ARAD - BACSU - GREMLIN Contacts

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ARAD - L-ribulose-5-phosphate 4-epimerase

UniProt:	P94525	Sequences: MLETLKKEVLAANLKLQEHQLVTFTWGNVSGIDREKERIVIKPSGVEYSDLTADDLVVLNLDGEVVEGSLKPSSDTPTHVYLYKAFPNIGGIVHTHSQWATSWAQSGRDIPPLGTTHADYFDSAIPCTREMYDEEIIHDYELNTGKVIAETFQHHNYEQVPGVLVNNHGPFCWGTDALNAIHNAVVLETVAEMAYHSIMLNKDVTPINTVLHEKHFYRKHGANAYYGQS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	229 (199)
Sequences:	6320 (3867)
Seq/√Len:	274.2

ECOLI - ARAD SGBE ULAF FUCA YGBL RHAD
BACSU - ARAD MTNB
HALSA - Q9HQE3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_N	64_E	4.798	1.00
175_T	179_N	3.189	1.00
99_W	196_H	3.113	1.00
192_E	196_H	3.067	1.00
38_R	58_V	2.866	1.00
209_T	213_E	2.663	1.00
5_L	31_G	2.607	1.00
108_R	198_I	2.588	1.00
40_V	56_L	2.516	1.00
39_I	80_V	2.454	1.00
8_E	178_L	2.449	1.00
89_I	173_W	2.200	1.00
81_Y	146_K	2.147	1.00
38_R	66_V	2.060	1.00
98_Q	192_E	2.055	1.00
102_S	196_H	2.041	1.00
99_W	192_E	2.025	1.00
208_N	211_L	1.978	1.00
10_L	53_A	1.947	1.00
81_Y	84_K	1.909	1.00
52_T	55_D	1.906	1.00
99_W	195_Y	1.886	1.00
7_K	11_A	1.866	1.00
140_Y	146_K	1.828	1.00
31_G	177_A	1.826	1.00
162_G	187_L	1.825	1.00
40_V	58_V	1.811	1.00
93_V	180_A	1.797	1.00
196_H	199_M	1.706	1.00
15_K	19_H	1.696	1.00
129_R	166_N	1.694	1.00
90_G	176_D	1.655	1.00
33_D	40_V	1.655	1.00
91_G	177_A	1.607	1.00
59_L	76_T	1.605	1.00
176_D	179_N	1.576	1.00
9_V	29_V	1.555	1.00
62_D	84_K	1.533	1.00
12_A	181_I	1.530	1.00
109_D	124_A	1.519	1.00
33_D	36_K	1.512	1.00
107_G	166_N	1.470	1.00
10_L	14_L	1.456	1.00
174_G	179_N	1.444	1.00
65_V	68_G	1.436	1.00
19_H	185_V	1.434	1.00
7_K	53_A	1.433	1.00
85_A	153_Q	1.432	1.00
9_V	56_L	1.420	1.00
4_T	8_E	1.413	1.00
126_P	155_H	1.399	1.00
14_L	18_E	1.391	1.00
95_T	184_A	1.365	1.00
170_P	187_L	1.360	1.00
111_P	194_A	1.354	1.00
39_I	61_L	1.341	1.00
135_E	147_V	1.340	1.00
98_Q	102_S	1.339	1.00
85_A	149_A	1.337	1.00
31_G	91_G	1.326	1.00
172_C	184_A	1.289	1.00
81_Y	85_A	1.285	1.00
86_F	89_I	1.275	1.00
96_H	168_H	1.245	1.00
10_L	56_L	1.232	1.00
80_V	84_K	1.231	1.00
110_I	191_A	1.227	1.00
30_S	92_I	1.222	1.00
211_L	214_K	1.218	1.00
103_W	198_I	1.214	1.00
123_S	213_E	1.202	1.00
58_V	67_E	1.184	1.00
15_K	18_E	1.176	1.00
146_K	150_E	1.161	1.00
30_S	83_Y	1.157	1.00
98_Q	189_T	1.148	1.00
161_P	183_N	1.145	1.00
83_Y	92_I	1.141	1.00
100_A	170_P	1.131	1.00
129_R	150_E	1.126	1.00
195_Y	200_L	1.123	1.00
101_T	104_A	1.121	1.00
16_L	29_V	1.113	1.00
46_V	55_D	1.109	1.00
198_I	202_K	1.102	1.00
107_G	205_T	1.102	1.00
12_A	177_A	1.100	1.00
165_V	171_F	1.090	1.00
147_V	150_E	1.089	1.00
194_A	198_I	1.082	1.00
17_Q	49_S	1.080	1.00
32_I	90_G	1.077	1.00
94_H	168_H	1.072	1.00
33_D	58_V	1.071	1.00
95_T	170_P	1.070	1.00
16_L	93_V	1.062	1.00
41_I	73_S	1.037	1.00
99_W	188_E	1.031	1.00
188_E	192_E	1.028	1.00
106_S	200_L	1.027	1.00
152_F	173_W	1.026	1.00
148_I	165_V	1.025	1.00
162_G	172_C	1.016	1.00
113_L	194_A	1.016	1.00
195_Y	199_M	1.012	1.00
46_V	70_L	1.009	1.00
13_N	29_V	1.001	1.00
100_A	187_L	0.991	1.00
86_F	173_W	0.982	1.00
189_T	192_E	0.965	1.00
39_I	76_T	0.964	1.00
109_D	127_C	0.962	1.00
97_S	100_A	0.959	1.00
12_A	29_V	0.956	1.00
33_D	38_R	0.948	1.00
174_G	183_N	0.945	1.00
55_D	70_L	0.939	1.00
19_H	181_I	0.933	1.00
43_P	46_V	0.929	1.00
207_I	211_L	0.924	1.00
5_L	33_D	0.919	1.00
51_L	55_D	0.910	1.00
107_G	203_D	0.909	1.00
61_L	84_K	0.906	1.00
8_E	11_A	0.903	1.00
152_F	163_V	0.902	1.00
128_T	147_V	0.899	1.00
122_D	209_T	0.897	1.00
210_V	214_K	0.890	1.00
57_V	71_K	0.888	1.00
39_I	59_L	0.883	1.00
123_S	209_T	0.881	1.00
8_E	31_G	0.879	1.00
16_L	181_I	0.876	1.00
82_L	152_F	0.872	1.00
93_V	184_A	0.871	1.00
213_E	216_F	0.865	1.00
129_R	147_V	0.865	1.00
60_N	66_V	0.858	1.00
43_P	56_L	0.847	1.00
10_L	51_L	0.842	1.00
55_D	69_S	0.841	1.00
210_V	213_E	0.834	1.00
98_Q	196_H	0.830	1.00
41_I	75_D	0.829	0.99
102_S	195_Y	0.827	0.99
110_I	190_V	0.822	0.99
170_P	184_A	0.819	0.99
81_Y	149_A	0.813	0.99
110_I	164_L	0.812	0.99
166_N	205_T	0.808	0.99
82_L	89_I	0.804	0.99
37_E	61_L	0.804	0.99
126_P	163_V	0.803	0.99
50_D	178_L	0.799	0.99
4_T	7_K	0.798	0.99
78_T	171_F	0.795	0.99
150_E	153_Q	0.793	0.99
6_K	67_E	0.789	0.99
97_S	184_A	0.787	0.99
32_I	37_E	0.780	0.99
105_Q	113_L	0.779	0.99
32_I	61_L	0.777	0.99
179_N	183_N	0.776	0.99
85_A	150_E	0.771	0.99
11_A	50_D	0.768	0.99
125_I	187_L	0.763	0.99
15_K	181_I	0.763	0.99
44_S	71_K	0.760	0.99
206_P	209_T	0.760	0.99
97_S	188_E	0.759	0.99
128_T	165_V	0.758	0.99
134_E	138_H	0.755	0.99
13_N	48_Y	0.752	0.99
35_E	38_R	0.740	0.99
207_I	212_H	0.738	0.99
187_L	191_A	0.738	0.99
6_K	40_V	0.737	0.99
78_T	148_I	0.735	0.99
211_L	215_H	0.729	0.99
42_K	83_Y	0.728	0.99
106_S	202_K	0.725	0.99
46_V	51_L	0.720	0.99
76_T	80_V	0.715	0.99
103_W	194_A	0.715	0.99
30_S	41_I	0.714	0.98
90_G	175_T	0.713	0.98
22_V	29_V	0.713	0.98
141_E	147_V	0.712	0.98
82_L	171_F	0.712	0.98
20_Q	192_E	0.703	0.98
151_T	163_V	0.697	0.98
172_C	183_N	0.697	0.98
42_K	51_L	0.696	0.98
205_T	208_N	0.695	0.98
24_F	182_H	0.689	0.98
135_E	142_L	0.687	0.98
84_K	149_A	0.683	0.98
108_R	202_K	0.682	0.98
77_P	140_Y	0.678	0.98
109_D	155_H	0.678	0.98
128_T	151_T	0.673	0.98
208_N	214_K	0.670	0.98
209_T	212_H	0.670	0.98
101_T	193_M	0.668	0.98
25_T	44_S	0.666	0.98
113_L	198_I	0.664	0.98
27_G	48_Y	0.664	0.98
58_V	66_V	0.664	0.98
50_D	55_D	0.663	0.98
47_E	50_D	0.661	0.98
149_A	152_F	0.660	0.97
5_L	8_E	0.654	0.97
6_K	58_V	0.652	0.97
139_D	142_L	0.643	0.97
179_N	182_H	0.642	0.97
109_D	126_P	0.641	0.97
86_F	152_F	0.633	0.97
16_L	21_L	0.633	0.97
197_S	203_D	0.630	0.97
124_A	155_H	0.628	0.97
91_G	180_A	0.628	0.97
111_P	206_P	0.626	0.97
106_S	195_Y	0.626	0.97
101_T	169_G	0.625	0.97
167_N	205_T	0.619	0.96
28_N	75_D	0.619	0.96
23_T	26_W	0.616	0.96
32_I	39_I	0.615	0.96
23_T	189_T	0.611	0.96
61_L	80_V	0.609	0.96
125_I	162_G	0.598	0.96
197_S	201_N	0.596	0.95
103_W	191_A	0.596	0.95
44_S	73_S	0.596	0.95
104_A	164_L	0.596	0.95
17_Q	22_V	0.592	0.95
97_S	170_P	0.592	0.95
161_P	179_N	0.591	0.95
88_N	175_T	0.591	0.95
116_T	186_V	0.589	0.95
5_L	40_V	0.586	0.95
28_N	73_S	0.586	0.95
105_Q	114_G	0.582	0.95
163_V	171_F	0.582	0.95
8_E	176_D	0.580	0.95
102_S	193_M	0.578	0.95
120_Y	183_N	0.577	0.95
129_R	135_E	0.574	0.94
147_V	151_T	0.571	0.94
9_V	40_V	0.571	0.94
103_W	108_R	0.570	0.94
100_A	164_L	0.568	0.94
38_R	61_L	0.567	0.94
134_E	137_I	0.567	0.94
129_R	205_T	0.566	0.94
6_K	56_L	0.565	0.94
106_S	197_S	0.564	0.94
99_W	102_S	0.563	0.94
103_W	195_Y	0.562	0.94
28_N	42_K	0.557	0.94
120_Y	186_V	0.556	0.93
141_E	146_K	0.551	0.93
112_P	117_H	0.550	0.93
77_P	81_Y	0.550	0.93
164_L	170_P	0.548	0.93
81_Y	142_L	0.548	0.93
161_P	175_T	0.546	0.93
124_A	206_P	0.545	0.93
82_L	92_I	0.544	0.93
100_A	191_A	0.543	0.93
63_G	80_V	0.543	0.93
60_N	63_G	0.543	0.93
17_Q	48_Y	0.542	0.93
59_L	80_V	0.540	0.92
86_F	161_P	0.539	0.92
17_Q	23_T	0.539	0.92
9_V	13_N	0.534	0.92
9_V	31_G	0.533	0.92
77_P	145_G	0.530	0.92
44_S	74_S	0.528	0.92
151_T	154_H	0.528	0.92
100_A	184_A	0.526	0.91
26_W	189_T	0.526	0.91
93_V	172_C	0.524	0.91
140_Y	145_G	0.523	0.91
15_K	24_F	0.523	0.91
13_N	42_K	0.522	0.91
114_G	117_H	0.521	0.91
11_A	14_L	0.520	0.91
82_L	149_A	0.519	0.91
83_Y	91_G	0.513	0.90
115_T	118_A	0.513	0.90
29_V	177_A	0.512	0.90
18_E	49_S	0.511	0.90
127_C	166_N	0.507	0.90
161_P	173_W	0.504	0.90
19_H	24_F	0.500	0.89

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
4c24A	3	0.9039	100	0.143	Contact Map
1k0wA	3	0.9301	100	0.148	Contact Map
1e4cP	3	0.8908	100	0.169	Contact Map
3ocrA	4	0.9476	100	0.18	Contact Map
2opiA	3	0.8777	100	0.195	Contact Map
2z7bA	3	0.9476	100	0.203	Contact Map
4xxfA	3	0.9127	100	0.206	Contact Map
2v9lA	3	0.952	100	0.211	Contact Map
2fk5A	4	0.821	100	0.219	Contact Map
4m6rA	3	0.8865	100	0.225	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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