KITH - BACSU - GREMLIN Contacts

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KITH - Thymidine kinase

UniProt:	Q03221	Sequences: MYIMKQSGWLELICGSMFSGKSEELIRRVKRATYAKQEVRVFKPVIDNRYSEAAVVSHNGTSMTSYAISSAADIWDHISESTDVVAVDEVQFFDQEIVEVLSSLADKGYRVIAAGLDMDFRGEPFGVVPNIMAIAESVTKLQAVCSVCGSPASRTQRLIDGKPASYDDPVILVGAAESYEARCRHHHEVPGKSKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	195 (180)
Sequences:	2056 (1130)
Seq/√Len:	84.2

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
148_C	183_C	4.006	1.00
156_Q	182_R	3.180	1.00
183_C	186_H	2.936	1.00
54_A	62_S	2.755	1.00
9_W	137_S	2.752	1.00
148_C	186_H	2.654	1.00
33_T	63_M	2.614	1.00
99_E	130_N	2.385	1.00
172_L	178_S	2.319	1.00
41_V	55_V	2.252	1.00
119_D	170_V	2.167	1.00
23_E	27_R	2.158	1.00
75_W	103_S	2.157	1.00
10_L	105_A	2.153	1.00
51_S	54_A	2.149	1.00
24_E	27_R	2.148	1.00
29_V	39_V	2.106	1.00
90_V	113_A	2.102	1.00
49_R	174_G	2.082	1.00
29_V	86_A	2.077	1.00
45_V	69_S	2.067	1.00
73_D	76_D	2.016	1.00
42_F	77_H	1.966	1.00
26_I	41_V	1.941	1.00
101_L	113_A	1.876	1.00
102_S	134_I	1.775	1.00
15_G	19_S	1.772	1.00
25_L	86_A	1.759	1.00
103_S	107_K	1.719	1.00
87_V	101_L	1.711	1.00
95_Q	126_G	1.695	1.00
106_D	184_R	1.691	1.00
95_Q	130_N	1.681	1.00
13_I	139_T	1.679	1.00
48_N	52_E	1.671	1.00
71_A	94_D	1.670	1.00
102_S	184_R	1.612	1.00
20_G	27_R	1.589	1.00
103_S	188_E	1.588	1.00
90_V	97_I	1.580	1.00
54_A	64_T	1.552	1.00
50_Y	56_V	1.550	1.00
20_G	23_E	1.510	0.99
129_P	133_A	1.497	0.99
13_I	112_I	1.487	0.99
73_D	100_V	1.473	0.99
159_I	163_P	1.465	0.99
117_D	140_K	1.458	0.99
126_G	129_P	1.391	0.99
102_S	188_E	1.374	0.99
96_E	100_V	1.351	0.99
28_R	112_I	1.341	0.99
40_R	66_Y	1.337	0.99
156_Q	164_A	1.331	0.99
71_A	96_E	1.329	0.99
78_I	104_L	1.325	0.99
50_Y	58_H	1.320	0.99
72_A	77_H	1.317	0.99
122_G	187_H	1.288	0.98
11_E	110_R	1.280	0.98
40_R	82_T	1.278	0.98
99_E	134_I	1.271	0.98
13_I	28_R	1.271	0.98
123_E	130_N	1.228	0.98
185_H	189_V	1.201	0.97
102_S	106_D	1.197	0.97
38_E	81_S	1.195	0.97
19_S	142_Q	1.189	0.97
43_K	47_D	1.188	0.97
84_V	112_I	1.185	0.97
95_Q	123_E	1.179	0.97
105_A	184_R	1.150	0.97
26_I	63_M	1.142	0.96
158_L	178_S	1.131	0.96
71_A	100_V	1.111	0.96
90_V	131_I	1.092	0.95
87_V	93_F	1.092	0.95
58_H	175_A	1.091	0.95
29_V	63_M	1.088	0.95
146_S	181_A	1.088	0.95
38_E	83_D	1.081	0.95
143_A	152_A	1.074	0.95
41_V	63_M	1.072	0.95
16_S	155_T	1.064	0.95
51_S	56_V	1.060	0.95
122_G	154_R	1.056	0.95
26_I	59_N	1.047	0.94
43_K	53_A	1.023	0.94
42_F	66_Y	1.017	0.93
157_R	172_L	1.004	0.93
27_R	31_R	1.003	0.93
56_V	62_S	0.999	0.93
76_D	79_S	0.992	0.92
82_T	109_Y	0.989	0.92
117_D	132_M	0.987	0.92
75_W	100_V	0.979	0.92
22_S	65_S	0.971	0.92
120_F	157_R	0.970	0.92
40_R	77_H	0.969	0.92
90_V	115_G	0.968	0.92
31_R	34_Y	0.968	0.92
169_P	172_L	0.967	0.91
11_E	28_R	0.961	0.91
24_E	141_L	0.948	0.91
69_S	73_D	0.941	0.90
126_G	170_V	0.936	0.90
105_A	136_E	0.933	0.90
38_E	82_T	0.929	0.90
12_L	135_A	0.916	0.89
145_C	148_C	0.915	0.89
31_R	144_V	0.911	0.89
13_I	24_E	0.905	0.89
22_S	58_H	0.904	0.88
35_A	144_V	0.884	0.87
32_A	37_Q	0.876	0.87
80_E	83_D	0.872	0.87
142_Q	151_P	0.871	0.87
113_A	128_V	0.866	0.86
124_P	129_P	0.862	0.86
55_V	158_L	0.861	0.86
70_S	73_D	0.861	0.86
69_S	76_D	0.858	0.86
32_A	84_V	0.851	0.85
113_A	131_I	0.851	0.85
145_C	183_C	0.848	0.85
130_N	133_A	0.845	0.85
119_D	123_E	0.843	0.85
146_S	186_H	0.839	0.84
130_N	134_I	0.830	0.84
32_A	110_R	0.829	0.84
134_I	188_E	0.828	0.84
70_S	94_D	0.825	0.83
20_G	24_E	0.812	0.82
122_G	133_A	0.805	0.82
136_E	184_R	0.799	0.81
118_M	133_A	0.797	0.81
78_I	109_Y	0.796	0.81
24_E	28_R	0.796	0.81
29_V	33_T	0.791	0.81
139_T	142_Q	0.778	0.80
69_S	72_A	0.759	0.78
164_A	169_P	0.758	0.78
28_R	86_A	0.758	0.78
175_A	178_S	0.756	0.78
37_Q	110_R	0.755	0.78
17_M	21_K	0.753	0.77
123_E	166_Y	0.751	0.77
16_S	142_Q	0.748	0.77
46_I	171_I	0.734	0.76
48_N	173_V	0.733	0.76
158_L	180_E	0.731	0.75
16_S	118_M	0.730	0.75
31_R	143_A	0.726	0.75
32_A	39_V	0.725	0.75
161_G	164_A	0.720	0.74
120_F	170_V	0.717	0.74
38_E	80_E	0.715	0.74
85_V	111_V	0.715	0.74
17_M	20_G	0.715	0.74
157_R	170_V	0.715	0.74
16_S	143_A	0.709	0.73
101_L	127_V	0.708	0.73
43_K	50_Y	0.701	0.72
23_E	57_S	0.693	0.71
100_V	104_L	0.688	0.71
42_F	74_I	0.688	0.71
10_L	101_L	0.688	0.71
169_P	189_V	0.676	0.70
186_H	189_V	0.673	0.69
143_A	181_A	0.672	0.69
52_E	64_T	0.670	0.69
101_L	105_A	0.669	0.69
80_E	107_K	0.667	0.69
136_E	153_S	0.666	0.68
85_V	109_Y	0.666	0.68
26_I	114_A	0.661	0.68
106_D	136_E	0.660	0.68
152_A	181_A	0.658	0.67
164_A	182_R	0.657	0.67
43_K	65_S	0.656	0.67
52_E	67_A	0.655	0.67
84_V	110_R	0.650	0.67
16_S	22_S	0.644	0.66
95_Q	129_P	0.641	0.65
77_H	108_G	0.639	0.65
19_S	34_Y	0.638	0.65
11_E	140_K	0.637	0.65
40_R	78_I	0.634	0.65
22_S	175_A	0.628	0.64
91_Q	171_I	0.626	0.64
75_W	107_K	0.625	0.64
108_G	185_H	0.622	0.63
112_I	152_A	0.620	0.63
49_R	175_A	0.618	0.63
62_S	150_S	0.617	0.63
53_A	64_T	0.616	0.62
86_A	112_I	0.615	0.62
33_T	38_E	0.613	0.62
90_V	128_V	0.613	0.62
31_R	35_A	0.611	0.62
111_V	144_V	0.608	0.61
174_G	184_R	0.605	0.61
13_I	141_L	0.604	0.61
44_P	68_I	0.602	0.61
38_E	160_D	0.600	0.60
142_Q	153_S	0.599	0.60
118_M	155_T	0.598	0.60
34_Y	181_A	0.597	0.60
141_L	153_S	0.597	0.60
110_R	151_P	0.593	0.59
137_S	142_Q	0.587	0.59
62_S	96_E	0.585	0.58
121_R	168_D	0.584	0.58
72_A	176_A	0.582	0.58
106_D	188_E	0.581	0.58
76_D	80_E	0.579	0.58
98_V	131_I	0.579	0.58
18_F	22_S	0.579	0.58
14_C	132_M	0.577	0.57
15_G	143_A	0.577	0.57
25_L	114_A	0.577	0.57
110_R	140_K	0.577	0.57
10_L	127_V	0.574	0.57
84_V	109_Y	0.572	0.57
8_G	105_A	0.569	0.56
76_D	103_S	0.568	0.56
18_F	34_Y	0.566	0.56
45_V	48_N	0.557	0.55
161_G	165_S	0.556	0.55
126_G	130_N	0.555	0.55
150_S	185_H	0.555	0.55
48_N	51_S	0.554	0.54
64_T	123_E	0.553	0.54
50_Y	54_A	0.553	0.54
14_C	181_A	0.553	0.54
69_S	185_H	0.553	0.54
32_A	144_V	0.551	0.54
73_D	79_S	0.548	0.54
97_I	127_V	0.544	0.53
120_F	187_H	0.543	0.53
23_E	58_H	0.543	0.53
99_E	188_E	0.539	0.52
74_I	77_H	0.538	0.52
182_R	187_H	0.537	0.52
57_S	151_P	0.537	0.52
18_F	181_A	0.533	0.52
75_W	79_S	0.532	0.51
91_Q	173_V	0.530	0.51
172_L	177_E	0.530	0.51
18_F	25_L	0.527	0.51
15_G	68_I	0.527	0.51
108_G	111_V	0.527	0.51
118_M	142_Q	0.526	0.51
45_V	67_A	0.524	0.50
52_E	76_D	0.522	0.50
60_G	168_D	0.521	0.50
26_I	57_S	0.520	0.50
43_K	48_N	0.519	0.50
19_S	37_Q	0.516	0.49
98_V	127_V	0.515	0.49
19_S	32_A	0.515	0.49
144_V	151_P	0.512	0.49
9_W	136_E	0.508	0.48
47_D	173_V	0.507	0.48
96_E	99_E	0.507	0.48
33_T	39_V	0.506	0.48
28_R	139_T	0.504	0.48
19_S	174_G	0.501	0.47
149_G	182_R	0.500	0.47
143_A	187_H	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	0.18	Contact Map
2orvA	3	0.8359	100	0.23	Contact Map
2j9rA	3	0.9026	100	0.361	Contact Map
3e2iA	3	0.8923	100	0.371	Contact Map
2b8tA	3	0.9641	100	0.412	Contact Map
1xx6A	4	0.9128	100	0.433	Contact Map
2orwA	3	0.8923	100	0.548	Contact Map
4uxhA	3	0.8872	100	0.587	Contact Map
3upuA	1	0.9744	98.4	0.846	Contact Map
1w36D	1	0.9641	98.4	0.847	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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