UDP - ECOLI - GREMLIN Contacts

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UDP - Uridine phosphorylase

UniProt:	P12758	Sequences: MSKSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11045
Length:	253 (214)
Sequences:	4863 (3325)
Seq/√Len:	227.3

ECOLI - UDP DEOD MTNN
BACSU - DEOD MTNN
HALSA - Q9HR25 Q9HP14
SULSO - PNPH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_T	219_V	3.397	1.00
206_C	213_A	3.217	1.00
82_A	211_L	3.196	1.00
133_D	212_R	2.884	1.00
40_K	56_E	2.753	1.00
111_T	153_V	2.711	1.00
88_T	212_R	2.704	1.00
141_V	153_V	2.686	1.00
199_S	215_M	2.538	1.00
112_A	155_V	2.535	1.00
112_A	131_V	2.456	1.00
110_T	156_T	2.382	1.00
56_E	61_P	2.296	1.00
32_E	36_A	2.248	1.00
46_S	51_T	2.246	1.00
141_V	145_K	2.212	1.00
99_Q	193_M	2.098	1.00
21_L	88_T	2.093	1.00
157_A	192_V	2.055	1.00
138_T	142_E	2.023	1.00
112_A	129_P	1.942	1.00
140_L	214_G	1.934	1.00
109_V	137_T	1.857	1.00
71_G	201_T	1.809	1.00
125_P	128_F	1.808	1.00
43_K	54_R	1.795	1.00
79_E	209_Q	1.794	1.00
87_R	211_L	1.771	1.00
103_N	106_D	1.699	1.00
33_K	239_S	1.672	1.00
137_T	153_V	1.660	1.00
95_T	194_N	1.654	1.00
71_G	158_S	1.653	1.00
24_V	67_T	1.644	1.00
79_E	83_Q	1.628	1.00
83_Q	209_Q	1.615	1.00
134_F	138_T	1.611	1.00
102_I	152_H	1.602	1.00
50_F	66_S	1.589	1.00
78_V	205_M	1.589	1.00
239_S	243_K	1.584	1.00
108_L	194_N	1.550	1.00
156_T	194_N	1.538	1.00
140_L	248_A	1.520	1.00
196_E	199_S	1.519	1.00
144_A	151_T	1.513	1.00
137_T	214_G	1.505	1.00
28_P	66_S	1.503	1.00
115_R	204_T	1.503	1.00
136_C	214_G	1.496	1.00
101_H	152_H	1.449	1.00
24_V	89_F	1.430	1.00
194_N	219_V	1.424	1.00
236_Q	240_H	1.421	1.00
25_P	31_V	1.414	1.00
156_T	217_A	1.405	1.00
154_G	193_M	1.403	1.00
43_K	46_S	1.392	1.00
109_V	151_T	1.369	1.00
39_D	56_E	1.367	1.00
147_I	247_E	1.353	1.00
78_V	89_F	1.335	1.00
113_S	203_L	1.310	1.00
44_L	51_T	1.301	1.00
52_T	65_C	1.288	1.00
113_S	199_S	1.277	1.00
54_R	63_I	1.272	1.00
57_L	246_V	1.269	1.00
230_N	233_T	1.254	1.00
26_G	30_R	1.252	1.00
222_N	225_Q	1.248	1.00
114_V	129_P	1.247	1.00
116_L	159_S	1.229	1.00
58_D	247_E	1.228	1.00
143_A	147_I	1.223	1.00
138_T	141_V	1.206	1.00
115_R	200_A	1.201	1.00
135_E	212_R	1.195	1.00
143_A	248_A	1.193	1.00
45_A	54_R	1.179	1.00
143_A	146_S	1.172	1.00
21_L	60_K	1.168	1.00
45_A	84_L	1.155	1.00
97_A	102_I	1.155	1.00
52_T	63_I	1.154	1.00
74_T	202_L	1.146	1.00
109_V	141_V	1.145	1.00
139_A	248_A	1.142	1.00
44_L	65_C	1.136	1.00
147_I	243_K	1.135	1.00
103_N	227_E	1.120	1.00
97_A	222_N	1.119	1.00
89_F	206_C	1.116	1.00
65_C	77_A	1.114	1.00
106_D	152_H	1.107	1.00
152_H	193_M	1.101	1.00
34_I	64_V	1.095	1.00
185_E	189_A	1.095	1.00
142_E	145_K	1.092	1.00
22_A	86_I	1.081	1.00
33_K	242_V	1.076	1.00
141_V	151_T	1.067	1.00
240_H	243_K	1.062	1.00
97_A	219_V	1.057	1.00
82_A	209_Q	1.055	1.00
108_L	193_M	1.047	1.00
82_A	89_F	1.037	1.00
109_V	214_G	1.022	1.00
103_N	225_Q	1.014	1.00
114_V	157_A	1.006	1.00
74_T	78_V	1.004	1.00
35_A	53_W	1.002	1.00
110_T	132_A	0.991	1.00
137_T	141_V	0.984	1.00
143_A	247_E	0.981	1.00
116_L	161_T	0.970	1.00
138_T	145_K	0.970	1.00
88_T	136_C	0.955	1.00
48_R	80_E	0.955	1.00
91_R	202_L	0.945	1.00
99_Q	102_I	0.943	1.00
74_T	201_T	0.943	1.00
139_A	143_A	0.936	1.00
33_K	36_A	0.934	1.00
119_A	123_F	0.932	1.00
31_V	64_V	0.927	1.00
25_P	92_I	0.926	1.00
135_E	139_A	0.923	1.00
76_I	205_M	0.922	1.00
232_E	236_Q	0.912	0.99
37_L	246_V	0.911	0.99
120_S	204_T	0.909	0.99
129_P	155_V	0.907	0.99
75_S	205_M	0.904	0.99
168_R	183_S	0.903	0.99
203_L	213_A	0.902	0.99
57_L	62_V	0.896	0.99
105_G	237_T	0.895	0.99
146_S	247_E	0.895	0.99
134_F	137_T	0.888	0.99
103_N	222_N	0.887	0.99
21_L	249_A	0.882	0.99
161_T	168_R	0.880	0.99
110_T	217_A	0.875	0.99
119_A	205_M	0.874	0.99
243_K	247_E	0.873	0.99
132_A	203_L	0.873	0.99
56_E	59_G	0.873	0.99
28_P	35_A	0.872	0.99
158_S	199_S	0.864	0.99
29_D	32_E	0.864	0.99
39_D	59_G	0.862	0.99
98_I	192_V	0.859	0.99
132_A	137_T	0.859	0.99
121_L	127_E	0.854	0.99
54_R	61_P	0.853	0.99
214_G	248_A	0.845	0.99
38_M	55_A	0.843	0.99
29_D	46_S	0.834	0.99
137_T	140_L	0.830	0.99
110_T	194_N	0.824	0.99
238_E	242_V	0.823	0.99
105_G	229_P	0.822	0.99
113_S	215_M	0.821	0.99
144_A	244_I	0.819	0.99
107_V	244_I	0.816	0.99
75_S	79_E	0.814	0.99
116_L	157_A	0.814	0.99
149_A	244_I	0.811	0.99
89_F	211_L	0.810	0.99
139_A	142_E	0.806	0.99
236_Q	239_S	0.803	0.99
98_I	195_Y	0.800	0.99
50_F	77_A	0.799	0.99
135_E	138_T	0.789	0.99
136_C	140_L	0.786	0.98
31_V	53_W	0.779	0.98
71_G	200_A	0.777	0.98
142_E	146_S	0.776	0.98
140_L	143_A	0.771	0.98
76_I	79_E	0.767	0.98
229_P	233_T	0.761	0.98
165_G	168_R	0.759	0.98
131_V	207_A	0.758	0.98
108_L	219_V	0.758	0.98
81_L	86_I	0.757	0.98
196_E	215_M	0.756	0.98
37_L	243_K	0.750	0.98
134_F	141_V	0.747	0.98
58_D	246_V	0.746	0.98
50_F	69_I	0.746	0.98
82_A	86_I	0.744	0.98
27_D	30_R	0.738	0.98
71_G	117_D	0.736	0.98
109_V	153_V	0.734	0.98
104_V	230_N	0.732	0.98
98_I	223_R	0.730	0.98
33_K	37_L	0.726	0.97
41_P	53_W	0.725	0.97
111_T	155_V	0.725	0.97
79_E	205_M	0.724	0.97
38_M	41_P	0.722	0.97
201_T	205_M	0.718	0.97
94_T	220_I	0.717	0.97
85_G	211_L	0.714	0.97
185_E	188_Q	0.714	0.97
52_T	80_E	0.707	0.97
239_S	242_V	0.703	0.97
133_D	136_C	0.702	0.97
235_K	239_S	0.697	0.97
22_A	63_I	0.696	0.97
75_S	201_T	0.696	0.97
36_A	239_S	0.696	0.97
37_L	239_S	0.691	0.97
99_Q	152_H	0.689	0.97
103_N	150_T	0.683	0.96
118_G	123_F	0.681	0.96
131_V	134_F	0.679	0.96
100_P	224_T	0.677	0.96
195_Y	223_R	0.677	0.96
71_G	119_A	0.669	0.96
110_T	113_S	0.667	0.96
130_A	204_T	0.665	0.96
111_T	134_F	0.664	0.96
50_F	65_C	0.664	0.96
199_S	217_A	0.660	0.96
115_R	118_G	0.656	0.95
65_C	81_L	0.649	0.95
97_A	104_V	0.644	0.95
102_I	219_V	0.641	0.95
67_T	78_V	0.639	0.95
195_Y	221_V	0.638	0.95
184_M	223_R	0.636	0.95
138_T	153_V	0.634	0.95
24_V	78_V	0.622	0.94
220_I	238_E	0.622	0.94
111_T	131_V	0.621	0.94
76_I	80_E	0.620	0.94
165_G	208_S	0.619	0.94
143_A	244_I	0.614	0.94
203_L	214_G	0.612	0.93
30_R	91_R	0.611	0.93
134_F	153_V	0.611	0.93
244_I	248_A	0.610	0.93
90_L	136_C	0.609	0.93
82_A	87_R	0.608	0.93
94_T	234_M	0.608	0.93
111_T	137_T	0.605	0.93
166_Q	169_Y	0.604	0.93
94_T	238_E	0.603	0.93
32_E	51_T	0.602	0.93
95_T	217_A	0.601	0.93
227_E	231_A	0.600	0.93
34_I	92_I	0.599	0.93
31_V	66_S	0.599	0.93
36_A	41_P	0.598	0.93
119_A	201_T	0.598	0.93
128_F	204_T	0.596	0.93
133_D	139_A	0.594	0.92
110_T	203_L	0.593	0.92
34_I	38_M	0.592	0.92
149_A	243_K	0.592	0.92
73_S	76_I	0.591	0.92
25_P	34_I	0.590	0.92
48_R	209_Q	0.589	0.92
114_V	192_V	0.589	0.92
149_A	240_H	0.589	0.92
91_R	94_T	0.585	0.92
41_P	44_L	0.584	0.92
95_T	108_L	0.583	0.92
45_A	52_T	0.581	0.92
113_S	156_T	0.580	0.92
145_K	150_T	0.578	0.91
80_E	83_Q	0.577	0.91
71_G	160_D	0.574	0.91
158_S	215_M	0.574	0.91
157_A	184_M	0.574	0.91
52_T	84_L	0.573	0.91
69_I	76_I	0.572	0.91
76_I	208_S	0.571	0.91
224_T	227_E	0.569	0.91
46_S	49_E	0.568	0.91
199_S	203_L	0.564	0.90
107_V	218_G	0.563	0.90
235_K	238_E	0.561	0.90
218_G	238_E	0.560	0.90
164_P	168_R	0.560	0.90
232_E	235_K	0.559	0.90
107_V	240_H	0.556	0.90
216_V	245_V	0.555	0.90
105_G	233_T	0.552	0.89
186_E	189_A	0.549	0.89
131_V	155_V	0.543	0.89
114_V	131_V	0.542	0.89
82_A	85_G	0.539	0.88
72_P	160_D	0.538	0.88
109_V	144_A	0.536	0.88
113_S	213_A	0.532	0.88
162_F	197_M	0.529	0.87
136_C	248_A	0.528	0.87
26_G	91_R	0.528	0.87
35_A	64_V	0.527	0.87
100_P	185_E	0.527	0.87
120_S	123_F	0.526	0.87
121_L	126_L	0.525	0.87
183_S	186_E	0.519	0.86
75_S	119_A	0.518	0.86
227_E	230_N	0.516	0.86
43_K	51_T	0.516	0.86
106_D	150_T	0.515	0.86
54_R	84_L	0.515	0.86
132_A	214_G	0.512	0.86
28_P	32_E	0.511	0.86
70_G	160_D	0.511	0.86
69_I	123_F	0.508	0.85
113_S	200_A	0.504	0.85
96_G	196_E	0.503	0.85
29_D	235_K	0.501	0.84
114_V	155_V	0.501	0.84
38_M	64_V	0.501	0.84
118_G	121_L	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
3bjeA	2	0.9881	100	0.202	Contact Map
3phcA	5	0.9328	100	0.24	Contact Map
3eufA	2	0.9921	100	0.257	Contact Map
2b94A	4	0.9091	100	0.257	Contact Map
3mb8A	4	0.9407	100	0.26	Contact Map
3qpbA	6	0.9684	100	0.265	Contact Map
4r31A	5	1	100	0.265	Contact Map
3p0fA	2	0.9881	100	0.279	Contact Map
4m7wA	5	0.917	100	0.28	Contact Map
4r2xC	3	0.9802	100	0.281	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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