NDK - BACSU - GREMLIN Contacts

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NDK - Nucleoside diphosphate kinase

UniProt:	P31103	Sequences: MMEKTFIMVKPDGVQRQLIGDILSRFERKGLQLAGAKLMRVTEQMAEKHYAEHQGKPFFGELVEFITSGPVFAMVWEGENVIEVTRQLIGKTNPKEALPGTIRGDYGMFVGKNIIHGSDSLESAEREINIFFKNEELVSYQQLMAGWIY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	149 (134)
Sequences:	3873 (2028)
Seq/√Len:	175.2

ECOLI - NDK
BACSU - NDK
HALSA - NDK
SULSO - NDK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_E	47_E	2.941	1.00
36_A	72_F	2.492	1.00
75_V	128_I	2.458	1.00
89_I	117_G	2.441	1.00
25_R	105_D	2.434	1.00
41_V	131_F	2.368	1.00
21_D	28_R	2.315	1.00
9_V	13_G	2.254	1.00
8_M	73_A	2.229	1.00
26_F	85_T	2.182	1.00
93_N	96_E	2.180	1.00
33_L	76_W	2.063	1.00
24_S	28_R	1.980	1.00
23_L	74_M	1.959	1.00
120_S	123_S	1.923	1.00
7_I	85_T	1.920	1.00
3_E	121_L	1.886	1.00
78_G	84_V	1.738	1.00
87_Q	98_L	1.725	1.00
48_K	130_I	1.723	1.00
46_A	66_I	1.722	1.00
34_A	77_E	1.717	1.00
52_E	126_R	1.706	1.00
31_L	84_V	1.623	1.00
89_I	115_I	1.620	1.00
43_E	64_E	1.605	1.00
31_L	81_V	1.596	1.00
80_N	83_E	1.587	1.00
119_D	123_S	1.568	1.00
47_E	54_Q	1.528	1.00
93_N	110_V	1.498	1.00
42_T	45_M	1.487	1.00
99_P	104_G	1.470	1.00
19_I	72_F	1.469	1.00
31_L	78_G	1.467	1.00
21_D	24_S	1.455	1.00
45_M	130_I	1.420	1.00
4_K	77_E	1.375	1.00
83_E	87_Q	1.345	1.00
39_M	73_A	1.335	1.00
85_T	117_G	1.329	1.00
61_E	111_G	1.329	1.00
63_V	67_T	1.314	1.00
82_I	121_L	1.311	1.00
124_A	128_I	1.277	1.00
91_K	98_L	1.274	1.00
125_E	129_N	1.269	1.00
60_G	64_E	1.269	1.00
48_K	51_A	1.266	1.00
123_S	126_R	1.257	1.00
84_V	87_Q	1.241	1.00
29_K	88_L	1.229	1.00
12_D	65_F	1.226	1.00
35_G	75_V	1.183	1.00
80_N	84_V	1.171	1.00
43_E	63_V	1.161	1.00
13_G	22_I	1.137	1.00
46_A	67_T	1.137	1.00
26_F	89_I	1.128	1.00
52_E	123_S	1.110	1.00
121_L	125_E	1.108	1.00
26_F	76_W	1.105	1.00
129_N	134_N	1.101	1.00
15_Q	112_K	1.101	1.00
41_V	46_A	1.080	1.00
4_K	34_A	1.069	1.00
23_L	36_A	1.059	1.00
8_M	71_V	1.046	1.00
32_Q	77_E	1.028	0.99
79_E	109_F	1.010	0.99
55_G	60_G	1.009	0.99
85_T	89_I	1.001	0.99
16_R	114_I	0.997	0.99
68_S	112_K	0.996	0.99
38_L	72_F	0.993	0.99
13_G	114_I	0.991	0.99
47_E	59_F	0.990	0.99
91_K	96_E	0.979	0.99
14_V	19_I	0.974	0.99
23_L	72_F	0.963	0.99
43_E	60_G	0.962	0.99
36_A	74_M	0.961	0.99
14_V	38_L	0.934	0.99
47_E	63_V	0.933	0.99
85_T	115_I	0.928	0.99
41_V	66_I	0.905	0.99
116_H	127_E	0.898	0.98
94_P	110_V	0.883	0.98
22_I	114_I	0.879	0.98
108_M	112_K	0.875	0.98
5_T	85_T	0.867	0.98
100_G	105_D	0.865	0.98
39_M	45_M	0.864	0.98
84_V	88_L	0.849	0.98
16_R	108_M	0.844	0.98
49_H	130_I	0.841	0.98
65_F	68_S	0.835	0.98
25_R	102_I	0.829	0.97
43_E	67_T	0.828	0.97
18_L	114_I	0.826	0.97
53_H	62_L	0.819	0.97
53_H	58_F	0.812	0.97
109_F	112_K	0.810	0.97
18_L	21_D	0.809	0.97
15_Q	68_S	0.799	0.97
20_G	36_A	0.797	0.97
25_R	29_K	0.796	0.97
7_I	74_M	0.794	0.97
7_I	26_F	0.794	0.97
41_V	71_V	0.790	0.97
94_P	109_F	0.788	0.97
7_I	76_W	0.783	0.96
102_I	115_I	0.782	0.96
126_R	130_I	0.782	0.96
45_M	48_K	0.782	0.96
44_Q	47_E	0.779	0.96
122_E	125_E	0.774	0.96
53_H	56_K	0.761	0.96
31_L	85_T	0.746	0.95
49_H	131_F	0.742	0.95
46_A	63_V	0.733	0.95
76_W	85_T	0.732	0.95
51_A	54_Q	0.727	0.95
91_K	97_A	0.726	0.95
51_A	59_F	0.720	0.94
3_E	82_I	0.713	0.94
29_K	84_V	0.711	0.94
57_P	61_E	0.704	0.94
9_V	22_I	0.702	0.94
33_L	36_A	0.695	0.93
94_P	107_G	0.680	0.92
19_I	38_L	0.676	0.92
17_Q	32_Q	0.666	0.92
55_G	61_E	0.664	0.92
86_R	116_H	0.659	0.91
54_Q	63_V	0.659	0.91
25_R	28_R	0.656	0.91
4_K	128_I	0.645	0.90
38_L	70_P	0.638	0.90
19_I	27_E	0.638	0.90
58_F	62_L	0.631	0.89
103_R	113_N	0.630	0.89
61_E	64_E	0.627	0.89
78_G	81_V	0.620	0.89
24_S	27_E	0.620	0.89
86_R	92_T	0.618	0.88
20_G	27_E	0.618	0.88
118_S	127_E	0.617	0.88
21_D	106_Y	0.616	0.88
14_V	72_F	0.616	0.88
51_A	126_R	0.615	0.88
34_A	75_V	0.614	0.88
90_G	103_R	0.614	0.88
82_I	120_S	0.613	0.88
3_E	80_N	0.612	0.88
23_L	27_E	0.609	0.88
50_Y	116_H	0.608	0.88
61_E	110_V	0.606	0.87
4_K	125_E	0.605	0.87
5_T	76_W	0.604	0.87
20_G	38_L	0.600	0.87
20_G	23_L	0.599	0.87
41_V	45_M	0.593	0.86
120_S	126_R	0.591	0.86
104_G	114_I	0.591	0.86
12_D	16_R	0.589	0.86
107_G	114_I	0.582	0.85
65_F	108_M	0.580	0.85
54_Q	60_G	0.579	0.85
98_L	101_T	0.573	0.84
14_V	69_G	0.571	0.84
108_M	114_I	0.570	0.84
80_N	87_Q	0.568	0.84
6_F	73_A	0.564	0.83
35_G	133_K	0.563	0.83
45_M	49_H	0.560	0.83
129_N	133_K	0.558	0.83
59_F	63_V	0.555	0.82
60_G	63_V	0.554	0.82
71_V	131_F	0.553	0.82
8_M	66_I	0.550	0.82
52_E	130_I	0.542	0.81
90_G	97_A	0.542	0.81
82_I	126_R	0.540	0.81
3_E	83_E	0.540	0.81
5_T	81_V	0.540	0.81
95_K	108_M	0.540	0.81
10_K	113_N	0.537	0.80
2_M	79_E	0.537	0.80
96_E	110_V	0.537	0.80
91_K	94_P	0.536	0.80
15_Q	18_L	0.534	0.80
82_I	123_S	0.526	0.79
102_I	114_I	0.520	0.78
33_L	38_L	0.519	0.78
23_L	33_L	0.514	0.77
58_F	92_T	0.514	0.77
12_D	108_M	0.511	0.77
10_K	94_P	0.503	0.76
7_I	117_G	0.503	0.76
63_V	66_I	0.500	0.76

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
2vu5A	5	0.9933	100	-0.013	Contact Map
5bxiA	6	1	100	-0.01	Contact Map
1w7wA	5	1	100	-0.005	Contact Map
3q8uA	3	0.9933	100	-0.005	Contact Map
3l7uA	5	1	100	-0.005	Contact Map
1xiqA	4	0.9866	100	-0.004	Contact Map
3b54A	4	0.953	100	-0.004	Contact Map
3r9lA	4	0.745	100	-0.003	Contact Map
1zs6A	5	1	100	-0.002	Contact Map
3bbbA	5	1	100	0.001	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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