RMLC - ECOLI - GREMLIN Contacts

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RMLC - dTDP-4-dehydrorhamnose 3,5-epimerase

UniProt:	P37745	Sequences: MNVIRTEIEDVLILEPRVFGDDRGFFYESFNQSAFEHILGYPVSFVQDNHSRSSKNVLRGLHFQRGEYAQDKLVRCTHGAVFDVAVDIRPNSVSFGKWVGVLLSADNKQQLWIPKGFAHGFLVLSDIAEFQYKTTNYYHPESDCGICWNDERIAIDWPQTSGLILSPKDERLFTLDELIRLKLIA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11979
Length:	185 (174)
Sequences:	4541 (2990)
Seq/√Len:	226.7

ECOLI - RMLC
BACSU - SPSL
SULSO - Q97X30 Q7LXE5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
145_G	172_L	3.383	1.00
80_A	102_L	3.278	1.00
32_Q	44_S	3.237	1.00
125_S	128_A	2.776	1.00
81_V	130_F	2.516	1.00
5_R	12_L	2.414	1.00
7_E	99_V	2.408	1.00
139_H	142_S	2.383	1.00
15_E	109_Q	2.360	1.00
152_R	176_D	2.349	1.00
61_L	118_A	2.316	1.00
65_R	144_C	2.274	1.00
71_D	112_W	2.226	1.00
82_F	100_G	2.185	1.00
36_E	42_P	2.157	1.00
48_D	133_K	2.142	1.00
58_L	122_L	2.103	1.00
78_H	105_A	2.092	1.00
51_S	121_F	2.091	1.00
55_K	126_D	2.026	1.00
4_I	15_E	1.978	1.00
33_S	137_Y	1.967	1.00
32_Q	36_E	1.943	1.00
7_E	97_K	1.941	1.00
77_T	131_Q	1.916	1.00
71_D	135_T	1.911	1.00
78_H	127_I	1.902	1.00
115_K	135_T	1.855	1.00
68_Y	139_H	1.841	1.00
147_C	174_T	1.833	1.00
2_N	15_E	1.813	1.00
167_P	171_R	1.763	1.00
78_H	129_E	1.753	1.00
174_T	177_E	1.727	1.00
13_I	109_Q	1.716	1.00
80_A	125_S	1.691	1.00
52_R	129_E	1.671	1.00
50_H	129_E	1.629	1.00
71_D	115_K	1.621	1.00
8_I	117_F	1.611	1.00
13_I	101_V	1.604	1.00
167_P	170_E	1.589	1.00
104_S	107_N	1.579	1.00
88_I	118_A	1.573	1.00
82_F	158_P	1.546	1.00
63_F	144_C	1.518	1.00
33_S	37_H	1.513	1.00
68_Y	136_N	1.499	1.00
11_V	85_A	1.497	1.00
80_A	104_S	1.455	1.00
61_L	120_G	1.442	1.00
50_H	75_R	1.434	1.00
18_V	108_K	1.379	1.00
123_V	128_A	1.348	1.00
63_F	178_L	1.342	1.00
5_R	9_E	1.330	1.00
81_V	128_A	1.316	1.00
3_V	12_L	1.299	1.00
6_T	13_I	1.293	1.00
43_V	112_W	1.286	1.00
68_Y	142_S	1.247	1.00
43_V	115_K	1.230	1.00
115_K	136_N	1.228	1.00
25_F	52_R	1.223	1.00
11_V	99_V	1.222	1.00
31_N	34_A	1.180	1.00
58_L	163_L	1.177	1.00
2_N	17_R	1.170	1.00
84_V	157_W	1.128	1.00
122_L	159_Q	1.124	1.00
118_A	146_I	1.122	1.00
85_A	99_V	1.111	1.00
52_R	127_I	1.092	1.00
146_I	153_I	1.076	1.00
67_E	142_S	1.063	1.00
173_F	177_E	1.059	1.00
28_E	31_N	1.053	1.00
114_P	117_F	1.033	1.00
122_L	158_P	1.032	1.00
101_V	111_L	1.031	1.00
26_F	51_S	1.018	1.00
8_I	11_V	1.010	1.00
50_H	131_Q	0.979	1.00
63_F	118_A	0.979	1.00
31_N	137_Y	0.971	1.00
22_D	167_P	0.959	1.00
148_W	163_L	0.953	1.00
4_I	13_I	0.949	1.00
3_V	14_L	0.947	1.00
25_F	50_H	0.947	1.00
61_L	86_V	0.946	1.00
151_E	174_T	0.944	1.00
83_D	119_H	0.942	1.00
65_R	142_S	0.940	1.00
14_L	34_A	0.935	1.00
159_Q	163_L	0.935	1.00
102_L	124_L	0.932	1.00
55_K	125_S	0.931	1.00
88_I	146_I	0.928	1.00
122_L	163_L	0.913	0.99
82_F	98_W	0.904	0.99
28_E	47_Q	0.897	0.99
152_R	174_T	0.893	0.99
34_A	37_H	0.891	0.99
8_I	99_V	0.890	0.99
146_I	178_L	0.886	0.99
29_S	48_D	0.883	0.99
54_S	127_I	0.882	0.99
143_D	172_L	0.881	0.99
153_I	175_L	0.867	0.99
28_E	70_Q	0.862	0.99
101_V	109_Q	0.862	0.99
17_R	34_A	0.849	0.99
8_I	94_S	0.842	0.99
61_L	155_I	0.841	0.99
85_A	117_F	0.837	0.99
63_F	88_I	0.832	0.99
45_F	48_D	0.832	0.99
25_F	129_E	0.828	0.99
6_T	11_V	0.828	0.99
49_N	134_T	0.828	0.99
69_A	142_S	0.827	0.99
98_W	153_I	0.825	0.99
25_F	108_K	0.817	0.99
147_C	172_L	0.816	0.99
10_D	94_S	0.807	0.99
39_L	43_V	0.804	0.99
96_G	152_R	0.801	0.99
20_G	54_S	0.798	0.99
84_V	155_I	0.792	0.99
89_R	117_F	0.790	0.99
50_H	77_T	0.790	0.99
46_V	137_Y	0.788	0.99
103_L	111_L	0.779	0.98
164_I	167_P	0.778	0.98
123_V	127_I	0.774	0.98
11_V	111_L	0.765	0.98
77_T	129_E	0.761	0.98
67_E	139_H	0.755	0.98
131_Q	134_T	0.748	0.98
85_A	113_I	0.747	0.98
9_E	93_V	0.737	0.98
45_F	135_T	0.728	0.98
124_L	158_P	0.722	0.97
4_I	109_Q	0.720	0.97
41_Y	112_W	0.717	0.97
3_V	39_L	0.716	0.97
85_A	111_L	0.716	0.97
173_F	178_L	0.704	0.97
39_L	42_P	0.699	0.97
5_R	10_D	0.698	0.97
144_C	173_F	0.689	0.97
74_V	130_F	0.685	0.96
8_I	85_A	0.685	0.96
36_E	41_Y	0.684	0.96
13_I	111_L	0.678	0.96
148_W	165_L	0.677	0.96
41_Y	115_K	0.675	0.96
35_F	110_Q	0.675	0.96
35_F	39_L	0.674	0.96
13_I	99_V	0.672	0.96
9_E	94_S	0.667	0.96
100_G	158_P	0.667	0.96
20_G	108_K	0.666	0.96
75_R	131_Q	0.664	0.96
76_C	81_V	0.662	0.96
43_V	135_T	0.658	0.95
65_R	178_L	0.656	0.95
94_S	97_K	0.654	0.95
26_F	49_N	0.650	0.95
160_T	163_L	0.649	0.95
29_S	50_H	0.649	0.95
14_L	73_L	0.648	0.95
18_V	27_Y	0.646	0.95
96_G	175_L	0.644	0.95
112_W	135_T	0.642	0.95
144_C	178_L	0.641	0.95
80_A	128_A	0.637	0.95
55_K	160_T	0.636	0.95
145_G	173_F	0.635	0.95
29_S	75_R	0.635	0.95
76_C	128_A	0.634	0.95
63_F	146_I	0.631	0.94
28_E	49_N	0.627	0.94
3_V	34_A	0.627	0.94
34_A	39_L	0.623	0.94
168_K	172_L	0.623	0.94
105_A	129_E	0.621	0.94
32_Q	42_P	0.621	0.94
13_I	107_N	0.619	0.94
36_E	39_L	0.619	0.94
18_V	25_F	0.617	0.94
99_V	111_L	0.615	0.94
108_K	129_E	0.615	0.94
61_L	153_I	0.614	0.94
72_K	83_D	0.611	0.93
6_T	101_V	0.611	0.93
22_D	164_I	0.605	0.93
6_T	99_V	0.604	0.93
174_T	178_L	0.598	0.93
138_Y	143_D	0.597	0.93
31_N	35_F	0.596	0.93
29_S	131_Q	0.593	0.92
26_F	132_Y	0.593	0.92
90_P	93_V	0.592	0.92
11_V	117_F	0.588	0.92
69_A	115_K	0.581	0.92
21_D	24_G	0.573	0.91
3_V	35_F	0.568	0.91
58_L	157_W	0.567	0.91
53_S	57_V	0.567	0.91
54_S	164_I	0.566	0.90
105_A	108_K	0.563	0.90
86_V	146_I	0.559	0.90
123_V	126_D	0.558	0.90
70_Q	134_T	0.558	0.90
46_V	136_N	0.557	0.90
27_Y	108_K	0.556	0.90
65_R	68_Y	0.556	0.90
81_V	121_F	0.555	0.90
75_R	129_E	0.554	0.90
52_R	78_H	0.554	0.90
35_F	41_Y	0.553	0.89
136_N	142_S	0.548	0.89
12_L	114_P	0.548	0.89
29_S	133_K	0.546	0.89
105_A	125_S	0.545	0.89
112_W	115_K	0.545	0.89
144_C	172_L	0.545	0.89
86_V	118_A	0.544	0.89
45_F	133_K	0.544	0.89
90_P	96_G	0.543	0.89
53_S	59_R	0.540	0.88
143_D	168_K	0.538	0.88
80_A	105_A	0.535	0.88
140_P	171_R	0.535	0.88
80_A	124_L	0.534	0.88
7_E	11_V	0.532	0.88
84_V	100_G	0.532	0.88
49_N	132_Y	0.532	0.88
56_N	163_L	0.529	0.87
82_F	124_L	0.528	0.87
78_H	125_S	0.526	0.87
10_D	117_F	0.526	0.87
17_R	20_G	0.525	0.87
165_L	170_E	0.525	0.87
81_V	123_V	0.521	0.87
134_T	168_K	0.521	0.87
57_V	164_I	0.520	0.86
54_S	57_V	0.520	0.86
161_S	164_I	0.520	0.86
74_V	83_D	0.520	0.86
102_L	158_P	0.515	0.86
15_E	107_N	0.512	0.86
8_I	89_R	0.510	0.85
99_V	102_L	0.509	0.85
49_N	168_K	0.508	0.85
8_I	111_L	0.505	0.85
104_S	109_Q	0.502	0.84
16_P	110_Q	0.501	0.84
102_L	107_N	0.500	0.84

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
1upiA	2	0.9946	100	0.108	Contact Map
1oi6A	2	1	100	0.109	Contact Map
2c0zA	2	0.9946	100	0.111	Contact Map
4hn1A	3	0.9892	100	0.133	Contact Map
1dzrA	2	0.9838	100	0.135	Contact Map
3rykA	2	0.9351	100	0.138	Contact Map
2ixkA	2	0.9784	100	0.142	Contact Map
1ep0A	2	0.973	100	0.154	Contact Map
1wltA	2	0.9405	100	0.19	Contact Map
5buvA	2	0.9243	100	0.198	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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