PYRH - ECOLI - GREMLIN Contacts

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PYRH - Uridylate kinase

UniProt:	P0A7E9	Sequences: MATNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11539
Length:	241 (216)
Sequences:	11403 (6629)
Seq/√Len:	451.0

ECOLI - PYRH AK2H AK1H AK3 PROB
BACSU - PYRH AK2 AK1 AK3 PROJ PROB
HALSA - PYRH Q9HMV1
SULSO - PYRH Q97ZL7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
173_A	178_D	4.063	1.00
11_R	50_Q	3.813	1.00
228_R	233_E	2.863	1.00
39_Q	98_A	2.443	1.00
101_N	130_R	2.442	1.00
42_K	100_V	2.385	1.00
169_G	183_M	2.380	1.00
153_G	161_V	2.305	1.00
42_K	46_E	2.290	1.00
104_L	107_A	2.172	1.00
160_V	216_R	2.163	1.00
52_G	156_I	2.071	1.00
105_M	109_P	2.070	1.00
100_V	131_V	2.053	1.00
103_R	110_L	2.041	1.00
168_D	219_N	1.990	1.00
42_K	98_A	1.926	1.00
35_D	98_A	1.923	1.00
92_R	102_A	1.906	1.00
10_K	159_D	1.866	1.00
20_A	220_M	1.864	1.00
104_L	110_L	1.864	1.00
105_M	110_L	1.862	1.00
190_S	209_R	1.858	1.00
107_A	110_L	1.829	1.00
104_L	109_P	1.827	1.00
59_N	62_R	1.823	1.00
111_N	114_C	1.822	1.00
162_L	218_F	1.787	1.00
172_T	182_T	1.777	1.00
172_T	178_D	1.775	1.00
168_D	222_K	1.733	1.00
59_N	63_G	1.715	1.00
45_V	100_V	1.714	1.00
18_G	61_F	1.672	1.00
35_D	97_R	1.660	1.00
106_S	110_L	1.645	1.00
36_R	39_Q	1.612	1.00
173_A	180_T	1.609	1.00
174_D	177_K	1.605	1.00
45_V	129_N	1.604	1.00
75_V	78_H	1.591	1.00
154_I	213_L	1.582	1.00
43_E	227_R	1.576	1.00
227_R	231_M	1.566	1.00
83_A	87_N	1.509	1.00
165_T	217_V	1.503	1.00
111_N	115_D	1.502	1.00
45_V	50_Q	1.490	1.00
134_L	152_R	1.414	1.00
192_V	205_F	1.410	1.00
166_K	176_A	1.394	1.00
38_A	94_A	1.393	1.00
123_I	127_R	1.381	1.00
40_E	224_G	1.378	1.00
216_R	229_V	1.377	1.00
113_V	116_S	1.374	1.00
43_E	223_P	1.372	1.00
14_L	41_I	1.358	1.00
208_A	215_I	1.355	1.00
154_I	211_H	1.343	1.00
168_D	171_F	1.330	1.00
150_C	208_A	1.328	1.00
104_L	108_I	1.322	1.00
150_C	161_V	1.320	1.00
125_L	130_R	1.318	1.00
112_G	115_D	1.313	1.00
172_T	184_Y	1.309	1.00
95_L	102_A	1.295	1.00
106_S	109_P	1.276	1.00
35_D	94_A	1.275	1.00
43_E	46_E	1.269	1.00
122_A	134_L	1.266	1.00
11_R	123_I	1.260	1.00
13_L	158_A	1.259	1.00
103_R	106_S	1.258	1.00
76_G	80_G	1.242	1.00
36_R	40_E	1.239	1.00
103_R	107_A	1.237	1.00
114_C	117_Y	1.231	1.00
33_I	36_R	1.226	1.00
58_G	61_F	1.217	1.00
84_T	87_N	1.206	1.00
37_M	91_M	1.205	1.00
12_I	49_I	1.202	1.00
94_A	98_A	1.197	1.00
50_Q	127_R	1.195	1.00
60_L	63_G	1.189	1.00
45_V	131_V	1.170	1.00
85_V	88_G	1.158	1.00
121_E	125_L	1.155	1.00
219_N	222_K	1.143	1.00
95_L	100_V	1.134	1.00
60_L	141_P	1.133	1.00
124_S	127_R	1.114	1.00
218_F	225_A	1.104	1.00
10_K	49_I	1.098	1.00
35_D	39_Q	1.094	1.00
191_E	194_E	1.090	1.00
226_L	229_V	1.090	1.00
47_L	231_M	1.090	1.00
103_R	109_P	1.088	1.00
41_I	53_V	1.081	1.00
171_F	175_P	1.073	1.00
222_K	225_A	1.064	1.00
227_R	230_V	1.061	1.00
191_E	195_K	1.060	1.00
96_H	101_N	1.059	1.00
124_S	128_N	1.057	1.00
43_E	47_L	1.050	1.00
40_E	223_P	1.047	1.00
206_T	210_D	1.042	1.00
222_K	228_R	1.040	1.00
170_V	187_L	1.035	1.00
157_E	211_H	1.029	1.00
39_Q	42_K	1.025	1.00
81_M	84_T	1.023	1.00
225_A	228_R	1.017	1.00
82_L	86_M	1.009	1.00
19_E	22_Q	1.009	1.00
119_W	157_E	0.999	1.00
52_G	126_L	0.986	1.00
149_A	161_V	0.984	1.00
65_G	68_K	0.984	1.00
105_M	125_L	0.982	1.00
74_V	78_H	0.977	1.00
168_D	183_M	0.974	1.00
50_Q	129_N	0.962	1.00
218_F	229_V	0.955	1.00
83_A	86_M	0.954	1.00
34_L	94_A	0.952	1.00
119_W	123_I	0.949	1.00
84_T	88_G	0.948	1.00
112_G	116_S	0.947	1.00
78_H	82_L	0.942	1.00
121_E	124_S	0.938	1.00
33_I	221_N	0.932	1.00
23_G	32_S	0.927	1.00
172_T	181_A	0.926	1.00
66_L	70_G	0.920	1.00
184_Y	187_L	0.920	1.00
44_L	47_L	0.915	1.00
32_S	35_D	0.907	1.00
19_E	166_K	0.906	1.00
38_A	95_L	0.905	1.00
65_G	69_A	0.901	1.00
171_F	181_A	0.900	1.00
162_L	216_R	0.900	1.00
125_L	132_V	0.899	1.00
175_P	181_A	0.883	1.00
173_A	181_A	0.883	1.00
188_T	191_E	0.877	1.00
64_A	68_K	0.876	1.00
39_Q	43_E	0.872	1.00
134_L	156_I	0.869	1.00
183_M	219_N	0.864	1.00
112_G	117_Y	0.861	1.00
52_G	134_L	0.859	1.00
64_A	67_A	0.858	1.00
41_I	131_V	0.854	1.00
92_R	96_H	0.854	1.00
105_M	108_I	0.843	1.00
83_A	88_G	0.840	1.00
45_V	51_V	0.839	1.00
147_S	207_L	0.832	1.00
111_N	116_S	0.830	1.00
34_L	91_M	0.828	1.00
150_C	207_L	0.827	1.00
44_L	162_L	0.824	1.00
64_A	71_M	0.815	1.00
171_F	183_M	0.813	1.00
184_Y	195_K	0.813	1.00
209_R	215_I	0.808	1.00
94_A	97_R	0.805	1.00
173_A	177_K	0.802	1.00
161_V	208_A	0.801	1.00
65_G	70_G	0.798	1.00
44_L	49_I	0.796	1.00
39_Q	223_P	0.780	1.00
120_A	124_S	0.778	1.00
14_L	44_L	0.778	1.00
42_K	45_V	0.778	1.00
123_I	157_E	0.778	1.00
16_L	53_V	0.777	1.00
41_I	95_L	0.776	1.00
153_G	213_L	0.775	1.00
82_L	85_V	0.773	1.00
189_Y	205_F	0.773	1.00
80_G	83_A	0.771	1.00
43_E	224_G	0.770	1.00
135_S	139_G	0.770	1.00
170_V	217_V	0.756	1.00
78_H	81_M	0.752	1.00
103_R	108_I	0.752	1.00
42_K	131_V	0.735	1.00
130_R	133_I	0.732	1.00
36_R	220_M	0.729	1.00
67_A	71_M	0.727	1.00
203_A	207_L	0.727	1.00
170_V	184_Y	0.726	1.00
115_D	119_W	0.723	1.00
19_E	58_G	0.723	1.00
173_A	179_P	0.722	1.00
164_A	218_F	0.721	1.00
136_A	140_N	0.720	1.00
80_G	87_N	0.719	1.00
203_A	206_T	0.718	1.00
16_L	20_A	0.717	1.00
224_G	228_R	0.717	1.00
196_E	209_R	0.716	1.00
42_K	95_L	0.715	1.00
14_L	162_L	0.712	1.00
125_L	128_N	0.711	1.00
147_S	203_A	0.706	1.00
152_R	156_I	0.706	1.00
190_S	194_E	0.704	1.00
88_G	91_M	0.704	1.00
160_V	214_P	0.700	1.00
44_L	230_V	0.698	1.00
66_L	71_M	0.693	1.00
208_A	213_L	0.687	1.00
77_D	80_G	0.684	1.00
135_S	141_P	0.676	1.00
135_S	138_T	0.675	1.00
137_G	140_N	0.672	1.00
185_E	226_L	0.672	1.00
114_C	118_S	0.672	1.00
93_D	97_R	0.668	1.00
122_A	126_L	0.667	1.00
189_Y	192_V	0.664	1.00
41_I	51_V	0.663	1.00
93_D	96_H	0.662	1.00
168_D	224_G	0.660	1.00
16_L	21_L	0.656	1.00
194_E	206_T	0.652	1.00
166_K	221_N	0.650	1.00
162_L	226_L	0.647	1.00
77_D	81_M	0.646	1.00
59_N	198_K	0.646	1.00
207_L	211_H	0.644	1.00
160_V	229_V	0.642	0.99
81_M	138_T	0.637	0.99
57_G	83_A	0.637	0.99
23_G	33_I	0.635	0.99
81_M	86_M	0.634	0.99
63_G	67_A	0.633	0.99
44_L	51_V	0.632	0.99
228_R	231_M	0.631	0.99
115_D	118_S	0.625	0.99
224_G	227_R	0.624	0.99
11_R	159_D	0.622	0.99
80_G	84_T	0.620	0.99
65_G	71_M	0.617	0.99
81_M	87_N	0.616	0.99
36_R	223_P	0.607	0.99
12_I	160_V	0.604	0.99
89_L	92_R	0.603	0.99
95_L	98_A	0.603	0.99
81_M	85_V	0.599	0.99
40_E	43_E	0.598	0.99
177_K	198_K	0.595	0.99
38_A	98_A	0.595	0.99
40_E	222_K	0.590	0.99
163_K	166_K	0.589	0.99
39_Q	97_R	0.587	0.99
46_E	100_V	0.584	0.99
138_T	142_F	0.583	0.99
68_K	72_N	0.583	0.99
64_A	69_A	0.581	0.99
226_L	230_V	0.579	0.99
75_V	81_M	0.577	0.99
189_Y	193_L	0.573	0.99
141_P	144_T	0.568	0.99
64_A	70_G	0.564	0.99
58_G	63_G	0.564	0.99
58_G	62_R	0.563	0.99
109_P	115_D	0.561	0.99
47_L	227_R	0.560	0.99
138_T	141_P	0.560	0.99
139_G	142_F	0.557	0.99
171_F	174_D	0.556	0.99
154_I	207_L	0.554	0.99
66_L	69_A	0.554	0.99
64_A	72_N	0.553	0.98
86_M	90_A	0.552	0.98
78_H	124_S	0.552	0.98
52_G	152_R	0.551	0.98
96_H	102_A	0.546	0.98
104_L	117_Y	0.544	0.98
114_C	119_W	0.543	0.98
49_I	159_D	0.541	0.98
200_M	204_A	0.540	0.98
34_L	38_A	0.540	0.98
118_S	121_E	0.540	0.98
37_M	41_I	0.537	0.98
117_Y	121_E	0.531	0.98
200_M	215_I	0.531	0.98
193_L	202_L	0.526	0.98
33_I	37_M	0.525	0.98
186_Q	231_M	0.524	0.98
170_V	202_L	0.523	0.98
67_A	70_G	0.523	0.98
126_L	132_V	0.522	0.98
178_D	181_A	0.520	0.98
75_V	79_M	0.520	0.98
101_N	129_N	0.518	0.98
40_E	220_M	0.516	0.98
108_I	112_G	0.515	0.98
11_R	14_L	0.515	0.98
78_H	86_M	0.515	0.98
74_V	137_G	0.514	0.98
140_N	144_T	0.513	0.98
165_T	215_I	0.512	0.98
131_V	134_L	0.512	0.98
78_H	85_V	0.510	0.97
38_A	42_K	0.507	0.97
14_L	164_A	0.506	0.97
136_A	141_P	0.506	0.97
125_L	129_N	0.504	0.97
52_G	158_A	0.502	0.97
95_L	131_V	0.502	0.97
204_A	208_A	0.502	0.97
19_E	165_T	0.500	0.97
16_L	40_E	0.500	0.97

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
2a1fA	5	0.9502	100	0.277	Contact Map
3ab4A	7	0.9004	100	0.28	Contact Map
1ybdA	5	0.9793	100	0.283	Contact Map
3l76A	2	0.9212	100	0.287	Contact Map
3nwyA	5	0.9793	100	0.289	Contact Map
2jjxA	5	0.9751	100	0.292	Contact Map
2va1A	5	0.9959	100	0.293	Contact Map
3ek6A	5	0.9876	100	0.294	Contact Map
3c1mA	3	0.9295	100	0.303	Contact Map
1z9dA	5	0.9751	100	0.309	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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