NDK - SULSO - GREMLIN Contacts

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NDK - Nucleoside diphosphate kinase

UniProt:	Q980Q7	Sequences: MVAQRTFVMIKPDGVKRGLIGEIISRFEKRGLKIVSLKMVKMSRDTAEKLYEEHKGKSFFEELVNYVTSGPVVCMVIEGDDVVQVIRRMIGNTDPKEAPPGTIRGDYALSKSENVIHASDSIEKAQREMSLFFDKSDL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	138 (133)
Sequences:	3753 (1973)
Seq/√Len:	171.1

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
44_R	48_E	2.943	1.00
37_L	73_V	2.468	1.00
76_V	129_M	2.464	1.00
90_I	118_A	2.423	1.00
22_E	29_K	2.386	1.00
26_R	106_D	2.378	1.00
42_M	132_F	2.328	1.00
9_M	74_C	2.317	1.00
10_I	14_G	2.257	1.00
27_F	86_I	2.192	1.00
94_D	97_E	2.142	1.00
34_I	77_I	2.100	1.00
25_S	29_K	2.013	1.00
121_S	124_K	1.939	1.00
24_I	75_M	1.933	1.00
8_V	86_I	1.933	1.00
4_Q	122_I	1.795	1.00
47_A	67_V	1.775	1.00
53_E	127_R	1.769	1.00
88_R	99_P	1.759	1.00
79_G	85_V	1.734	1.00
32_L	82_V	1.697	1.00
49_K	131_L	1.694	1.00
32_L	85_V	1.646	1.00
35_V	78_E	1.622	1.00
90_I	116_I	1.608	1.00
120_D	124_K	1.588	1.00
44_R	65_N	1.573	1.00
32_L	79_G	1.546	1.00
48_E	55_K	1.521	1.00
43_S	46_T	1.504	1.00
81_D	84_Q	1.481	1.00
22_E	25_S	1.468	1.00
46_T	131_L	1.462	1.00
94_D	111_K	1.449	1.00
20_I	73_V	1.434	1.00
100_P	105_G	1.365	1.00
64_V	68_T	1.360	1.00
84_Q	88_R	1.340	1.00
40_V	74_C	1.331	1.00
86_I	118_A	1.310	1.00
125_A	129_M	1.307	1.00
83_V	122_I	1.301	1.00
5_R	78_E	1.300	1.00
126_Q	130_S	1.297	1.00
49_K	52_E	1.278	1.00
85_V	88_R	1.271	1.00
62_E	112_S	1.268	1.00
124_K	127_R	1.261	1.00
61_E	65_N	1.249	1.00
30_R	89_M	1.248	1.00
13_D	66_Y	1.241	1.00
47_A	68_T	1.211	1.00
92_N	99_P	1.205	1.00
42_M	47_A	1.191	1.00
44_R	64_V	1.184	1.00
36_S	76_V	1.176	1.00
14_G	23_I	1.130	1.00
81_D	85_V	1.129	1.00
27_F	77_I	1.128	1.00
53_E	124_K	1.122	1.00
122_I	126_Q	1.117	1.00
130_S	135_K	1.109	1.00
27_F	90_I	1.077	1.00
24_I	37_L	1.064	1.00
16_K	113_E	1.048	0.99
33_K	78_E	1.047	0.99
86_I	90_I	1.045	0.99
56_G	61_E	1.033	0.99
48_E	60_F	1.025	0.99
5_R	35_V	1.024	0.99
14_G	115_V	1.008	0.99
9_M	72_V	1.006	0.99
80_D	110_S	1.002	0.99
69_S	113_E	0.996	0.99
39_M	73_V	0.993	0.99
92_N	97_E	0.968	0.99
17_R	115_V	0.967	0.99
24_I	73_V	0.964	0.99
15_V	39_M	0.945	0.99
48_E	64_V	0.943	0.99
44_R	61_E	0.943	0.99
37_L	75_M	0.929	0.99
15_V	20_I	0.922	0.99
42_M	67_V	0.920	0.99
6_T	86_I	0.917	0.99
23_I	115_V	0.909	0.98
109_L	113_E	0.899	0.98
17_R	109_L	0.884	0.98
86_I	116_I	0.880	0.98
54_H	57_K	0.878	0.98
54_H	59_F	0.863	0.98
85_V	89_M	0.862	0.98
42_M	72_V	0.855	0.98
95_P	111_K	0.845	0.98
50_L	131_L	0.843	0.98
101_G	106_D	0.843	0.98
21_G	37_L	0.833	0.97
40_V	46_T	0.831	0.97
127_R	131_L	0.828	0.97
66_Y	69_S	0.827	0.97
19_L	115_V	0.818	0.97
16_K	69_S	0.817	0.97
95_P	110_S	0.812	0.97
26_R	30_R	0.812	0.97
54_H	63_L	0.811	0.97
8_V	75_M	0.807	0.97
110_S	113_E	0.799	0.97
117_H	128_E	0.797	0.97
19_L	22_E	0.790	0.96
44_R	68_T	0.790	0.96
77_I	86_I	0.787	0.96
26_R	103_I	0.783	0.96
47_A	64_V	0.782	0.96
10_I	23_I	0.782	0.96
46_T	49_K	0.771	0.96
32_L	86_I	0.770	0.96
92_N	98_A	0.764	0.96
103_I	116_I	0.763	0.96
8_V	77_I	0.761	0.96
8_V	27_F	0.759	0.95
52_E	60_F	0.757	0.95
45_D	48_E	0.745	0.95
52_E	55_K	0.744	0.95
95_P	108_A	0.741	0.95
123_E	126_Q	0.738	0.95
34_I	37_L	0.735	0.95
30_R	85_V	0.704	0.93
4_Q	83_V	0.699	0.93
87_R	117_H	0.689	0.93
5_R	129_M	0.671	0.92
58_S	62_E	0.669	0.91
56_G	62_E	0.667	0.91
62_E	65_N	0.661	0.91
50_L	132_F	0.660	0.91
20_I	39_M	0.658	0.91
25_S	28_E	0.652	0.90
24_I	28_E	0.651	0.90
42_M	46_T	0.646	0.90
18_G	33_K	0.633	0.89
21_G	39_M	0.628	0.89
26_R	29_K	0.627	0.89
87_R	93_T	0.626	0.88
15_V	70_G	0.626	0.88
21_G	28_E	0.625	0.88
6_T	77_I	0.623	0.88
15_V	73_V	0.621	0.88
83_V	121_S	0.619	0.88
121_S	127_R	0.619	0.88
79_G	82_V	0.613	0.87
4_Q	81_D	0.611	0.87
108_A	115_V	0.610	0.87
39_M	71_P	0.610	0.87
20_I	28_E	0.609	0.87
105_G	115_V	0.598	0.86
21_G	24_I	0.593	0.86
59_F	63_L	0.589	0.85
52_E	127_R	0.587	0.85
35_V	76_V	0.587	0.85
91_G	104_R	0.585	0.85
13_D	17_R	0.585	0.85
130_S	134_D	0.580	0.84
55_K	64_V	0.576	0.84
62_E	111_K	0.569	0.83
99_P	102_T	0.568	0.83
53_E	131_L	0.568	0.83
9_M	67_V	0.564	0.83
22_E	107_Y	0.561	0.82
61_E	64_V	0.558	0.82
8_V	118_A	0.558	0.82
96_K	109_L	0.555	0.82
5_R	126_Q	0.555	0.82
46_T	50_L	0.552	0.81
83_V	124_K	0.552	0.81
51_Y	117_H	0.551	0.81
66_Y	109_L	0.545	0.81
7_F	74_C	0.545	0.81
55_K	61_E	0.544	0.80
119_S	128_E	0.541	0.80
86_I	98_A	0.536	0.79
63_L	67_V	0.529	0.79
83_V	127_R	0.529	0.79
42_M	50_L	0.528	0.78
109_L	115_V	0.526	0.78
60_F	64_V	0.525	0.78
97_E	111_K	0.525	0.78
48_E	56_G	0.524	0.78
55_K	60_F	0.521	0.78
103_I	115_V	0.520	0.77
36_S	134_D	0.515	0.77
83_V	125_A	0.512	0.76
81_D	88_R	0.511	0.76
6_T	82_V	0.509	0.76
72_V	132_F	0.508	0.76
59_F	120_D	0.507	0.76
92_N	95_P	0.503	0.75
127_R	130_S	0.502	0.75
13_D	109_L	0.502	0.75
104_R	114_N	0.502	0.75
40_V	72_V	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
4kpcA	4	0.9928	100	-0.008	Contact Map
1w7wA	5	1	100	-0.007	Contact Map
3r9lA	4	0.8043	100	-0.007	Contact Map
4c6aA	1	1	100	-0.005	Contact Map
1ehwA	4	1	100	-0.005	Contact Map
3ztpA	3	0.9928	100	-0.004	Contact Map
3mpdA	4	0.9855	100	-0.004	Contact Map
4w98A	2	1	100	-0.004	Contact Map
2vu5A	5	0.9855	100	-0.001	Contact Map
3l7uA	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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