ULAD - ECOLI - GREMLIN Contacts

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ULAD - 3-keto-L-gulonate-6-phosphate decarboxylase UlaD

UniProt:	P39304	Sequences: MSLPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGDVQIELTGYWTWEQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPLFKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12496
Length:	216 (205)
Sequences:	3278 (2195)
Seq/√Len:	153.3

ECOLI - ULAD SGBH PYRF
BACSU - HPS PYRF
SULSO - Q980S5 PYRF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_R	53_L	3.839	1.00
14_T	17_S	3.618	1.00
199_S	202_E	3.520	1.00
88_C	110_Q	3.294	1.00
51_K	82_D	3.229	1.00
90_A	94_T	2.506	1.00
45_R	48_R	2.479	1.00
201_V	205_R	2.383	1.00
19_Y	49_D	2.343	1.00
178_P	210_S	2.331	1.00
92_I	96_K	2.278	1.00
197_A	203_A	2.273	1.00
150_E	175_E	2.241	1.00
202_E	206_Q	2.220	1.00
119_W	130_I	2.193	1.00
99_L	103_K	2.168	1.00
15_M	49_D	2.110	1.00
157_K	186_H	2.098	1.00
73_S	100_D	2.075	1.00
6_L	190_A	2.050	1.00
36_T	40_V	1.994	1.00
178_P	182_G	1.859	1.00
28_E	205_R	1.824	1.00
179_L	182_G	1.818	1.00
175_E	183_I	1.794	1.00
157_K	167_T	1.762	1.00
119_W	123_Q	1.750	1.00
92_I	124_Q	1.745	1.00
156_I	167_T	1.660	1.00
73_S	101_V	1.630	1.00
12_N	21_T	1.622	1.00
185_I	188_F	1.602	1.00
118_T	121_Q	1.596	1.00
142_Q	161_D	1.593	1.00
15_M	46_A	1.572	1.00
7_Q	31_I	1.521	1.00
40_V	65_I	1.507	1.00
15_M	42_E	1.502	1.00
93_N	96_K	1.499	1.00
20_E	24_L	1.492	1.00
96_K	100_D	1.480	1.00
58_I	82_D	1.479	1.00
49_D	52_A	1.459	1.00
17_S	20_E	1.454	1.00
34_V	50_L	1.452	1.00
129_G	132_Q	1.450	1.00
21_T	25_I	1.446	1.00
135_Y	159_L	1.405	1.00
93_N	121_Q	1.397	1.00
6_L	204_A	1.393	1.00
92_I	144_A	1.379	1.00
38_L	42_E	1.370	1.00
128_A	136_H	1.343	1.00
24_L	200_P	1.328	1.00
205_R	209_R	1.318	1.00
6_L	211_I	1.315	1.00
8_V	29_V	1.309	1.00
150_E	172_L	1.304	1.00
113_L	117_W	1.301	1.00
92_I	143_A	1.298	1.00
179_L	183_I	1.294	1.00
9_A	191_G	1.290	1.00
32_I	57_K	1.284	1.00
18_A	38_L	1.281	1.00
24_L	199_S	1.281	1.00
76_C	84_V	1.260	1.00
92_I	140_D	1.253	1.00
119_W	129_G	1.251	1.00
206_Q	210_S	1.234	1.00
8_V	195_R	1.224	1.00
15_M	19_Y	1.220	1.00
206_Q	209_R	1.218	1.00
202_E	205_R	1.214	1.00
22_T	32_I	1.201	1.00
128_A	132_Q	1.196	1.00
203_A	206_Q	1.192	1.00
7_Q	187_V	1.190	1.00
167_T	186_H	1.188	1.00
48_R	52_A	1.175	1.00
154_T	183_I	1.171	1.00
169_T	185_I	1.158	1.00
133_V	137_R	1.151	1.00
120_E	124_Q	1.144	1.00
24_L	201_V	1.131	1.00
139_R	159_L	1.130	1.00
154_T	158_R	1.130	1.00
142_Q	160_S	1.127	1.00
65_I	72_L	1.122	1.00
85_T	109_V	1.113	0.99
72_L	94_T	1.112	0.99
97_G	100_D	1.109	0.99
101_V	105_F	1.104	0.99
85_T	111_I	1.101	0.99
31_I	58_I	1.091	0.99
72_L	98_A	1.089	0.99
13_Q	17_S	1.087	0.99
156_I	160_S	1.086	0.99
155_A	159_L	1.079	0.99
70_K	74_R	1.068	0.99
69_G	94_T	1.061	0.99
113_L	133_V	1.047	0.99
38_L	46_A	1.046	0.99
19_Y	23_R	1.046	0.99
117_W	121_Q	1.037	0.99
123_Q	127_D	1.033	0.99
29_V	204_A	1.032	0.99
122_A	126_R	1.015	0.99
31_I	83_W	1.015	0.99
27_E	201_V	1.005	0.99
89_C	137_R	0.992	0.99
93_N	97_G	0.990	0.99
153_I	185_I	0.978	0.99
84_V	102_A	0.957	0.98
6_L	208_K	0.956	0.98
86_V	108_D	0.954	0.98
22_T	50_L	0.954	0.98
61_A	81_A	0.954	0.98
76_C	102_A	0.944	0.98
30_D	57_K	0.942	0.98
181_K	211_I	0.940	0.98
47_V	79_A	0.936	0.98
42_E	45_R	0.929	0.98
166_V	186_H	0.927	0.98
78_E	105_F	0.920	0.98
135_Y	139_R	0.919	0.98
41_G	78_E	0.906	0.98
181_K	188_F	0.906	0.98
201_V	204_A	0.901	0.98
89_C	133_V	0.882	0.97
44_V	47_V	0.880	0.97
37_I	74_R	0.879	0.97
123_Q	128_A	0.878	0.97
148_W	167_T	0.877	0.97
19_Y	22_T	0.871	0.97
109_V	168_V	0.867	0.97
92_I	95_A	0.864	0.97
39_C	63_A	0.861	0.97
28_E	201_V	0.855	0.97
153_I	167_T	0.855	0.97
148_W	156_I	0.854	0.97
135_Y	155_A	0.853	0.97
5_M	58_I	0.851	0.97
85_T	95_A	0.849	0.97
95_A	144_A	0.842	0.97
194_I	204_A	0.842	0.97
97_G	101_V	0.842	0.97
86_V	95_A	0.841	0.96
88_C	141_A	0.840	0.96
32_I	50_L	0.840	0.96
204_A	208_K	0.829	0.96
193_S	207_F	0.829	0.96
112_E	115_G	0.829	0.96
72_L	90_A	0.829	0.96
99_L	108_D	0.826	0.96
26_A	32_I	0.822	0.96
39_C	44_V	0.822	0.96
47_V	51_K	0.821	0.96
175_E	179_L	0.816	0.96
15_M	45_R	0.815	0.96
47_V	59_V	0.805	0.96
121_Q	125_W	0.805	0.96
4_P	30_D	0.805	0.96
74_R	196_D	0.800	0.95
128_A	133_V	0.798	0.95
10_L	34_V	0.795	0.95
203_A	210_S	0.790	0.95
12_N	18_A	0.790	0.95
26_A	29_V	0.784	0.95
89_C	117_W	0.781	0.95
25_I	201_V	0.780	0.95
8_V	25_I	0.772	0.94
17_S	24_L	0.769	0.94
60_L	85_T	0.769	0.94
83_W	109_V	0.768	0.94
190_A	207_F	0.764	0.94
167_T	187_V	0.764	0.94
76_C	108_D	0.760	0.94
65_I	75_M	0.760	0.94
21_T	24_L	0.757	0.94
89_C	113_L	0.755	0.94
131_G	155_A	0.753	0.94
46_A	49_D	0.753	0.94
83_W	187_V	0.752	0.94
139_R	160_S	0.749	0.93
50_L	53_L	0.748	0.93
155_A	158_R	0.745	0.93
30_D	204_A	0.742	0.93
10_L	50_L	0.741	0.93
207_F	210_S	0.736	0.93
103_K	106_N	0.734	0.93
42_E	46_A	0.733	0.93
77_F	106_N	0.733	0.93
151_A	175_E	0.732	0.93
110_Q	141_A	0.731	0.93
121_Q	124_Q	0.730	0.93
31_I	82_D	0.724	0.92
37_I	195_R	0.723	0.92
146_V	165_K	0.722	0.92
8_V	194_I	0.722	0.92
89_C	126_R	0.721	0.92
135_Y	160_S	0.720	0.92
59_V	81_A	0.719	0.92
49_D	53_L	0.712	0.92
146_V	156_I	0.706	0.91
27_E	30_D	0.702	0.91
19_Y	53_L	0.700	0.91
139_R	143_A	0.699	0.91
4_P	58_I	0.696	0.91
66_A	89_C	0.695	0.91
104_E	107_G	0.693	0.90
36_T	75_M	0.691	0.90
26_A	57_K	0.689	0.90
166_V	187_V	0.687	0.90
45_R	49_D	0.686	0.90
160_S	165_K	0.686	0.90
16_D	20_E	0.682	0.90
8_V	21_T	0.680	0.90
126_R	133_V	0.678	0.90
7_Q	168_V	0.678	0.90
20_E	23_R	0.675	0.89
85_T	165_K	0.671	0.89
36_T	65_I	0.671	0.89
146_V	167_T	0.666	0.89
12_N	195_R	0.665	0.89
77_F	105_F	0.663	0.88
149_G	152_D	0.663	0.88
65_I	76_C	0.661	0.88
203_A	207_F	0.655	0.88
16_D	19_Y	0.651	0.88
188_F	211_I	0.647	0.87
136_H	140_D	0.644	0.87
98_A	101_V	0.640	0.87
22_T	42_E	0.639	0.87
199_S	203_A	0.637	0.86
50_L	57_K	0.635	0.86
29_V	57_K	0.634	0.86
110_Q	113_L	0.634	0.86
10_L	22_T	0.629	0.86
21_T	200_P	0.629	0.86
141_A	145_G	0.625	0.85
112_E	116_Y	0.624	0.85
5_M	181_K	0.623	0.85
177_L	188_F	0.621	0.85
100_D	104_E	0.620	0.85
138_S	142_Q	0.617	0.85
34_V	38_L	0.614	0.84
146_V	149_G	0.611	0.84
153_I	157_K	0.610	0.84
77_F	84_V	0.601	0.83
120_E	123_Q	0.598	0.83
110_Q	114_T	0.597	0.83
45_R	52_A	0.596	0.83
177_L	184_P	0.593	0.82
34_V	46_A	0.592	0.82
28_E	208_K	0.591	0.82
51_K	59_V	0.589	0.82
64_K	67_D	0.585	0.81
76_C	98_A	0.585	0.81
25_I	204_A	0.584	0.81
29_V	208_K	0.581	0.81
201_V	209_R	0.581	0.81
25_I	57_K	0.579	0.81
177_L	207_F	0.570	0.80
34_V	39_C	0.568	0.80
60_L	115_G	0.567	0.79
73_S	97_G	0.566	0.79
87_I	170_G	0.565	0.79
125_W	130_I	0.564	0.79
27_E	57_K	0.562	0.79
37_I	71_I	0.559	0.78
31_I	57_K	0.557	0.78
40_V	63_A	0.555	0.78
139_R	142_Q	0.554	0.78
86_V	98_A	0.550	0.77
66_A	87_I	0.550	0.77
113_L	137_R	0.543	0.76
152_D	173_A	0.540	0.76
38_L	41_G	0.538	0.76
133_V	136_H	0.538	0.76
124_Q	128_A	0.538	0.76
87_I	114_T	0.535	0.75
161_D	164_F	0.533	0.75
60_L	83_W	0.528	0.74
29_V	32_I	0.525	0.74
133_V	156_I	0.523	0.74
112_E	146_V	0.523	0.74
66_A	117_W	0.521	0.73
6_L	167_T	0.520	0.73
10_L	18_A	0.518	0.73
31_I	187_V	0.516	0.73
9_A	195_R	0.516	0.73
157_K	187_V	0.515	0.73
100_D	103_K	0.515	0.73
110_Q	115_G	0.514	0.72
22_T	54_Y	0.511	0.72
119_W	122_A	0.510	0.72
32_I	194_I	0.509	0.72
153_I	184_P	0.508	0.72
77_F	102_A	0.507	0.71
13_Q	74_R	0.506	0.71
83_W	147_A	0.505	0.71
208_K	211_I	0.505	0.71
33_E	170_G	0.504	0.71
131_G	135_Y	0.504	0.71
26_A	30_D	0.501	0.71
152_D	156_I	0.501	0.71
109_V	116_Y	0.501	0.71
92_I	125_W	0.500	0.70

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
3gdmA	2	0.9583	100	0.3	Contact Map
3qw4B	4	0.9676	100	0.307	Contact Map
3qw3A	2	0.963	100	0.319	Contact Map
2ffcA	2	0.9815	100	0.33	Contact Map
4mjzA	2	0.9769	100	0.343	Contact Map
3ldvA	2	0.9676	100	0.345	Contact Map
3r89A	2	0.9907	100	0.352	Contact Map
3tr2A	2	0.963	100	0.355	Contact Map
1eixA	2	0.9722	100	0.357	Contact Map
3tfxA	2	0.9769	100	0.358	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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