URK - BACSU - GREMLIN Contacts

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URK - Uridine kinase

UniProt:	O32033	Sequences: MGKNPVVIGIAGGSGSGKTSVTRSIYEQFKGHSILMIQQDLYYKDQSHLPFEERLNTNYDHPLAFDNDYLIEHIQDLLNYRPIEKPIYDYKLHTRSEETVHVEPKDVIILEGILVLEDKRLRDLMDIKLYVDTDADLRIIRRIMRDINERGRSIDSVIEQYVSVVRPMHNQFVEPTKRYADIIIPEGGQNHVAIDLMVTKIQTILEQNAIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	211 (184)
Sequences:	4771 (2853)
Seq/√Len:	210.3

ECOLI - URK YGGC COAA
BACSU - URK COAA
HALSA - URK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_D	81_R	4.953	1.00
89_D	96_S	4.893	1.00
42_Y	73_H	4.323	1.00
72_E	76_D	3.072	1.00
69_Y	73_H	3.010	1.00
70_L	110_L	2.897	1.00
9_G	125_M	2.885	1.00
82_P	101_H	2.849	1.00
139_I	162_V	2.791	1.00
122_R	179_Y	2.390	1.00
78_L	126_D	2.246	1.00
50_P	56_N	2.190	1.00
82_P	103_E	2.119	1.00
84_E	101_H	2.118	1.00
48_H	52_E	2.106	1.00
166_R	170_N	2.086	1.00
153_S	156_S	2.048	1.00
137_L	140_I	2.003	1.00
84_E	99_T	1.998	1.00
33_S	106_D	1.983	1.00
121_L	125_M	1.910	1.00
165_V	168_M	1.877	1.00
110_L	125_M	1.816	1.00
39_Q	115_V	1.808	1.00
26_Y	109_I	1.797	1.00
85_K	100_V	1.784	1.00
75_Q	124_L	1.739	1.00
75_Q	120_R	1.685	1.00
73_H	76_D	1.679	1.00
75_Q	79_N	1.662	1.00
66_D	95_R	1.660	1.00
46_Q	59_Y	1.657	1.00
88_Y	93_H	1.656	1.00
47_S	94_T	1.647	1.00
45_D	48_H	1.633	1.00
55_L	63_L	1.616	1.00
132_D	177_K	1.606	1.00
26_Y	36_M	1.584	1.00
139_I	143_I	1.567	1.00
11_A	116_L	1.565	1.00
45_D	94_T	1.537	1.00
89_D	92_L	1.532	1.00
8_I	107_V	1.503	1.00
24_S	27_E	1.483	1.00
46_Q	57_T	1.436	1.00
134_D	137_L	1.430	1.00
144_M	148_N	1.416	1.00
116_L	128_K	1.410	1.00
41_L	85_K	1.384	1.00
166_R	169_H	1.383	1.00
135_A	170_N	1.371	1.00
167_P	171_Q	1.364	1.00
127_I	182_I	1.359	1.00
22_T	36_M	1.353	1.00
13_G	138_R	1.312	1.00
154_I	158_I	1.310	1.00
140_I	144_M	1.296	1.00
71_I	75_Q	1.286	1.00
21_V	131_V	1.267	1.00
71_I	120_R	1.266	1.00
128_K	181_D	1.250	1.00
66_D	69_Y	1.238	1.00
174_E	177_K	1.229	1.00
22_T	109_I	1.221	1.00
61_H	172_F	1.205	1.00
6_V	127_I	1.201	1.00
44_K	48_H	1.185	1.00
68_D	120_R	1.177	1.00
156_S	159_E	1.172	1.00
7_V	78_L	1.165	1.00
6_V	107_V	1.159	1.00
35_L	105_K	1.144	1.00
38_Q	41_L	1.134	1.00
170_N	174_E	1.108	1.00
7_V	125_M	1.095	1.00
52_E	56_N	1.084	1.00
152_R	160_Q	1.075	1.00
165_V	169_H	1.070	1.00
77_L	108_I	1.066	1.00
87_I	98_E	1.065	1.00
21_V	25_I	1.052	1.00
152_R	156_S	1.049	1.00
52_E	55_L	1.037	1.00
157_V	160_Q	1.033	1.00
48_H	53_E	1.029	1.00
139_I	158_I	1.024	1.00
62_P	117_E	1.001	1.00
39_Q	67_N	1.000	1.00
92_L	96_S	0.997	1.00
71_I	121_L	0.996	1.00
26_Y	34_I	0.996	1.00
90_Y	93_H	0.970	1.00
147_I	157_V	0.961	1.00
46_Q	93_H	0.952	1.00
10_I	22_T	0.943	0.99
39_Q	65_F	0.942	0.99
46_Q	55_L	0.926	0.99
158_I	162_V	0.925	0.99
4_N	78_L	0.924	0.99
46_Q	94_T	0.916	0.99
164_V	168_M	0.912	0.99
30_K	33_S	0.912	0.99
43_Y	65_F	0.910	0.99
68_D	72_E	0.882	0.99
43_Y	60_D	0.876	0.99
22_T	26_Y	0.873	0.99
87_I	95_R	0.871	0.99
63_L	119_K	0.861	0.99
10_I	21_V	0.860	0.99
74_I	125_M	0.855	0.99
156_S	160_Q	0.855	0.99
8_I	109_I	0.848	0.99
87_I	96_S	0.848	0.99
146_D	150_R	0.845	0.99
76_D	79_N	0.843	0.99
33_S	105_K	0.841	0.99
23_R	26_Y	0.834	0.99
21_V	184_I	0.826	0.99
161_Y	164_V	0.825	0.99
116_L	180_A	0.814	0.98
159_E	164_V	0.811	0.98
38_Q	100_V	0.806	0.98
147_I	154_I	0.805	0.98
23_R	27_E	0.803	0.98
14_S	165_V	0.802	0.98
41_L	87_I	0.801	0.98
142_R	165_V	0.800	0.98
90_Y	96_S	0.800	0.98
69_Y	86_P	0.799	0.98
49_L	64_A	0.797	0.98
44_K	66_D	0.796	0.98
114_L	117_E	0.790	0.98
162_V	167_P	0.786	0.98
73_H	85_K	0.785	0.98
164_V	167_P	0.784	0.98
69_Y	97_E	0.780	0.98
87_I	100_V	0.777	0.98
138_R	169_H	0.774	0.98
177_K	183_I	0.771	0.98
73_H	83_I	0.771	0.98
46_Q	56_N	0.770	0.98
118_D	123_D	0.768	0.98
119_K	123_D	0.768	0.98
86_P	95_R	0.763	0.98
143_I	158_I	0.759	0.98
58_N	168_M	0.758	0.98
14_S	169_H	0.757	0.98
24_S	28_Q	0.753	0.97
135_A	138_R	0.753	0.97
155_D	158_I	0.749	0.97
37_I	102_V	0.748	0.97
49_L	57_T	0.746	0.97
9_G	116_L	0.735	0.97
74_I	121_L	0.733	0.97
155_D	159_E	0.731	0.97
29_F	107_V	0.729	0.97
117_E	176_T	0.728	0.97
22_T	38_Q	0.725	0.97
84_E	96_S	0.724	0.97
26_Y	30_K	0.723	0.97
35_L	108_I	0.721	0.97
135_A	174_E	0.714	0.96
59_Y	88_Y	0.711	0.96
9_G	121_L	0.710	0.96
132_D	185_P	0.706	0.96
102_V	108_I	0.706	0.96
103_E	106_D	0.704	0.96
140_I	158_I	0.702	0.96
39_Q	70_L	0.700	0.96
11_A	128_K	0.697	0.96
16_S	138_R	0.693	0.96
90_Y	95_R	0.688	0.96
58_N	61_H	0.679	0.95
33_S	103_E	0.678	0.95
120_R	123_D	0.667	0.95
41_L	100_V	0.664	0.95
50_P	53_E	0.660	0.95
13_G	130_Y	0.659	0.95
69_Y	95_R	0.656	0.94
45_D	95_R	0.654	0.94
170_N	178_R	0.653	0.94
136_D	140_I	0.650	0.94
60_D	168_M	0.650	0.94
67_N	71_I	0.648	0.94
13_G	169_H	0.643	0.94
30_K	34_I	0.642	0.94
82_P	104_P	0.640	0.94
37_I	85_K	0.636	0.93
30_K	106_D	0.630	0.93
74_I	110_L	0.629	0.93
44_K	49_L	0.628	0.93
35_L	100_V	0.627	0.93
26_Y	35_L	0.627	0.93
40_D	145_R	0.625	0.93
70_L	74_I	0.621	0.93
134_D	185_P	0.621	0.93
78_L	124_L	0.620	0.93
25_I	109_I	0.619	0.92
135_A	162_V	0.617	0.92
135_A	166_R	0.616	0.92
59_Y	90_Y	0.615	0.92
77_L	83_I	0.615	0.92
7_V	124_L	0.612	0.92
160_Q	164_V	0.612	0.92
87_I	99_T	0.610	0.92
28_Q	31_G	0.609	0.92
88_Y	94_T	0.608	0.92
139_I	166_R	0.608	0.92
143_I	154_I	0.607	0.92
12_G	17_G	0.604	0.92
58_N	165_V	0.604	0.92
55_L	93_H	0.600	0.91
72_E	75_Q	0.600	0.91
7_V	74_I	0.599	0.91
43_Y	142_R	0.599	0.91
47_S	50_P	0.596	0.91
29_F	34_I	0.590	0.91
162_V	166_R	0.590	0.91
89_D	94_T	0.590	0.91
67_N	115_V	0.587	0.90
46_Q	49_L	0.584	0.90
88_Y	91_K	0.584	0.90
8_I	129_L	0.581	0.90
147_I	153_S	0.581	0.90
98_E	101_H	0.578	0.90
42_Y	83_I	0.577	0.90
45_D	97_E	0.576	0.90
67_N	118_D	0.576	0.90
46_Q	50_P	0.575	0.89
82_P	99_T	0.573	0.89
115_V	125_M	0.572	0.89
60_D	142_R	0.568	0.89
44_K	84_E	0.566	0.89
23_R	123_D	0.566	0.89
7_V	108_I	0.563	0.88
59_Y	165_V	0.562	0.88
69_Y	72_E	0.562	0.88
14_S	43_Y	0.562	0.88
152_R	157_V	0.560	0.88
137_L	141_R	0.554	0.88
149_E	152_R	0.554	0.88
71_I	124_L	0.554	0.88
58_N	63_L	0.553	0.88
82_P	85_K	0.551	0.87
8_I	106_D	0.550	0.87
148_N	155_D	0.543	0.87
168_M	171_Q	0.540	0.86
60_D	64_A	0.539	0.86
61_H	64_A	0.539	0.86
23_R	36_M	0.536	0.86
35_L	102_V	0.534	0.86
43_Y	49_L	0.533	0.86
62_P	119_K	0.533	0.86
157_V	161_Y	0.531	0.85
159_E	162_V	0.528	0.85
58_N	171_Q	0.528	0.85
154_I	159_E	0.526	0.85
12_G	18_K	0.521	0.84
36_M	109_I	0.520	0.84
14_S	90_Y	0.518	0.84
41_L	98_E	0.516	0.84
14_S	142_R	0.515	0.84
9_G	12_G	0.514	0.84
102_V	105_K	0.513	0.83
123_D	179_Y	0.510	0.83
105_K	108_I	0.509	0.83
14_S	40_D	0.508	0.83
168_M	172_F	0.506	0.83
41_L	113_I	0.506	0.83
122_R	125_M	0.505	0.83
5_P	106_D	0.505	0.83
55_L	59_Y	0.504	0.82
9_G	115_V	0.504	0.82
88_Y	92_L	0.502	0.82
12_G	16_S	0.500	0.82
11_A	125_M	0.500	0.82

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
2jeoA	3	0.9573	100	0.439	Contact Map
3tqcA	2	0.9431	100	0.444	Contact Map
2ga8A	1	0.891	100	0.449	Contact Map
1a7jA	5	0.9621	100	0.465	Contact Map
1uj2A	3	0.9668	100	0.516	Contact Map
3w34A	2	0.9858	100	0.516	Contact Map
1rz3A	1	0.7583	100	0.517	Contact Map
2qt1A	1	0.872	99.9	0.549	Contact Map
4bfzA	2	0.9431	99.9	0.551	Contact Map
4ne2A	2	0.9384	99.9	0.554	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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