ULAF - ECOLI - GREMLIN Contacts

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ULAF - L-ribulose-5-phosphate 4-epimerase UlaF

UniProt:	P39306	Sequences: MQKLKQQVFEANMELPRYGLVTFTWGNVSAIDRERGLVVIKPSGVAYETMKAADMVVVDMSGKVVEGEYRPSSDTATHLELYRRYPSLGGIVHTHSTHATAWAQAGLAIPALGTTHADYFFGDIPCTRGLSEEEVQGEYELNTGKVIIETLGNAEPLHTPGIVVYQHGPFAWGKDAHDAVHNAVVMEEVAKMAWIARGINPQLNHIDSFLMNKHFMRKHGPNAYYGQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12498
Length:	228 (197)
Sequences:	6321 (3826)
Seq/√Len:	272.6

ECOLI - ULAF SGBE ARAD 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
59_D	63_K	5.053	1.00
174_K	178_D	3.376	1.00
191_K	195_I	3.194	1.00
98_H	195_I	3.193	1.00
37_L	57_V	2.971	1.00
4_L	30_A	2.776	1.00
107_L	197_R	2.687	1.00
38_V	79_L	2.588	1.00
208_S	212_N	2.588	1.00
39_V	55_M	2.560	1.00
7_Q	177_H	2.549	1.00
88_L	172_W	2.183	1.00
80_E	145_K	2.124	1.00
37_L	65_V	2.104	1.00
101_A	195_I	2.083	1.00
98_H	191_K	2.079	1.00
97_T	191_K	2.069	1.00
98_H	194_W	1.978	1.00
9_F	52_A	1.974	1.00
207_D	210_L	1.933	1.00
6_Q	10_E	1.928	1.00
51_K	54_D	1.915	1.00
30_A	176_A	1.900	1.00
80_E	83_R	1.897	1.00
161_G	186_M	1.880	1.00
39_V	57_V	1.832	1.00
92_V	179_A	1.781	1.00
89_G	175_D	1.733	1.00
14_E	18_Y	1.718	1.00
195_I	198_G	1.704	1.00
32_D	39_V	1.699	1.00
175_D	178_D	1.619	1.00
58_V	75_T	1.618	1.00
90_G	176_A	1.612	1.00
8_V	28_V	1.585	1.00
11_A	180_V	1.579	1.00
106_G	165_Y	1.530	1.00
18_Y	184_V	1.492	1.00
61_S	83_R	1.480	1.00
84_R	152_G	1.477	1.00
139_Y	145_K	1.470	1.00
9_F	13_M	1.432	1.00
173_G	178_D	1.428	1.00
169_P	186_M	1.426	1.00
134_E	146_V	1.412	1.00
108_A	123_D	1.406	1.00
97_T	101_A	1.403	1.00
13_M	17_R	1.395	1.00
64_V	67_G	1.372	1.00
110_P	193_A	1.371	1.00
125_P	154_A	1.364	1.00
85_Y	88_L	1.364	1.00
6_Q	52_A	1.364	1.00
94_T	183_A	1.360	1.00
8_V	55_M	1.346	1.00
38_V	60_M	1.345	1.00
80_E	84_R	1.337	1.00
30_A	90_G	1.319	1.00
109_I	190_A	1.304	1.00
79_L	83_R	1.295	1.00
84_R	148_I	1.286	1.00
95_H	167_H	1.283	1.00
171_A	183_A	1.279	1.00
57_V	66_E	1.243	1.00
102_W	197_R	1.235	1.00
210_L	213_K	1.234	1.00
9_F	55_M	1.233	1.00
29_S	91_I	1.228	1.00
122_G	212_N	1.221	1.00
14_E	17_R	1.210	1.00
29_S	82_Y	1.165	1.00
33_R	37_L	1.156	1.00
146_V	149_E	1.152	1.00
99_A	169_P	1.149	1.00
45_V	54_D	1.137	1.00
105_A	199_I	1.127	1.00
11_A	176_A	1.126	1.00
40_I	72_S	1.123	1.00
97_T	188_E	1.121	1.00
15_L	28_V	1.119	1.00
164_V	170_F	1.115	1.00
93_H	167_H	1.113	1.00
31_I	89_G	1.112	1.00
193_A	197_R	1.110	1.00
194_W	199_I	1.109	1.00
160_P	182_N	1.107	1.00
82_Y	91_I	1.096	1.00
161_G	171_A	1.091	1.00
100_T	103_A	1.089	1.00
197_R	201_P	1.088	1.00
16_P	48_E	1.070	1.00
15_L	92_V	1.069	1.00
145_K	149_E	1.060	1.00
32_D	57_V	1.059	1.00
94_T	169_P	1.055	1.00
85_Y	172_W	1.045	1.00
45_V	69_Y	1.044	1.00
147_I	164_V	1.037	1.00
194_W	198_G	1.036	1.00
32_D	35_R	1.024	1.00
98_H	187_E	1.018	1.00
99_A	186_M	1.014	1.00
187_E	191_K	1.007	1.00
12_N	28_V	0.997	1.00
112_L	193_A	0.996	1.00
59_D	65_V	0.991	1.00
4_L	32_D	0.989	1.00
151_L	172_W	0.986	1.00
151_L	162_I	0.971	1.00
60_M	83_R	0.963	1.00
188_E	191_K	0.957	1.00
206_I	210_L	0.955	1.00
132_E	136_Q	0.953	1.00
108_A	126_C	0.953	1.00
42_P	45_V	0.953	1.00
38_V	75_T	0.950	1.00
173_G	182_N	0.945	1.00
32_D	37_L	0.944	1.00
54_D	69_Y	0.943	1.00
96_S	99_A	0.931	1.00
212_N	215_F	0.930	1.00
7_Q	10_E	0.923	1.00
15_L	180_V	0.912	1.00
7_Q	30_A	0.908	1.00
196_A	203_L	0.907	1.00
11_A	28_V	0.907	1.00
54_D	68_E	0.906	1.00
92_V	183_A	0.904	1.00
42_P	55_M	0.898	1.00
18_Y	180_V	0.894	1.00
209_F	213_K	0.891	1.00
122_G	208_S	0.876	1.00
97_T	195_I	0.875	1.00
56_V	70_R	0.868	1.00
38_V	58_V	0.865	1.00
50_M	54_D	0.863	1.00
77_T	170_F	0.854	1.00
9_F	50_M	0.846	1.00
149_E	152_G	0.841	1.00
132_E	165_Y	0.834	1.00
121_F	208_S	0.834	1.00
31_I	36_G	0.830	0.99
81_L	88_L	0.829	0.99
101_A	194_W	0.827	0.99
77_T	147_I	0.824	0.99
125_P	162_I	0.820	0.99
133_E	136_Q	0.810	0.99
169_P	183_A	0.809	0.99
80_E	148_I	0.806	0.99
123_D	127_T	0.806	0.99
134_E	137_G	0.805	0.99
210_L	214_H	0.805	0.99
49_T	177_H	0.803	0.99
106_G	202_Q	0.800	0.99
209_F	212_N	0.799	0.99
206_I	211_M	0.798	0.99
81_L	151_L	0.796	0.99
104_Q	112_L	0.794	0.99
40_I	74_D	0.794	0.99
31_I	60_M	0.790	0.99
109_I	189_V	0.785	0.99
10_E	49_T	0.784	0.99
36_G	60_M	0.782	0.99
96_S	187_E	0.777	0.99
148_I	151_L	0.777	0.99
132_E	146_V	0.775	0.99
96_S	183_A	0.774	0.99
43_S	70_R	0.773	0.99
12_N	47_Y	0.770	0.99
5_K	39_V	0.766	0.99
89_G	174_K	0.763	0.99
84_R	149_E	0.758	0.99
109_I	163_V	0.758	0.99
14_E	180_V	0.755	0.99
5_K	66_E	0.753	0.99
178_D	182_N	0.749	0.99
29_S	40_I	0.745	0.99
127_T	146_V	0.745	0.99
133_E	137_G	0.744	0.99
19_G	191_K	0.740	0.99
102_W	193_A	0.734	0.99
207_D	213_K	0.730	0.99
106_G	204_N	0.723	0.99
186_M	190_A	0.722	0.99
75_T	79_L	0.722	0.99
33_R	36_G	0.712	0.98
45_V	50_M	0.700	0.98
4_L	7_Q	0.698	0.98
103_A	163_V	0.692	0.98
107_L	201_P	0.690	0.98
41_K	50_M	0.689	0.98
21_V	28_V	0.687	0.98
83_R	148_I	0.686	0.98
132_E	149_E	0.685	0.98
24_T	43_S	0.684	0.98
111_A	116_H	0.672	0.98
41_K	82_Y	0.663	0.98
96_S	169_P	0.656	0.97
196_A	202_Q	0.655	0.97
49_T	54_D	0.653	0.97
23_F	181_H	0.650	0.97
171_A	182_N	0.650	0.97
81_L	170_F	0.650	0.97
90_G	179_A	0.648	0.97
112_L	197_R	0.645	0.97
133_E	138_E	0.644	0.97
46_A	49_T	0.641	0.97
208_S	211_M	0.631	0.97
127_T	164_V	0.630	0.97
108_A	125_P	0.628	0.97
104_Q	113_G	0.628	0.97
102_W	190_A	0.628	0.97
22_T	188_E	0.627	0.97
100_T	192_M	0.626	0.97
43_S	72_S	0.625	0.96
105_A	201_P	0.623	0.96
57_V	65_V	0.622	0.96
15_L	20_L	0.619	0.96
178_D	181_H	0.619	0.96
26_G	47_Y	0.614	0.96
100_T	168_G	0.609	0.96
27_N	72_S	0.609	0.96
27_N	74_D	0.607	0.96
62_G	79_L	0.607	0.96
160_P	174_K	0.606	0.96
31_I	38_V	0.602	0.96
22_T	25_W	0.598	0.95
81_L	91_I	0.597	0.95
124_I	186_M	0.597	0.95
114_T	117_A	0.596	0.95
5_K	57_V	0.594	0.95
4_L	39_V	0.592	0.95
199_I	203_L	0.591	0.95
146_V	150_T	0.590	0.95
134_E	138_E	0.589	0.95
92_V	171_A	0.586	0.95
108_A	154_A	0.585	0.95
119_Y	182_N	0.584	0.95
87_S	174_K	0.583	0.95
37_L	60_M	0.580	0.95
76_A	80_E	0.580	0.95
160_P	178_D	0.575	0.94
8_V	39_V	0.573	0.94
127_T	150_T	0.573	0.94
16_P	21_V	0.573	0.94
8_V	12_N	0.567	0.94
148_I	152_G	0.565	0.94
150_T	162_I	0.564	0.94
201_P	204_N	0.563	0.94
102_W	194_W	0.562	0.94
58_V	64_V	0.561	0.94
101_A	192_M	0.560	0.94
43_S	73_S	0.558	0.94
150_T	154_A	0.558	0.94
99_A	183_A	0.557	0.93
60_M	79_L	0.555	0.93
98_H	101_A	0.554	0.93
123_D	154_A	0.554	0.93
62_G	65_V	0.554	0.93
211_M	214_H	0.552	0.93
99_A	163_V	0.547	0.93
85_Y	151_L	0.546	0.93
8_V	30_A	0.544	0.93
123_D	126_C	0.543	0.93
150_T	153_N	0.541	0.92
85_Y	160_P	0.540	0.92
147_I	162_I	0.538	0.92
16_P	22_T	0.537	0.92
105_A	194_W	0.537	0.92
12_N	41_K	0.536	0.92
198_G	201_P	0.534	0.92
16_P	47_Y	0.533	0.92
105_A	196_A	0.532	0.92
12_N	50_M	0.531	0.92
162_I	170_F	0.529	0.92
106_G	203_L	0.528	0.92
7_Q	175_D	0.528	0.92
119_Y	185_V	0.528	0.92
5_K	52_A	0.524	0.91
37_L	59_D	0.523	0.91
163_V	169_P	0.522	0.91
5_K	55_M	0.520	0.91
7_Q	176_A	0.519	0.91
5_K	42_P	0.517	0.91
99_A	190_A	0.516	0.91
135_V	138_E	0.513	0.90
59_D	62_G	0.512	0.90
27_N	41_K	0.509	0.90
122_G	215_F	0.507	0.90
102_W	107_L	0.507	0.90
100_T	113_G	0.506	0.90
14_E	23_F	0.505	0.90
112_L	116_H	0.503	0.89
181_H	188_E	0.502	0.89
115_T	185_V	0.501	0.89
113_G	116_H	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	0.9035	100	0.126	Contact Map
1k0wA	3	0.9386	100	0.142	Contact Map
1e4cP	3	0.8904	100	0.153	Contact Map
3ocrA	4	0.9474	100	0.154	Contact Map
4xxfA	3	0.9123	100	0.181	Contact Map
2opiA	3	0.8772	100	0.182	Contact Map
2z7bA	3	0.9298	100	0.188	Contact Map
2v9lA	3	0.9518	100	0.204	Contact Map
1pvtA	3	0.8465	100	0.207	Contact Map
2fk5A	4	0.8246	100	0.211	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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