NDK - HALSA - GREMLIN Contacts

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NDK - Nucleoside diphosphate kinase

UniProt:	P61136	Sequences: MTDHDERTFVMVKPDGVQRGLIGDIVTRLETKGLKMVGGKFMRIDEELAHEHYAEHEDKPFFDGLVSFITSGPVFAMVWEGADATRQVRQLMGATDAQDAAPGTIRGDYGNDLGHNLIHGSDHEDEGANEREIALFFDDDELVDWDRDASAWVYEDLADHD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	161 (135)
Sequences:	3870 (2032)
Seq/√Len:	174.9

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
46_E	50_H	2.853	1.00
28_R	108_D	2.459	1.00
92_M	120_G	2.436	1.00
39_G	75_F	2.418	1.00
78_V	133_I	2.410	1.00
44_I	136_F	2.327	1.00
24_D	31_T	2.297	1.00
11_M	76_A	2.271	1.00
12_V	16_G	2.228	1.00
29_L	88_V	2.191	1.00
96_D	99_D	2.172	1.00
36_M	79_W	2.032	1.00
26_V	77_M	1.982	1.00
27_T	31_T	1.968	1.00
123_H	126_E	1.912	1.00
10_V	88_V	1.903	1.00
81_G	87_Q	1.786	1.00
6_E	124_E	1.777	1.00
90_Q	101_A	1.773	1.00
51_E	135_L	1.742	1.00
37_V	80_E	1.723	1.00
49_A	69_I	1.716	1.00
92_M	118_I	1.658	1.00
34_L	87_Q	1.648	1.00
55_E	131_R	1.637	1.00
122_D	126_E	1.564	1.00
34_L	84_A	1.563	1.00
46_E	67_S	1.551	1.00
45_D	48_L	1.520	1.00
96_D	113_L	1.510	1.00
83_D	86_R	1.495	1.00
50_H	57_E	1.477	1.00
22_I	75_F	1.467	1.00
24_D	27_T	1.466	1.00
138_D	141_E	1.456	1.00
34_L	81_G	1.434	1.00
102_P	107_G	1.425	1.00
48_L	135_L	1.407	1.00
7_R	80_E	1.362	1.00
86_R	90_Q	1.340	1.00
66_V	70_T	1.338	1.00
42_M	76_A	1.330	1.00
88_V	120_G	1.318	1.00
85_T	124_E	1.314	1.00
94_A	101_A	1.312	1.00
130_E	134_A	1.309	1.00
64_G	114_G	1.283	1.00
126_E	131_R	1.280	1.00
127_G	133_I	1.246	1.00
63_D	67_S	1.233	1.00
51_E	54_A	1.231	1.00
15_D	68_F	1.229	1.00
32_K	91_L	1.197	1.00
87_Q	90_Q	1.193	1.00
83_D	87_Q	1.192	1.00
46_E	66_V	1.188	1.00
16_G	25_I	1.170	1.00
49_A	70_T	1.141	1.00
29_L	79_W	1.123	1.00
11_M	74_V	1.119	1.00
38_G	78_V	1.119	1.00
124_E	130_E	1.111	1.00
134_A	139_D	1.107	1.00
26_V	39_G	1.100	1.00
29_L	92_M	1.078	1.00
18_Q	115_H	1.076	1.00
55_E	126_E	1.070	1.00
40_K	141_E	1.062	1.00
88_V	92_M	1.045	1.00
44_I	49_A	1.042	0.99
35_K	80_E	1.035	0.99
7_R	37_V	1.032	0.99
50_H	62_F	1.027	0.99
16_G	117_L	1.007	0.99
41_F	75_F	1.003	0.99
17_V	22_I	0.998	0.99
46_E	63_D	0.994	0.99
71_S	115_H	0.993	0.99
19_R	117_L	0.979	0.99
44_I	69_I	0.969	0.99
39_G	77_M	0.950	0.99
88_V	118_I	0.947	0.99
26_V	75_F	0.945	0.99
17_V	41_F	0.941	0.99
94_A	99_D	0.927	0.99
82_A	112_D	0.924	0.99
58_D	63_D	0.909	0.99
50_H	66_V	0.907	0.99
68_F	71_S	0.900	0.99
8_T	88_V	0.896	0.98
25_I	117_L	0.893	0.98
119_H	132_E	0.891	0.98
19_R	111_N	0.880	0.98
97_A	113_L	0.877	0.98
52_H	135_L	0.875	0.98
21_L	117_L	0.852	0.98
103_G	108_D	0.843	0.98
111_N	115_H	0.837	0.98
56_H	59_K	0.836	0.98
56_H	65_L	0.832	0.98
56_H	61_F	0.823	0.97
87_Q	91_L	0.822	0.97
38_G	141_E	0.812	0.97
42_M	48_L	0.812	0.97
10_V	29_L	0.801	0.97
46_E	70_T	0.801	0.97
10_V	79_W	0.799	0.97
10_V	77_M	0.798	0.97
44_I	74_V	0.796	0.97
28_R	105_I	0.794	0.97
125_D	130_E	0.791	0.97
6_E	85_T	0.791	0.97
48_L	51_E	0.788	0.97
54_A	57_E	0.785	0.96
131_R	135_L	0.780	0.96
28_R	32_K	0.772	0.96
18_Q	71_S	0.769	0.96
34_L	88_V	0.766	0.96
47_E	50_H	0.758	0.96
21_L	24_D	0.755	0.96
12_V	25_I	0.752	0.96
97_A	112_D	0.751	0.95
79_W	88_V	0.745	0.95
23_G	39_G	0.744	0.95
105_I	118_I	0.743	0.95
112_D	115_H	0.740	0.95
49_A	66_V	0.739	0.95
52_H	136_F	0.738	0.95
22_I	41_F	0.734	0.95
36_M	39_G	0.712	0.94
32_K	87_Q	0.702	0.94
97_A	110_G	0.668	0.92
41_F	73_P	0.667	0.92
54_A	62_F	0.665	0.92
7_R	133_I	0.660	0.91
20_G	35_K	0.653	0.91
17_V	75_F	0.648	0.91
58_D	64_G	0.647	0.90
5_D	80_E	0.639	0.90
22_I	30_E	0.633	0.90
28_R	31_T	0.633	0.90
89_R	119_H	0.627	0.89
27_T	30_E	0.624	0.89
54_A	131_R	0.621	0.89
68_F	111_N	0.618	0.88
64_G	67_S	0.617	0.88
23_G	30_E	0.617	0.88
93_G	106_R	0.615	0.88
24_D	109_Y	0.614	0.88
7_R	130_E	0.614	0.88
123_H	131_R	0.609	0.88
106_R	116_N	0.609	0.88
101_A	104_T	0.609	0.88
17_V	72_G	0.608	0.88
6_E	83_D	0.608	0.88
94_A	100_A	0.606	0.87
81_G	84_A	0.604	0.87
121_S	132_E	0.601	0.87
53_Y	119_H	0.599	0.87
8_T	79_W	0.593	0.86
63_D	66_V	0.593	0.86
57_E	66_V	0.592	0.86
60_P	64_G	0.592	0.86
110_G	117_L	0.591	0.86
23_G	26_V	0.588	0.86
57_E	63_D	0.581	0.85
99_D	113_L	0.581	0.85
23_G	41_F	0.581	0.85
9_F	76_A	0.578	0.85
85_T	123_H	0.575	0.85
44_I	48_L	0.574	0.84
85_T	131_R	0.572	0.84
107_G	117_L	0.571	0.84
37_V	78_V	0.571	0.84
105_I	117_L	0.571	0.84
62_F	66_V	0.568	0.84
13_K	116_N	0.566	0.84
26_V	30_E	0.562	0.83
61_F	65_L	0.561	0.83
111_N	117_L	0.560	0.83
94_A	97_A	0.558	0.83
18_Q	21_L	0.558	0.83
89_R	95_T	0.554	0.82
74_V	136_F	0.547	0.82
98_Q	111_N	0.547	0.82
15_D	19_R	0.544	0.81
11_M	69_I	0.544	0.81
10_V	120_G	0.540	0.81
134_A	138_D	0.532	0.80
93_G	100_A	0.526	0.79
9_F	132_E	0.523	0.79
85_T	126_E	0.523	0.79
26_V	36_M	0.522	0.78
89_R	122_D	0.519	0.78
48_L	52_H	0.517	0.78
85_T	127_G	0.516	0.78
55_E	135_L	0.515	0.78
44_I	52_H	0.514	0.77
64_G	113_L	0.510	0.77
61_F	95_T	0.510	0.77
13_K	97_A	0.501	0.76
98_Q	113_L	0.500	0.75

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
2az3A	6	0.9379	100	0.013	Contact Map
3b54A	4	0.9006	100	0.021	Contact Map
3l7uA	5	0.9503	100	0.036	Contact Map
5bxiA	6	0.9814	100	0.039	Contact Map
1w7wA	5	0.9379	100	0.046	Contact Map
1zs6A	5	0.9441	100	0.047	Contact Map
3bbbA	5	0.9379	100	0.05	Contact Map
1s57A	5	0.9441	100	0.05	Contact Map
3q8uA	3	0.9255	100	0.05	Contact Map
2dxeA	5	0.9503	100	0.052	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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