702	0.99
108_T	128_V	0.701	0.99
111_K	171_S	0.700	0.99
159_L	164_F	0.699	0.99
54_P	128_V	0.698	0.99
158_L	161_D	0.693	0.99
75_L	150_W	0.691	0.99
104_A	129_A	0.687	0.99
60_L	176_V	0.685	0.99
23_T	43_R	0.683	0.99
51_M	168_R	0.682	0.99
113_L	170_V	0.680	0.99
55_I	60_L	0.679	0.99
50_V	88_V	0.679	0.99
41_R	68_V	0.675	0.99
73_Y	144_P	0.672	0.99
139_G	142_P	0.669	0.99
116_A	120_F	0.666	0.99
44_P	48_E	0.663	0.99
63_I	145_L	0.657	0.99
78_S	96_L	0.657	0.99
13_V	43_R	0.649	0.98
57_D	133_Y	0.648	0.98
89_Y	127_V	0.645	0.98
112_K	165_N	0.645	0.98
62_L	155_M	0.644	0.98
55_I	130_Q	0.638	0.98
111_K	175_L	0.638	0.98
55_I	58_D	0.637	0.98
140_D	143_E	0.630	0.98
152_L	177_R	0.626	0.98
55_I	176_V	0.626	0.98
151_P	156_M	0.624	0.98
54_P	104_A	0.620	0.98
155_M	159_L	0.620	0.98
24_V	42_M	0.616	0.98
137_L	147_Q	0.616	0.98
54_P	77_F	0.616	0.98
11_L	28_D	0.609	0.98
115_M	167_A	0.609	0.98
60_L	152_L	0.608	0.98
54_P	63_I	0.606	0.98
49_A	81_L	0.606	0.98
123_K	165_N	0.603	0.97
106_D	109_F	0.595	0.97
154_H	163_D	0.590	0.97
152_L	156_M	0.588	0.97
82_I	125_N	0.586	0.97
92_A	127_V	0.586	0.97
174_F	177_R	0.585	0.97
44_P	119_Y	0.582	0.97
14_E	38_V	0.581	0.97
33_N	144_P	0.581	0.97
52_I	78_S	0.577	0.97
136_S	139_G	0.573	0.97
92_A	96_L	0.573	0.97
19_S	26_S	0.573	0.97
8_P	29_L	0.572	0.96
56_V	61_I	0.569	0.96
171_S	175_L	0.567	0.96
27_V	71_E	0.566	0.96
75_L	158_L	0.566	0.96
135_E	138_E	0.565	0.96
47_R	81_L	0.565	0.96
74_E	114_S	0.564	0.96
131_D	134_P	0.562	0.96
12_N	15_T	0.562	0.96
153_A	156_M	0.560	0.96
52_I	96_L	0.558	0.96
159_L	173_L	0.557	0.96
51_M	79_K	0.551	0.96
148_V	158_L	0.551	0.96
110_L	176_V	0.550	0.96
60_L	155_M	0.549	0.96
104_A	132_L	0.545	0.95
167_A	171_S	0.545	0.95
108_T	111_K	0.542	0.95
8_P	32_S	0.541	0.95
83_D	91_A	0.541	0.95
10_I	13_V	0.540	0.95
150_W	154_H	0.540	0.95
164_F	169_N	0.536	0.95
111_K	162_P	0.536	0.95
31_F	35_V	0.536	0.95
48_E	81_L	0.532	0.95
115_M	120_F	0.530	0.95
79_K	168_R	0.528	0.95
173_L	177_R	0.526	0.94
111_K	170_V	0.526	0.94
29_L	37_R	0.526	0.94
87_S	127_V	0.525	0.94
79_K	118_S	0.525	0.94
59_H	154_H	0.522	0.94
41_R	44_P	0.519	0.94
39_Y	44_P	0.519	0.94
128_V	175_L	0.519	0.94
29_L	68_V	0.518	0.94
158_L	164_F	0.518	0.94
30_E	34_G	0.516	0.94
67_A	118_S	0.514	0.94
155_M	177_R	0.511	0.94
170_V	174_F	0.510	0.93
104_A	131_D	0.508	0.93
52_I	107_L	0.507	0.93
31_F	37_R	0.504	0.93
79_K	116_A	0.504	0.93
44_P	120_F	0.501	0.93
103_G	135_E	0.500	0.93

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
1vhzA	2	1	100	0.287	Contact Map
1g0sA	2	0.9839	100	0.309	Contact Map
2dscA	2	0.9355	100	0.324	Contact Map
1mk1A	2	0.8817	100	0.377	Contact Map
2yvpA	2	0.9516	100	0.407	Contact Map
3o6zA	2	0.9355	100	0.417	Contact Map
1v8yA	2	0.8011	100	0.44	Contact Map
3q91A	2	0.6989	100	0.482	Contact Map
2w4eA	2	0.7312	99.9	0.526	Contact Map
2fvvA	1	0.7151	99.9	0.572	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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