KAD - BACSU - GREMLIN Contacts

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KAD - Adenylate kinase

UniProt:	P16304	Sequences: MNLVLMGLPGAGKGTQGERIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVDKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQTQPLLDFYSEKGYLANVNGQQDIQDVYADVKDLLGGLKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (207)
Sequences:	4140 (2444)
Seq/√Len:	169.9

ECOLI - KAD AROL AROK
BACSU - KAD YQAC AROK
HALSA - KAD KCY Y2452 KAD6
SULSO - KCY Y1041 KAD6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_K	176_M	3.545	1.00
50_K	54_D	2.926	1.00
71_R	76_D	2.823	1.00
122_E	140_V	2.743	1.00
35_F	64_T	2.715	1.00
52_Y	60_P	2.642	1.00
97_E	189_K	2.630	1.00
199_Q	207_D	2.584	1.00
23_D	209_K	2.434	1.00
48_E	51_S	2.406	1.00
128_R	139_L	2.376	1.00
161_A	164_N	2.349	1.00
199_Q	203_D	2.295	1.00
38_A	70_E	2.284	1.00
37_A	41_E	2.242	1.00
113_I	197_G	2.226	1.00
173_E	177_K	2.223	1.00
130_C	133_C	2.219	1.00
19_R	205_Y	2.211	1.00
112_N	194_N	2.208	1.00
65_I	86_F	2.202	1.00
114_E	194_N	2.187	1.00
126_G	138_H	2.164	1.00
131_S	158_Y	2.075	1.00
187_S	194_N	2.063	1.00
131_S	155_G	1.958	1.00
44_P	48_E	1.827	1.00
24_Y	209_K	1.798	1.00
65_I	95_A	1.775	1.00
150_C	153_D	1.749	1.00
42_E	47_L	1.739	1.00
165_E	169_S	1.680	1.00
109_Y	193_A	1.644	1.00
124_L	168_V	1.630	1.00
97_E	185_F	1.629	1.00
193_A	211_L	1.626	1.00
170_K	173_E	1.601	1.00
44_P	47_L	1.598	1.00
130_C	153_D	1.594	1.00
23_D	205_Y	1.582	1.00
48_E	66_G	1.572	1.00
149_I	156_E	1.568	1.00
75_D	78_E	1.547	1.00
39_M	53_I	1.525	1.00
133_C	153_D	1.510	1.00
180_Q	184_D	1.487	1.00
71_R	74_K	1.485	1.00
16_Q	208_V	1.416	1.00
116_D	198_Q	1.400	1.00
130_C	150_C	1.400	1.00
119_V	198_Q	1.390	1.00
119_V	122_E	1.389	1.00
51_S	55_K	1.386	1.00
131_S	156_E	1.373	1.00
200_D	203_D	1.363	1.00
132_V	153_D	1.355	1.00
146_T	149_I	1.352	1.00
19_R	202_Q	1.350	1.00
174_V	178_Q	1.350	1.00
11_A	115_V	1.329	1.00
115_V	197_G	1.316	1.00
205_Y	209_K	1.309	1.00
126_G	139_L	1.306	1.00
133_C	150_C	1.295	1.00
206_A	210_D	1.272	1.00
38_A	43_T	1.251	1.00
164_N	167_T	1.238	1.00
27_P	71_R	1.233	1.00
121_M	169_S	1.230	1.00
38_A	67_I	1.220	1.00
203_D	207_D	1.209	1.00
10_G	124_L	1.193	1.00
38_A	41_E	1.183	1.00
91_A	94_E	1.182	1.00
60_P	63_V	1.168	1.00
2_N	105_K	1.166	1.00
128_R	159_Q	1.164	1.00
125_T	165_E	1.160	1.00
129_I	136_T	1.152	1.00
184_D	188_E	1.141	1.00
135_T	152_K	1.141	1.00
63_V	66_G	1.137	1.00
111_I	208_V	1.132	1.00
117_K	169_S	1.131	1.00
117_K	173_E	1.129	1.00
176_M	180_Q	1.125	1.00
43_T	46_G	1.123	1.00
199_Q	204_V	1.112	1.00
138_H	141_F	1.104	1.00
32_G	36_R	1.103	1.00
4_V	107_I	1.102	1.00
170_K	174_V	1.096	1.00
196_N	199_Q	1.084	1.00
69_K	103_Y	1.084	1.00
121_M	125_T	1.082	1.00
52_Y	57_E	1.076	1.00
18_E	22_E	1.072	1.00
112_N	183_L	1.066	1.00
48_E	62_E	1.053	0.99
6_M	183_L	1.051	0.99
34_M	38_A	1.051	0.99
5_L	20_I	1.047	0.99
150_C	155_G	1.045	0.99
25_G	79_R	1.041	0.99
37_A	71_R	1.025	0.99
195_V	204_V	1.018	0.99
71_R	77_C	1.016	0.99
94_E	97_E	1.011	0.99
81_F	107_I	1.010	0.99
117_K	172_L	1.001	0.99
35_F	39_M	0.999	0.99
130_C	155_G	0.998	0.99
8_L	175_N	0.997	0.99
69_K	73_G	0.994	0.99
26_I	81_F	0.982	0.99
145_K	151_D	0.981	0.99
169_S	173_E	0.977	0.99
97_E	186_Y	0.971	0.99
5_L	113_I	0.970	0.99
160_R	163_D	0.952	0.99
95_A	98_E	0.951	0.99
196_N	204_V	0.947	0.99
16_Q	205_Y	0.945	0.99
49_A	66_G	0.945	0.99
172_L	176_M	0.939	0.99
110_V	192_L	0.932	0.99
20_I	208_V	0.931	0.99
144_P	151_D	0.928	0.99
128_R	157_L	0.925	0.99
49_A	52_Y	0.925	0.99
19_R	22_E	0.924	0.99
5_L	17_G	0.924	0.99
21_V	28_H	0.924	0.99
94_E	98_E	0.923	0.99
57_E	170_K	0.919	0.99
153_D	156_E	0.919	0.99
27_P	77_C	0.897	0.98
135_T	142_N	0.897	0.98
61_D	92_Q	0.889	0.98
66_G	69_K	0.886	0.98
14_G	84_D	0.885	0.98
203_D	206_A	0.874	0.98
5_L	82_L	0.869	0.98
26_I	80_G	0.868	0.98
184_D	187_S	0.867	0.98
49_A	53_I	0.866	0.98
38_A	49_A	0.862	0.98
121_M	168_V	0.862	0.98
94_E	185_F	0.846	0.98
195_V	208_V	0.843	0.97
195_V	211_L	0.842	0.97
2_N	107_I	0.840	0.97
20_I	82_L	0.837	0.97
135_T	153_D	0.836	0.97
107_I	191_Y	0.832	0.97
41_E	74_K	0.828	0.97
90_V	94_E	0.827	0.97
175_N	179_T	0.824	0.97
167_T	170_K	0.818	0.97
182_L	192_L	0.813	0.97
146_T	151_D	0.813	0.97
6_M	182_L	0.804	0.97
2_N	108_D	0.801	0.97
106_P	191_Y	0.800	0.97
73_G	103_Y	0.799	0.97
201_I	205_Y	0.794	0.96
130_C	135_T	0.791	0.96
27_P	76_D	0.790	0.96
126_G	141_F	0.787	0.96
118_D	169_S	0.779	0.96
93_A	186_Y	0.773	0.96
39_M	46_G	0.773	0.96
65_I	68_V	0.754	0.95
114_E	183_L	0.752	0.95
185_F	189_K	0.752	0.95
133_C	155_G	0.750	0.95
206_A	209_K	0.743	0.95
143_P	147_P	0.740	0.95
32_G	88_R	0.732	0.94
207_D	210_D	0.728	0.94
133_C	152_K	0.725	0.94
179_T	182_L	0.719	0.94
37_A	74_K	0.716	0.94
71_R	75_D	0.714	0.94
15_T	123_R	0.714	0.94
118_D	122_E	0.707	0.93
16_Q	195_V	0.702	0.93
153_D	157_L	0.702	0.93
135_T	150_C	0.699	0.93
110_V	191_Y	0.698	0.93
120_L	168_V	0.694	0.93
116_D	119_V	0.691	0.92
159_Q	164_N	0.688	0.92
38_A	46_G	0.687	0.92
137_Y	144_P	0.686	0.92
163_D	167_T	0.684	0.92
70_E	74_K	0.683	0.92
126_G	140_V	0.680	0.92
45_L	66_G	0.675	0.92
71_R	80_G	0.674	0.92
34_M	67_I	0.674	0.92
6_M	175_N	0.673	0.91
36_R	88_R	0.673	0.91
35_F	68_V	0.672	0.91
28_H	33_D	0.670	0.91
18_E	28_H	0.670	0.91
89_T	92_Q	0.669	0.91
207_D	211_L	0.668	0.91
125_T	164_N	0.666	0.91
30_S	33_D	0.664	0.91
115_V	120_L	0.663	0.91
198_Q	204_V	0.662	0.91
3_L	109_Y	0.662	0.91
196_N	207_D	0.661	0.91
155_G	158_Y	0.658	0.91
7_G	10_G	0.658	0.91
12_G	15_T	0.652	0.90
22_E	152_K	0.652	0.90
47_L	51_S	0.652	0.90
38_A	66_G	0.644	0.90
77_C	80_G	0.644	0.90
208_V	211_L	0.639	0.89
112_N	192_L	0.638	0.89
14_G	36_R	0.633	0.89
87_P	92_Q	0.633	0.89
138_H	144_P	0.633	0.89
6_M	110_V	0.632	0.89
64_T	68_V	0.632	0.89
150_C	154_G	0.632	0.89
47_L	50_K	0.627	0.88
10_G	168_V	0.626	0.88
70_E	73_G	0.626	0.88
58_L	88_R	0.623	0.88
48_E	52_Y	0.621	0.88
42_E	50_K	0.618	0.88
129_I	158_Y	0.616	0.87
51_S	54_D	0.616	0.87
27_P	80_G	0.616	0.87
18_E	21_V	0.616	0.87
16_Q	204_V	0.612	0.87
2_N	6_M	0.611	0.87
8_L	11_A	0.609	0.87
149_I	154_G	0.604	0.86
121_M	165_E	0.597	0.86
120_L	172_L	0.595	0.86
52_Y	55_K	0.591	0.85
35_F	53_I	0.591	0.85
130_C	156_E	0.583	0.84
109_Y	211_L	0.583	0.84
151_D	154_G	0.581	0.84
148_G	151_D	0.580	0.84
132_V	155_G	0.578	0.84
61_D	89_T	0.578	0.84
22_E	25_G	0.577	0.84
109_Y	191_Y	0.575	0.84
9_P	167_T	0.574	0.84
52_Y	63_V	0.574	0.84
85_G	88_R	0.571	0.83
12_G	123_R	0.571	0.83
24_Y	205_Y	0.571	0.83
144_P	148_G	0.570	0.83
76_D	80_G	0.569	0.83
62_E	66_G	0.568	0.83
51_S	63_V	0.567	0.83
41_E	49_A	0.566	0.83
160_R	171_R	0.564	0.82
6_M	28_H	0.563	0.82
3_L	107_I	0.558	0.82
49_A	55_K	0.555	0.81
20_I	212_L	0.552	0.81
49_A	60_P	0.549	0.81
2_N	81_F	0.542	0.80
20_I	205_Y	0.542	0.80
198_Q	207_D	0.542	0.80
138_H	143_P	0.542	0.80
127_R	163_D	0.541	0.80
7_G	12_G	0.540	0.80
72_L	77_C	0.538	0.79
149_I	155_G	0.537	0.79
14_G	58_L	0.530	0.78
90_V	185_F	0.529	0.78
109_Y	212_L	0.528	0.78
182_L	186_Y	0.527	0.78
45_L	67_I	0.527	0.78
31_T	68_V	0.527	0.78
162_D	171_R	0.526	0.78
130_C	152_K	0.523	0.78
11_A	17_G	0.523	0.78
9_P	120_L	0.521	0.77
29_I	34_M	0.520	0.77
88_R	127_R	0.518	0.77
6_M	168_V	0.517	0.77
32_G	58_L	0.517	0.77
72_L	81_F	0.516	0.77
32_G	163_D	0.515	0.76
35_F	49_A	0.515	0.76
56_G	61_D	0.515	0.76
49_A	67_I	0.515	0.76
166_E	170_K	0.512	0.76
86_F	92_Q	0.512	0.76
134_G	137_Y	0.509	0.76
111_I	195_V	0.508	0.76
188_E	191_Y	0.508	0.76
49_A	59_V	0.505	0.75
29_I	81_F	0.504	0.75
113_I	208_V	0.504	0.75
151_D	155_G	0.504	0.75
117_K	121_M	0.500	0.74
54_D	161_A	0.500	0.74
197_G	204_V	0.500	0.74

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
4qbgB	1	1	100	0.309	Contact Map
4jzkA	1	0.9631	100	0.34	Contact Map
3be4A	1	0.9677	100	0.345	Contact Map
3tlxA	1	0.9862	100	0.347	Contact Map
3gmtA	1	0.8848	100	0.347	Contact Map
2xb4A	4	0.977	100	0.351	Contact Map
4pzlA	2	0.9724	100	0.352	Contact Map
1ak2A	1	1	100	0.355	Contact Map
1akyA	1	0.9908	100	0.366	Contact Map
4nu0A	1	0.9724	100	0.376	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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