KITH - HALSA - GREMLIN Contacts

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KITH - Thymidine kinase

UniProt:	Q9HPQ9	Sequences: MHAITNSGWVEVITGSMFSGKTEELLRRLRRAEIAGQDVAAVTPAVDDRYGEATLGSHAGRSWAATVVEPTAEGVASIPTLLNGEQVVAIDEANFFPAELVDVCQELAADGRRVVLSGTDQTFRGEPFEPVPQLMAIAEYVDKMRAICMQCGEPATRNQRLIEGEPAHYDDPTVMVGAEETYEARCRNCHVVRRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	195 (181)
Sequences:	2083 (1111)
Seq/√Len:	82.6

ECOLI - KITH
BACSU - KITH
HALSA - KITH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
151_C	186_C	3.991	1.00
159_Q	185_R	3.135	1.00
186_C	189_C	2.955	1.00
9_W	140_Y	2.767	1.00
33_E	63_W	2.756	1.00
151_C	189_C	2.641	1.00
175_M	181_T	2.448	1.00
54_T	62_S	2.380	1.00
102_D	133_Q	2.363	1.00
41_A	55_L	2.321	1.00
51_G	54_T	2.261	1.00
10_V	108_A	2.234	1.00
29_L	39_V	2.218	1.00
73_E	76_A	2.213	1.00
23_E	27_R	2.146	1.00
122_T	173_T	2.126	1.00
93_A	116_L	2.111	1.00
24_E	27_R	2.035	1.00
29_L	89_A	2.014	1.00
45_A	69_E	1.988	1.00
26_L	41_A	1.917	1.00
49_R	177_G	1.914	1.00
104_C	116_L	1.901	1.00
42_V	77_S	1.901	1.00
106_E	110_D	1.889	1.00
109_A	187_R	1.828	1.00
105_Q	137_I	1.765	1.00
78_I	107_L	1.761	1.00
75_V	106_E	1.753	1.00
25_L	89_A	1.747	1.00
15_G	19_S	1.742	1.00
98_A	129_E	1.708	1.00
13_I	142_D	1.669	1.00
90_I	104_C	1.657	1.00
150_Q	189_C	1.643	1.00
93_A	100_L	1.629	1.00
98_A	133_Q	1.621	1.00
48_D	52_E	1.604	1.00
105_Q	187_R	1.593	1.00
106_E	191_V	1.565	1.00
132_P	136_A	1.561	1.00
20_G	27_R	1.554	1.00
72_A	77_S	1.545	1.00
20_G	23_E	1.525	0.99
50_Y	56_G	1.523	0.99
13_I	115_V	1.471	0.99
120_D	143_K	1.441	0.99
71_T	97_P	1.438	0.99
162_I	166_P	1.423	0.99
71_T	99_E	1.422	0.99
73_E	103_V	1.388	0.99
129_E	132_P	1.378	0.99
159_Q	167_A	1.364	0.99
28_R	115_V	1.357	0.99
105_Q	191_V	1.339	0.99
99_E	103_V	1.337	0.99
43_T	47_D	1.325	0.99
54_T	64_A	1.317	0.98
50_Y	58_H	1.301	0.98
126_E	133_Q	1.267	0.98
40_A	85_E	1.261	0.98
13_I	28_R	1.255	0.98
11_E	113_R	1.246	0.98
188_N	192_V	1.240	0.98
105_Q	109_A	1.220	0.97
102_D	137_I	1.206	0.97
125_G	190_H	1.200	0.97
87_V	115_V	1.191	0.97
150_Q	183_E	1.190	0.97
40_A	66_T	1.186	0.97
19_S	145_R	1.178	0.97
42_V	66_T	1.170	0.97
98_A	126_E	1.166	0.97
161_L	181_T	1.160	0.97
29_L	63_W	1.146	0.96
93_A	134_L	1.138	0.96
51_G	56_G	1.122	0.96
108_A	187_R	1.118	0.96
38_D	86_Q	1.117	0.96
125_G	157_R	1.114	0.96
90_I	96_F	1.112	0.96
43_T	53_A	1.105	0.95
146_A	155_A	1.103	0.95
38_D	84_G	1.086	0.95
58_H	178_A	1.079	0.95
26_L	63_W	1.071	0.95
85_E	112_R	1.058	0.94
148_C	151_C	1.043	0.94
41_A	63_W	1.018	0.93
120_D	135_M	1.016	0.93
16_S	158_N	1.009	0.93
56_G	62_S	1.005	0.93
27_R	31_R	1.004	0.93
129_E	173_T	1.001	0.92
172_P	175_M	0.995	0.92
38_D	85_E	0.988	0.92
22_T	58_H	0.982	0.92
32_A	37_Q	0.968	0.91
26_L	59_A	0.966	0.91
13_I	24_E	0.964	0.91
93_A	118_G	0.961	0.91
108_A	139_E	0.937	0.90
11_E	28_R	0.932	0.89
24_E	144_M	0.932	0.89
74_G	77_S	0.930	0.89
123_F	160_R	0.928	0.89
160_R	175_M	0.922	0.89
69_E	73_E	0.918	0.89
31_R	34_I	0.914	0.89
29_L	33_E	0.893	0.87
12_V	138_A	0.892	0.87
69_E	72_A	0.880	0.87
150_Q	185_R	0.875	0.86
22_T	65_A	0.874	0.86
127_P	132_P	0.867	0.86
148_C	186_C	0.865	0.86
139_E	187_R	0.864	0.86
31_R	147_I	0.864	0.86
83_N	86_Q	0.859	0.85
71_T	75_V	0.859	0.85
32_A	87_V	0.852	0.85
35_A	147_I	0.844	0.84
17_M	21_K	0.842	0.84
116_L	131_V	0.838	0.84
116_L	134_L	0.832	0.83
32_A	113_R	0.831	0.83
55_L	161_L	0.826	0.83
133_Q	136_A	0.822	0.83
126_E	169_Y	0.816	0.82
69_E	76_A	0.809	0.82
20_G	24_E	0.807	0.81
145_R	154_P	0.802	0.81
70_P	97_P	0.789	0.80
121_Q	136_A	0.788	0.80
32_A	39_V	0.787	0.80
178_A	181_T	0.779	0.79
133_Q	137_I	0.778	0.79
19_S	34_I	0.773	0.79
31_R	146_A	0.770	0.78
125_G	136_A	0.768	0.78
122_T	126_E	0.768	0.78
37_Q	113_R	0.766	0.78
46_V	174_V	0.765	0.78
161_L	183_E	0.760	0.77
43_T	50_Y	0.760	0.77
71_T	103_V	0.758	0.77
160_R	173_T	0.756	0.77
137_I	191_V	0.752	0.77
24_E	28_R	0.752	0.77
28_R	89_A	0.749	0.76
167_A	172_P	0.745	0.76
123_F	173_T	0.743	0.76
40_A	77_S	0.738	0.75
62_S	153_E	0.737	0.75
142_D	145_R	0.735	0.75
16_S	146_A	0.732	0.75
87_V	113_R	0.727	0.74
78_I	112_R	0.722	0.74
16_S	145_R	0.722	0.74
111_G	188_N	0.720	0.74
75_V	103_V	0.715	0.73
53_A	64_A	0.714	0.73
109_A	139_E	0.708	0.72
104_C	130_P	0.705	0.72
88_V	112_R	0.703	0.72
17_M	20_G	0.698	0.71
83_N	110_D	0.693	0.71
38_D	83_N	0.686	0.70
82_L	85_E	0.684	0.70
66_T	77_S	0.683	0.70
43_T	65_A	0.679	0.69
10_V	104_C	0.676	0.69
18_F	22_T	0.674	0.69
139_E	156_T	0.672	0.68
77_S	111_G	0.670	0.68
16_S	22_T	0.668	0.68
146_A	184_A	0.665	0.68
57_S	154_P	0.665	0.68
20_G	25_L	0.662	0.67
129_E	133_Q	0.661	0.67
52_E	67_V	0.658	0.67
16_S	121_Q	0.657	0.67
88_V	114_V	0.654	0.66
115_V	155_A	0.654	0.66
70_P	74_G	0.648	0.66
62_S	99_E	0.645	0.65
103_V	107_L	0.644	0.65
124_R	171_D	0.641	0.65
48_D	176_V	0.640	0.65
87_V	112_R	0.637	0.64
104_C	108_A	0.635	0.64
26_L	117_S	0.633	0.64
23_E	57_S	0.632	0.64
31_R	35_A	0.629	0.63
38_D	163_E	0.629	0.63
22_T	178_A	0.626	0.63
101_V	134_L	0.625	0.63
52_E	64_A	0.621	0.62
167_A	185_R	0.618	0.62
14_T	184_A	0.617	0.62
89_A	115_V	0.616	0.62
140_Y	145_R	0.614	0.61
144_M	156_T	0.611	0.61
18_F	34_I	0.609	0.61
11_E	143_K	0.608	0.61
50_Y	54_T	0.605	0.60
14_T	135_M	0.604	0.60
77_S	82_L	0.600	0.60
75_V	110_D	0.597	0.59
76_A	81_L	0.597	0.59
8_G	108_A	0.596	0.59
68_V	74_G	0.596	0.59
45_A	48_D	0.594	0.59
177_G	187_R	0.592	0.59
8_G	11_E	0.592	0.59
100_L	130_P	0.591	0.58
25_L	117_S	0.590	0.58
18_F	25_L	0.589	0.58
48_D	51_G	0.589	0.58
15_G	68_V	0.586	0.58
23_E	58_H	0.586	0.58
98_A	132_P	0.585	0.58
93_A	131_V	0.585	0.58
121_Q	158_N	0.583	0.57
44_P	68_V	0.580	0.57
175_M	180_E	0.579	0.57
34_I	179_E	0.576	0.57
113_R	143_K	0.575	0.56
124_R	170_D	0.573	0.56
34_I	184_A	0.566	0.55
164_G	167_A	0.565	0.55
32_A	147_I	0.564	0.55
155_A	184_A	0.564	0.55
123_F	190_H	0.562	0.55
164_G	181_T	0.561	0.55
19_S	37_Q	0.558	0.54
84_G	98_A	0.555	0.54
145_R	156_T	0.554	0.54
33_E	38_D	0.554	0.54
147_I	154_P	0.553	0.54
11_E	57_S	0.553	0.54
10_V	130_P	0.553	0.54
13_I	144_M	0.548	0.53
26_L	57_S	0.546	0.53
19_S	32_A	0.545	0.52
49_R	178_A	0.542	0.52
111_G	153_E	0.538	0.52
94_N	174_V	0.536	0.51
18_F	58_H	0.532	0.51
101_V	130_P	0.531	0.51
114_V	147_I	0.531	0.51
36_G	152_G	0.530	0.50
94_N	176_V	0.527	0.50
71_T	106_E	0.527	0.50
185_R	190_H	0.527	0.50
189_C	192_V	0.527	0.50
44_P	174_V	0.526	0.50
121_Q	145_R	0.525	0.50
19_S	177_G	0.524	0.50
110_D	192_V	0.524	0.50
60_G	171_D	0.522	0.49
43_T	48_D	0.521	0.49
162_I	181_T	0.516	0.49
153_E	188_N	0.511	0.48
22_T	41_A	0.510	0.48
113_R	154_P	0.509	0.48
15_G	146_A	0.508	0.48
109_A	191_V	0.507	0.47
156_T	174_V	0.506	0.47
18_F	184_A	0.506	0.47
45_A	67_V	0.504	0.47
9_W	139_E	0.500	0.47

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
1w4rA	3	0.8923	100	0.181	Contact Map
2orvA	3	0.8359	100	0.238	Contact Map
2j9rA	3	0.8974	100	0.379	Contact Map
3e2iA	3	0.8974	100	0.39	Contact Map
2b8tA	3	0.9641	100	0.411	Contact Map
1xx6A	4	0.9128	100	0.448	Contact Map
2orwA	3	0.8923	100	0.56	Contact Map
4uxhA	3	0.8872	100	0.584	Contact Map
3upuA	1	0.9692	98.5	0.84	Contact Map
3e1sA	1	0.9282	98.5	0.841	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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