PUUR - ECOLI - GREMLIN Contacts

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PUUR - HTH-type transcriptional regulator PuuR

UniProt:	P0A9U6	Sequences: MSDEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEPQVVINQDDLIEMGSQGVSMKLVHNGNPNRTLAMIFETYQPGTTTGERIKHQGEEIGTVLEGEIVLTINGQDYHLVAGQSYAINTGIPHSFSNTSAGICRIISAHTPTTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12431
Length:	185 (172)
Sequences:	6011 (4046)
Seq/√Len:	308.5

ECOLI - PUUR YDCN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
138_E	151_V	3.981	1.00
136_E	175_R	3.724	1.00
140_V	147_D	3.115	1.00
140_V	167_S	3.064	1.00
139_I	174_C	2.999	1.00
140_V	149_H	2.954	1.00
140_V	169_T	2.916	1.00
111_F	175_R	2.840	1.00
138_E	149_H	2.687	1.00
113_T	173_I	2.589	1.00
113_T	175_R	2.315	1.00
115_Q	173_I	2.295	1.00
136_E	152_A	2.229	1.00
25_R	29_L	2.181	1.00
23_Q	37_I	2.033	1.00
24_R	28_E	2.021	1.00
85_L	96_K	1.964	1.00
144_N	162_I	1.962	1.00
142_T	147_D	1.935	1.00
14_E	18_Q	1.907	1.00
141_L	156_Y	1.869	1.00
15_I	61_L	1.856	1.00
26_A	59_Y	1.793	1.00
119_T	167_S	1.760	1.00
25_R	28_E	1.730	1.00
24_R	34_H	1.694	1.00
81_N	154_Q	1.686	1.00
135_L	177_I	1.656	1.00
142_T	167_S	1.653	1.00
109_M	131_I	1.628	1.00
21_L	29_L	1.592	1.00
142_T	165_S	1.584	1.00
138_E	170_S	1.535	1.00
150_L	154_Q	1.520	1.00
136_E	172_G	1.501	1.00
139_I	176_I	1.497	1.00
132_G	178_S	1.495	1.00
96_K	111_F	1.492	1.00
126_H	130_E	1.448	1.00
132_G	156_Y	1.447	1.00
109_M	179_A	1.435	1.00
7_A	43_D	1.424	1.00
130_E	164_H	1.414	1.00
133_T	177_I	1.399	1.00
138_E	169_T	1.378	1.00
149_H	169_T	1.368	1.00
36_A	40_I	1.366	1.00
33_T	36_A	1.360	1.00
82_Q	154_Q	1.352	1.00
136_E	173_I	1.343	1.00
32_L	51_T	1.332	1.00
96_K	113_T	1.328	1.00
15_I	19_Q	1.326	1.00
94_S	115_Q	1.313	1.00
19_Q	60_G	1.297	1.00
40_I	47_P	1.277	1.00
11_R	14_E	1.273	1.00
79_V	156_Y	1.265	1.00
134_V	174_C	1.255	1.00
142_T	145_G	1.252	1.00
62_S	65_E	1.246	1.00
151_V	154_Q	1.242	1.00
81_N	84_D	1.232	1.00
38_S	42_Q	1.209	1.00
87_E	96_K	1.203	1.00
129_E	157_A	1.203	1.00
21_L	26_A	1.176	1.00
170_S	174_C	1.151	1.00
94_S	113_T	1.150	1.00
13_S	17_Q	1.145	1.00
131_I	155_S	1.145	1.00
126_H	164_H	1.143	1.00
119_T	165_S	1.132	1.00
127_Q	161_G	1.115	1.00
26_A	58_V	1.110	1.00
30_S	58_V	1.096	1.00
116_P	172_G	1.092	1.00
36_A	45_V	1.082	1.00
143_I	162_I	1.078	1.00
15_I	59_Y	1.075	1.00
114_Y	176_I	1.075	1.00
111_F	133_T	1.069	1.00
168_N	173_I	1.059	1.00
134_V	139_I	1.053	1.00
135_L	175_R	1.032	1.00
16_R	41_E	1.032	1.00
89_G	94_S	1.028	1.00
143_I	158_I	1.014	1.00
32_L	36_A	1.008	1.00
77_Q	148_Y	1.001	1.00
144_N	163_P	0.995	1.00
9_G	43_D	0.987	1.00
116_P	173_I	0.981	1.00
79_V	148_Y	0.980	1.00
21_L	25_R	0.979	1.00
87_E	94_S	0.972	1.00
111_F	135_L	0.970	1.00
56_L	61_L	0.969	1.00
56_L	66_F	0.968	1.00
111_F	177_I	0.967	1.00
112_E	176_I	0.953	1.00
15_I	18_Q	0.947	1.00
23_Q	38_S	0.945	1.00
36_A	51_T	0.937	1.00
107_L	157_A	0.928	1.00
133_T	155_S	0.908	1.00
116_P	168_N	0.897	1.00
134_V	176_I	0.887	1.00
27_A	34_H	0.882	1.00
36_A	39_T	0.882	1.00
105_R	129_E	0.878	1.00
39_T	44_K	0.871	1.00
8_P	52_L	0.864	1.00
32_L	37_I	0.859	1.00
105_R	157_A	0.843	1.00
35_S	38_S	0.833	1.00
52_L	63_L	0.824	1.00
29_L	58_V	0.821	1.00
124_I	164_H	0.814	1.00
39_T	45_V	0.812	1.00
10_K	14_E	0.812	1.00
40_I	55_L	0.810	1.00
82_Q	152_A	0.795	1.00
53_Q	57_K	0.795	1.00
81_N	151_V	0.787	1.00
131_I	179_A	0.787	1.00
93_V	112_E	0.785	1.00
23_Q	34_H	0.780	0.99
12_L	59_Y	0.778	0.99
130_E	160_T	0.766	0.99
107_L	179_A	0.756	0.99
80_I	84_D	0.756	0.99
158_I	164_H	0.755	0.99
11_R	69_E	0.754	0.99
30_S	34_H	0.753	0.99
77_Q	80_I	0.751	0.99
37_I	55_L	0.748	0.99
23_Q	30_S	0.736	0.99
12_L	55_L	0.734	0.99
40_I	46_S	0.729	0.99
30_S	37_I	0.728	0.99
35_S	39_T	0.727	0.99
11_R	15_I	0.726	0.99
124_I	161_G	0.725	0.99
158_I	166_F	0.724	0.99
124_I	166_F	0.724	0.99
75_E	78_V	0.718	0.99
114_Y	174_C	0.717	0.99
138_E	152_A	0.715	0.99
124_I	130_E	0.715	0.99
46_S	50_S	0.709	0.99
61_L	66_F	0.706	0.99
12_L	56_L	0.701	0.99
143_I	148_Y	0.700	0.99
99_H	109_M	0.697	0.99
80_I	85_L	0.697	0.99
95_M	110_I	0.688	0.99
114_Y	118_T	0.687	0.99
117_G	171_A	0.686	0.99
109_M	157_A	0.686	0.99
116_P	170_S	0.685	0.99
10_K	13_S	0.681	0.99
107_L	131_I	0.679	0.99
97_L	110_I	0.679	0.99
168_N	171_A	0.668	0.98
148_Y	156_Y	0.668	0.98
79_V	154_Q	0.667	0.98
49_I	52_L	0.665	0.98
27_A	37_I	0.659	0.98
38_S	67_F	0.653	0.98
64_S	108_A	0.651	0.98
30_S	54_K	0.649	0.98
53_Q	63_L	0.647	0.98
128_G	160_T	0.647	0.98
11_R	66_F	0.642	0.98
80_I	86_I	0.641	0.98
108_A	180_H	0.641	0.98
160_T	164_H	0.640	0.98
30_S	59_Y	0.634	0.98
79_V	150_L	0.632	0.98
99_H	157_A	0.630	0.98
131_I	157_A	0.630	0.98
29_L	60_G	0.628	0.98
22_S	25_R	0.624	0.98
7_A	10_K	0.622	0.98
134_V	151_V	0.620	0.97
112_E	178_S	0.620	0.97
63_L	67_F	0.618	0.97
114_Y	139_I	0.616	0.97
55_L	59_Y	0.615	0.97
42_Q	45_V	0.614	0.97
51_T	54_K	0.614	0.97
124_I	127_Q	0.614	0.97
95_M	99_H	0.613	0.97
77_Q	84_D	0.611	0.97
129_E	159_N	0.607	0.97
23_Q	33_T	0.606	0.97
115_Q	118_T	0.604	0.97
36_A	48_A	0.604	0.97
12_L	38_S	0.604	0.97
46_S	51_T	0.604	0.97
106_T	181_T	0.602	0.97
22_S	34_H	0.591	0.97
92_G	115_Q	0.590	0.97
21_L	59_Y	0.576	0.96
81_N	85_L	0.576	0.96
123_R	163_P	0.574	0.96
34_H	51_T	0.572	0.96
116_P	171_A	0.569	0.96
150_L	156_Y	0.569	0.96
76_P	146_Q	0.569	0.96
64_S	131_I	0.568	0.96
33_T	51_T	0.566	0.96
147_D	169_T	0.564	0.96
65_E	68_S	0.562	0.96
23_Q	42_Q	0.559	0.95
32_L	47_P	0.557	0.95
83_D	151_V	0.557	0.95
60_G	65_E	0.556	0.95
146_Q	162_I	0.555	0.95
131_I	158_I	0.553	0.95
109_M	133_T	0.553	0.95
147_D	167_S	0.550	0.95
45_V	49_I	0.549	0.95
14_E	17_Q	0.547	0.95
121_G	165_S	0.546	0.95
32_L	58_V	0.544	0.95
117_G	168_N	0.541	0.95
49_I	63_L	0.540	0.94
47_P	51_T	0.539	0.94
152_A	175_R	0.533	0.94
45_V	48_A	0.530	0.94
49_I	95_M	0.530	0.94
134_V	150_L	0.530	0.94
82_Q	151_V	0.529	0.94
27_A	31_G	0.529	0.94
166_F	178_S	0.527	0.94
37_I	132_G	0.523	0.93
149_H	171_A	0.523	0.93
98_V	109_M	0.523	0.93
53_Q	166_F	0.521	0.93
10_K	17_Q	0.519	0.93
54_K	58_V	0.516	0.93
61_L	65_E	0.516	0.93
139_I	166_F	0.515	0.93
132_G	139_I	0.515	0.93
86_I	94_S	0.514	0.93
23_Q	27_A	0.513	0.93
91_Q	115_Q	0.512	0.93
145_G	162_I	0.512	0.93
117_G	170_S	0.510	0.93
67_F	114_Y	0.506	0.92
116_P	169_T	0.506	0.92
98_V	155_S	0.505	0.92
132_G	141_L	0.504	0.92
33_T	45_V	0.504	0.92
107_L	181_T	0.504	0.92
50_S	108_A	0.500	0.92

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
1y9qA	1	0.9459	100	0.367	Contact Map
2bnmA	3	0.973	100	0.369	Contact Map
4yarA	2	0.9676	100	0.384	Contact Map
4b29A	1	0.9568	100	0.445	Contact Map
4qm9A	1	0.7351	100	0.465	Contact Map
2p5tA	2	0.5189	99.9	0.501	Contact Map
4lukA	2	0.7784	99.9	0.526	Contact Map
1j58A	5	0.7892	99.9	0.53	Contact Map
4e2qA	6	0.7243	99.9	0.534	Contact Map
3bu7A	3	0.8541	99.8	0.595	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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