KITH - ECOLI - GREMLIN Contacts

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KITH - Thymidine kinase

UniProt:	P23331	Sequences: MAQLYFYYSAMNAGKSTALLQSSYNYQERGMRTVVYTAEIDDRFGAGKVSSRIGLSSPAKLFNQNSSLFDEIRAEHEQQAIHCVLVDECQFLTRQQVYELSEVVDQLDIPVLCYGLRTDFRGELFIGSQYLLAWSDKLVELKTICFCGRKASMVLRLDQAGRPYNEGEQVVIGGNERYVSVCRKHYKEALQVDSLTAIQERHRHD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10994
Length:	205 (181)
Sequences:	2158 (1098)
Seq/√Len:	81.6

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
147_C	182_C	3.826	1.00
155_L	181_V	2.925	1.00
182_C	185_H	2.811	1.00
48_K	56_S	2.674	1.00
3_Q	137_K	2.616	1.00
147_C	185_H	2.554	1.00
27_Q	57_S	2.489	1.00
171_V	177_R	2.375	1.00
35_V	49_V	2.234	1.00
98_Y	130_Y	2.156	1.00
146_F	185_H	2.126	1.00
45_G	48_K	2.110	1.00
17_T	21_Q	2.100	1.00
18_A	21_Q	2.078	1.00
119_D	169_Q	2.070	1.00
67_S	70_D	2.069	1.00
23_S	33_T	2.010	1.00
89_C	113_C	1.997	1.00
43_R	173_G	1.993	1.00
23_S	85_L	1.978	1.00
39_E	63_N	1.919	1.00
36_Y	71_E	1.869	1.00
20_L	35_V	1.838	1.00
100_L	104_V	1.801	1.00
69_F	107_L	1.799	1.00
9_S	13_A	1.708	1.00
94_R	126_I	1.674	1.00
19_L	85_L	1.665	1.00
86_V	100_L	1.644	1.00
7_Y	139_V	1.630	1.00
101_S	183_R	1.623	1.00
102_E	106_Q	1.623	1.00
14_G	21_Q	1.570	1.00
102_E	187_K	1.568	1.00
65_N	93_T	1.530	0.99
129_Q	133_A	1.520	0.99
158_D	162_R	1.511	0.99
48_K	58_P	1.508	0.99
4_L	104_V	1.502	0.99
94_R	130_Y	1.499	0.99
14_G	17_T	1.472	0.99
69_F	102_E	1.470	0.99
65_N	95_Q	1.470	0.99
103_V	107_L	1.447	0.99
7_Y	112_L	1.447	0.99
42_D	46_A	1.441	0.99
72_I	103_V	1.437	0.99
117_R	140_E	1.425	0.99
44_F	50_S	1.425	0.99
89_C	96_Q	1.425	0.99
126_I	129_Q	1.405	0.99
100_L	113_C	1.398	0.99
101_S	134_W	1.384	0.99
34_V	81_I	1.370	0.99
22_S	112_L	1.366	0.99
5_Y	110_P	1.330	0.99
155_L	163_P	1.317	0.98
66_S	71_E	1.305	0.98
95_Q	99_E	1.289	0.98
122_G	186_Y	1.287	0.98
7_Y	22_S	1.287	0.98
70_D	73_R	1.287	0.98
44_F	52_R	1.267	0.98
47_G	58_P	1.257	0.98
184_K	188_E	1.236	0.98
32_R	80_A	1.224	0.97
94_R	123_E	1.216	0.97
67_S	99_E	1.206	0.97
83_C	112_L	1.202	0.97
37_T	41_D	1.201	0.97
123_E	130_Y	1.199	0.97
101_S	187_K	1.188	0.97
37_T	47_G	1.185	0.97
146_F	179_V	1.183	0.97
98_Y	134_W	1.178	0.97
32_R	79_Q	1.147	0.96
20_L	57_S	1.144	0.96
34_V	60_K	1.140	0.96
23_S	57_S	1.127	0.96
36_Y	60_K	1.111	0.95
143_T	151_A	1.106	0.95
13_A	142_K	1.100	0.95
86_V	92_L	1.097	0.95
32_R	82_H	1.090	0.95
146_F	181_V	1.073	0.95
104_V	183_R	1.069	0.94
89_C	131_L	1.064	0.94
81_I	109_I	1.060	0.94
69_F	99_E	1.046	0.94
122_G	153_M	1.045	0.94
52_R	174_G	1.034	0.93
120_F	156_R	1.033	0.93
146_F	189_A	1.018	0.93
25_N	28_E	1.000	0.92
155_L	189_A	0.993	0.92
117_R	132_L	0.992	0.92
64_Q	67_S	0.986	0.92
50_S	56_S	0.981	0.91
32_R	81_I	0.980	0.91
157_L	177_R	0.977	0.91
126_I	169_Q	0.976	0.91
21_Q	25_N	0.971	0.91
174_G	177_R	0.959	0.90
168_E	171_V	0.959	0.90
10_A	154_V	0.952	0.90
6_F	135_S	0.952	0.90
136_D	183_R	0.949	0.90
89_C	115_G	0.948	0.90
35_V	57_S	0.940	0.90
26_Y	31_M	0.932	0.89
25_N	144_I	0.930	0.89
7_Y	18_A	0.926	0.89
20_L	53_I	0.915	0.88
5_Y	22_S	0.914	0.88
18_A	141_L	0.912	0.88
99_E	103_V	0.910	0.88
96_Q	99_E	0.906	0.88
16_S	52_R	0.898	0.87
29_R	144_I	0.896	0.87
156_R	171_V	0.890	0.87
34_V	71_E	0.885	0.87
26_Y	83_C	0.880	0.86
63_N	66_S	0.878	0.86
16_S	59_A	0.865	0.85
23_S	27_Q	0.864	0.85
63_N	70_D	0.864	0.85
119_D	123_E	0.853	0.84
26_Y	110_P	0.851	0.84
63_N	67_S	0.851	0.84
14_G	18_A	0.846	0.84
145_C	182_C	0.846	0.84
73_R	107_L	0.845	0.84
72_I	109_I	0.843	0.84
130_Y	134_W	0.842	0.84
130_Y	133_A	0.840	0.84
165_N	189_A	0.835	0.83
31_M	110_P	0.826	0.83
122_G	133_A	0.826	0.83
124_L	129_Q	0.820	0.82
113_C	128_S	0.820	0.82
10_A	143_T	0.817	0.82
118_T	133_A	0.808	0.81
113_C	131_L	0.802	0.81
18_A	22_S	0.799	0.80
142_K	150_K	0.799	0.80
64_Q	93_T	0.796	0.80
22_S	85_L	0.781	0.79
134_W	187_K	0.780	0.79
136_D	152_S	0.775	0.78
121_R	167_G	0.773	0.78
49_V	157_L	0.771	0.78
45_G	50_S	0.771	0.78
10_A	142_K	0.767	0.78
42_D	172_I	0.761	0.77
120_F	169_Q	0.759	0.77
13_A	28_E	0.756	0.77
11_M	15_K	0.755	0.76
101_S	104_V	0.747	0.76
83_C	110_P	0.745	0.76
17_T	51_S	0.741	0.75
156_R	169_Q	0.724	0.73
165_N	188_E	0.724	0.73
65_N	99_E	0.722	0.73
11_M	14_G	0.720	0.73
157_L	179_V	0.719	0.73
4_L	127_G	0.716	0.73
84_V	111_V	0.716	0.73
26_Y	33_T	0.715	0.73
100_L	127_G	0.715	0.73
40_I	170_V	0.714	0.72
25_N	143_T	0.705	0.71
63_N	73_R	0.699	0.71
25_N	29_R	0.697	0.71
12_N	28_E	0.696	0.70
37_T	44_F	0.696	0.70
84_V	109_I	0.696	0.70
60_K	71_E	0.688	0.70
139_V	142_K	0.677	0.68
90_Q	170_V	0.677	0.68
141_L	152_S	0.674	0.68
137_K	142_K	0.671	0.68
143_T	180_S	0.670	0.68
90_Q	172_I	0.667	0.67
83_C	109_I	0.667	0.67
142_K	152_S	0.666	0.67
106_Q	187_K	0.664	0.67
10_A	118_T	0.660	0.66
98_Y	104_V	0.658	0.66
163_P	168_E	0.657	0.66
66_S	175_N	0.656	0.66
123_E	165_N	0.654	0.66
104_V	136_D	0.653	0.66
97_V	131_L	0.652	0.65
108_D	184_K	0.650	0.65
68_L	71_E	0.648	0.65
112_L	151_A	0.641	0.64
12_N	16_S	0.640	0.64
16_S	174_G	0.640	0.64
151_A	180_S	0.639	0.64
10_A	16_S	0.635	0.63
28_E	180_S	0.634	0.63
26_Y	144_I	0.632	0.63
173_G	183_R	0.628	0.63
111_V	144_I	0.628	0.63
94_R	129_Q	0.628	0.63
163_P	181_V	0.627	0.62
27_Q	32_R	0.625	0.62
85_L	112_L	0.624	0.62
56_S	149_R	0.623	0.62
126_I	130_Y	0.621	0.62
20_L	114_Y	0.621	0.62
110_P	150_K	0.620	0.62
7_Y	141_L	0.619	0.61
38_A	170_V	0.618	0.61
89_C	128_S	0.617	0.61
51_S	150_K	0.615	0.61
118_T	154_V	0.611	0.60
120_F	186_Y	0.609	0.60
34_V	72_I	0.608	0.60
37_T	59_A	0.607	0.60
79_Q	82_H	0.600	0.59
98_Y	101_S	0.596	0.59
168_E	188_E	0.595	0.58
8_Y	132_L	0.593	0.58
9_S	143_T	0.591	0.58
46_A	61_L	0.590	0.58
5_Y	140_E	0.590	0.58
44_F	48_K	0.589	0.58
80_A	94_R	0.586	0.57
8_Y	180_S	0.585	0.57
118_T	142_K	0.583	0.57
158_D	171_V	0.582	0.57
67_S	73_R	0.581	0.57
27_Q	33_T	0.573	0.56
181_V	186_Y	0.570	0.55
12_N	180_S	0.568	0.55
22_S	139_V	0.565	0.55
17_T	52_R	0.564	0.54
99_E	104_V	0.564	0.54
171_V	176_E	0.563	0.54
19_L	114_Y	0.560	0.54
12_N	52_R	0.553	0.53
9_S	62_F	0.551	0.53
173_G	176_E	0.551	0.53
97_V	127_G	0.550	0.53
36_Y	68_L	0.547	0.52
98_Y	187_K	0.547	0.52
13_A	31_M	0.546	0.52
160_A	164_Y	0.545	0.52
16_S	35_V	0.545	0.52
39_E	42_D	0.543	0.52
12_N	19_L	0.530	0.50
13_A	118_T	0.529	0.50
37_T	50_S	0.526	0.50
28_E	175_N	0.520	0.49
5_Y	51_S	0.519	0.49
149_R	184_K	0.519	0.49
143_T	186_Y	0.518	0.48
158_D	177_R	0.518	0.48
14_G	19_L	0.517	0.48
17_T	53_I	0.515	0.48
6_F	128_S	0.515	0.48
108_D	111_V	0.514	0.48
42_D	45_G	0.513	0.48
27_Q	107_L	0.512	0.48
166_E	171_V	0.509	0.47
7_Y	21_Q	0.509	0.47
20_L	51_S	0.505	0.47
12_N	175_N	0.505	0.47
96_Q	127_G	0.504	0.47
23_S	35_V	0.501	0.46
152_S	170_V	0.500	0.46

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	0.8439	100	0.202	Contact Map
2orvA	3	0.7902	100	0.261	Contact Map
2j9rA	3	0.8195	100	0.414	Contact Map
3e2iA	3	0.8439	100	0.424	Contact Map
2b8tA	3	0.9659	100	0.444	Contact Map
1xx6A	4	0.8341	100	0.483	Contact Map
2orwA	3	0.8439	100	0.584	Contact Map
4uxhA	3	0.839	99.9	0.614	Contact Map
3e1sA	1	0.9415	98.4	0.855	Contact Map
1w36D	1	0.9268	98.2	0.863	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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