URK - HALSA - GREMLIN Contacts

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URK - Uridine kinase

UniProt:	Q9HQC9	Sequences: MTIPSFAIGIAGGTGAGKTTVAREITDNVGESATLIPLDNYYEDLSDRPFEERANANYDHPSAFEWELLRTHIDALLSGQSIEMPQYDFERHVRKADRVVVEPTDVIVLEGILALSDETVNDMLDLHIYVETDADVRILRRIERDVVERGRELEGVMDQYLSTVKPMHEQFIEPTKRHADIIIPEGANSVAVNLLEEKVQAETSEMTAWAARDDTAFEDATYNPQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	225 (187)
Sequences:	4535 (2653)
Seq/√Len:	194.0

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
75_A	80_Q	5.160	1.00
88_D	95_K	5.085	1.00
41_Y	72_H	4.401	1.00
68_L	72_H	3.269	1.00
71_T	75_A	3.237	1.00
69_L	109_L	2.980	1.00
9_G	124_L	2.744	1.00
138_I	161_L	2.740	1.00
121_N	178_H	2.579	1.00
47_D	51_E	2.553	1.00
77_L	125_D	2.374	1.00
165_K	169_E	2.208	1.00
81_S	100_V	2.164	1.00
83_E	98_R	2.136	1.00
152_E	155_G	2.055	1.00
38_L	114_A	2.026	1.00
158_D	162_S	1.929	1.00
164_V	167_M	1.896	1.00
109_L	124_L	1.896	1.00
72_H	75_A	1.893	1.00
83_E	100_V	1.889	1.00
65_E	94_R	1.846	1.00
136_V	139_L	1.836	1.00
11_A	115_L	1.779	1.00
86_Q	97_D	1.763	1.00
131_E	176_K	1.762	1.00
88_D	91_R	1.751	1.00
26_T	108_V	1.733	1.00
120_V	124_L	1.726	1.00
74_D	78_S	1.716	1.00
44_D	47_D	1.701	1.00
46_S	93_V	1.690	1.00
74_D	123_M	1.658	1.00
138_I	142_I	1.645	1.00
45_L	58_Y	1.615	1.00
81_S	102_E	1.608	1.00
8_I	106_V	1.606	1.00
26_T	35_L	1.581	1.00
24_E	27_D	1.528	1.00
54_A	62_S	1.526	1.00
165_K	168_H	1.481	1.00
134_A	169_E	1.471	1.00
45_L	56_A	1.470	1.00
87_Y	92_H	1.444	1.00
40_N	84_M	1.442	1.00
74_D	119_T	1.420	1.00
44_D	93_V	1.418	1.00
13_G	137_R	1.414	1.00
126_L	181_I	1.404	1.00
118_E	122_D	1.390	1.00
49_P	55_N	1.386	1.00
60_H	171_F	1.367	1.00
166_P	170_Q	1.365	1.00
133_D	136_V	1.364	1.00
115_L	127_H	1.351	1.00
22_A	35_L	1.327	1.00
50_F	56_A	1.324	1.00
22_A	108_V	1.316	1.00
127_H	180_D	1.296	1.00
84_M	99_V	1.290	1.00
91_R	95_K	1.279	1.00
6_F	106_V	1.246	1.00
70_R	74_D	1.244	1.00
156_V	159_Q	1.235	1.00
70_R	119_T	1.231	1.00
50_F	54_A	1.228	1.00
37_P	40_N	1.227	1.00
151_R	159_Q	1.224	1.00
164_V	168_H	1.200	1.00
67_E	119_T	1.187	1.00
153_L	157_M	1.180	1.00
76_L	107_I	1.177	1.00
139_L	143_E	1.167	1.00
65_E	68_L	1.137	1.00
7_A	124_L	1.136	1.00
34_T	104_T	1.130	1.00
6_F	126_L	1.128	1.00
21_V	130_V	1.125	1.00
155_G	158_D	1.105	1.00
47_D	52_E	1.092	1.00
173_E	176_K	1.090	1.00
7_A	77_L	1.083	1.00
155_G	159_Q	1.066	1.00
138_I	157_M	1.063	1.00
43_E	47_D	1.042	1.00
45_L	93_V	1.042	1.00
143_E	147_V	1.021	1.00
38_L	64_F	1.009	1.00
86_Q	95_K	1.000	1.00
157_M	161_L	0.988	0.99
151_R	155_G	0.987	0.99
38_L	66_W	0.984	0.99
89_F	92_H	0.970	0.99
81_S	98_R	0.964	0.99
10_I	22_A	0.956	0.99
81_S	103_P	0.951	0.99
42_Y	64_F	0.948	0.99
68_L	85_P	0.940	0.99
86_Q	94_R	0.936	0.99
50_F	55_N	0.934	0.99
21_V	25_I	0.927	0.99
45_L	54_A	0.926	0.99
146_V	156_V	0.925	0.99
43_E	65_E	0.920	0.99
67_E	71_T	0.915	0.99
137_R	168_H	0.914	0.99
154_E	157_M	0.909	0.99
134_A	137_R	0.903	0.99
141_R	164_V	0.901	0.99
145_D	149_R	0.881	0.99
4_P	77_L	0.878	0.99
73_I	124_L	0.878	0.99
51_E	55_N	0.878	0.99
22_A	26_T	0.876	0.99
61_P	116_S	0.875	0.99
169_E	173_E	0.875	0.99
70_R	120_V	0.868	0.99
86_Q	99_V	0.860	0.99
115_L	179_A	0.854	0.99
72_H	82_I	0.853	0.99
10_I	21_V	0.844	0.98
26_T	33_A	0.839	0.98
34_T	107_I	0.839	0.98
21_V	183_I	0.836	0.98
75_A	78_S	0.825	0.98
45_L	92_H	0.825	0.98
42_Y	59_D	0.822	0.98
14_T	164_V	0.820	0.98
41_Y	82_I	0.813	0.98
8_I	108_V	0.811	0.98
154_E	158_D	0.800	0.98
134_A	173_E	0.795	0.98
73_I	120_V	0.795	0.98
40_N	86_Q	0.794	0.98
101_V	104_T	0.791	0.98
48_R	63_A	0.788	0.97
40_N	97_D	0.787	0.97
88_D	93_V	0.787	0.97
45_L	55_N	0.779	0.97
85_P	94_R	0.778	0.97
113_L	116_S	0.770	0.97
7_A	107_I	0.768	0.97
126_L	190_V	0.763	0.97
24_E	189_S	0.761	0.97
151_R	156_V	0.760	0.97
30_G	105_D	0.754	0.97
16_A	137_R	0.751	0.97
23_R	27_D	0.748	0.97
51_E	54_A	0.748	0.97
13_G	168_H	0.743	0.96
49_P	52_E	0.741	0.96
176_K	182_I	0.741	0.96
22_A	37_P	0.731	0.96
89_F	95_K	0.726	0.96
26_T	30_G	0.726	0.96
9_G	115_L	0.724	0.96
54_A	92_H	0.717	0.96
14_T	168_H	0.712	0.95
34_T	99_V	0.708	0.95
153_L	156_V	0.706	0.95
38_L	69_L	0.706	0.95
146_V	153_L	0.704	0.95
58_Y	89_F	0.701	0.95
69_L	73_I	0.698	0.95
138_I	165_K	0.690	0.95
13_G	129_Y	0.689	0.95
48_R	56_A	0.686	0.94
59_D	167_M	0.686	0.94
73_I	109_L	0.686	0.94
57_N	60_H	0.685	0.94
133_D	184_P	0.681	0.94
169_E	177_R	0.677	0.94
42_Y	141_R	0.676	0.94
7_A	123_M	0.672	0.94
11_A	127_H	0.672	0.94
134_A	165_K	0.670	0.94
72_H	84_M	0.668	0.94
79_G	101_V	0.666	0.94
131_E	184_P	0.664	0.93
122_D	127_H	0.662	0.93
25_I	108_V	0.660	0.93
24_E	28_N	0.659	0.93
142_I	157_M	0.654	0.93
15_G	185_E	0.649	0.93
43_E	48_R	0.648	0.93
83_E	95_K	0.647	0.93
116_S	175_T	0.641	0.92
57_N	167_M	0.640	0.92
66_W	70_R	0.637	0.92
23_R	26_T	0.636	0.92
161_L	166_P	0.632	0.92
44_D	94_R	0.630	0.92
39_D	144_R	0.630	0.92
68_L	94_R	0.629	0.92
9_G	120_V	0.627	0.91
4_P	78_S	0.623	0.91
135_D	139_L	0.619	0.91
9_G	114_A	0.619	0.91
139_L	190_V	0.618	0.91
29_V	106_V	0.617	0.91
52_E	55_N	0.612	0.90
59_D	141_R	0.609	0.90
21_V	24_E	0.608	0.90
87_Y	93_V	0.602	0.90
146_V	150_G	0.601	0.90
109_L	172_I	0.601	0.90
83_E	86_Q	0.600	0.90
142_I	153_L	0.599	0.89
49_P	54_A	0.598	0.89
156_V	160_Y	0.596	0.89
129_Y	175_T	0.596	0.89
68_L	71_T	0.595	0.89
26_T	34_T	0.592	0.89
161_L	165_K	0.590	0.89
44_D	96_A	0.588	0.89
70_R	124_L	0.588	0.89
121_N	160_Y	0.584	0.88
68_L	96_A	0.584	0.88
54_A	58_Y	0.580	0.88
117_D	122_D	0.580	0.88
135_D	180_D	0.580	0.88
58_Y	164_V	0.579	0.88
12_G	17_G	0.578	0.88
163_T	168_H	0.576	0.88
57_N	164_V	0.572	0.87
163_T	167_M	0.571	0.87
77_L	123_M	0.568	0.87
14_T	89_F	0.568	0.87
129_Y	132_T	0.566	0.87
36_I	84_M	0.562	0.86
127_H	178_H	0.561	0.86
102_E	105_D	0.559	0.86
23_R	35_L	0.555	0.86
19_T	164_V	0.554	0.85
57_N	170_Q	0.553	0.85
119_T	122_D	0.553	0.85
42_Y	48_R	0.553	0.85
15_G	38_L	0.550	0.85
34_T	101_V	0.548	0.85
90_E	155_G	0.547	0.85
151_R	154_E	0.546	0.85
70_R	123_M	0.545	0.85
122_D	178_H	0.545	0.85
114_A	124_L	0.545	0.85
8_I	128_I	0.543	0.84
121_N	125_D	0.543	0.84
66_W	114_A	0.542	0.84
66_W	117_D	0.541	0.84
35_L	108_V	0.538	0.84
139_L	157_M	0.537	0.84
104_T	107_I	0.535	0.83
87_Y	149_R	0.535	0.83
30_G	33_A	0.535	0.83
57_N	62_S	0.535	0.83
89_F	141_R	0.534	0.83
12_G	18_K	0.533	0.83
11_A	172_I	0.533	0.83
19_T	23_R	0.530	0.83
121_N	124_L	0.529	0.83
71_T	78_S	0.529	0.83
135_D	184_P	0.528	0.83
162_S	166_P	0.524	0.82
76_L	82_I	0.524	0.82
40_N	112_I	0.523	0.82
14_T	39_D	0.523	0.82
84_M	98_R	0.522	0.82
14_T	141_R	0.517	0.81
159_Q	164_V	0.516	0.81
91_R	97_D	0.515	0.81
60_H	63_A	0.514	0.81
83_E	99_V	0.513	0.81
48_R	51_E	0.510	0.80
130_V	185_E	0.510	0.80
129_Y	176_K	0.510	0.80
39_D	87_Y	0.509	0.80
11_A	124_L	0.507	0.80
42_Y	89_F	0.506	0.80
89_F	149_R	0.506	0.80
32_S	103_P	0.504	0.80
14_T	42_Y	0.500	0.79

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
3tqcA	2	0.88	100	0.462	Contact Map
2jeoA	3	0.8889	100	0.463	Contact Map
2ga8A	1	0.8311	100	0.481	Contact Map
1a7jA	5	0.9644	100	0.507	Contact Map
1uj2A	3	0.8978	100	0.541	Contact Map
1rz3A	1	0.7067	100	0.545	Contact Map
3w34A	2	0.92	99.9	0.547	Contact Map
4bfzA	2	0.8756	99.9	0.561	Contact Map
4ne2A	2	0.8756	99.9	0.57	Contact Map
2qt1A	1	0.8178	99.9	0.579	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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