NDK - ECOLI - GREMLIN Contacts

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NDK - Nucleoside diphosphate kinase

UniProt:	P0A763	Sequences: MAIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10650
Length:	143 (134)
Sequences:	3844 (2042)
Seq/√Len:	176.4

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_V	48_R	2.899	1.00
37_T	73_V	2.518	1.00
26_R	106_D	2.440	1.00
76_V	129_I	2.409	1.00
90_L	118_G	2.404	1.00
42_L	132_F	2.386	1.00
22_N	29_A	2.349	1.00
10_I	14_A	2.339	1.00
9_I	74_V	2.265	1.00
94_N	97_N	2.198	1.00
27_F	86_H	2.165	1.00
34_I	77_L	2.097	1.00
25_A	29_A	2.046	1.00
24_F	75_S	1.966	1.00
121_S	124_S	1.943	1.00
8_S	86_H	1.919	1.00
4_E	122_V	1.858	1.00
53_E	127_R	1.815	1.00
47_A	67_M	1.810	1.00
35_V	78_E	1.747	1.00
49_G	131_Y	1.746	1.00
79_G	85_R	1.721	1.00
32_F	85_R	1.657	1.00
88_D	99_L	1.640	1.00
90_L	116_T	1.623	1.00
32_F	82_A	1.617	1.00
120_D	124_S	1.572	1.00
81_N	84_Q	1.518	1.00
44_V	65_E	1.518	1.00
48_R	55_D	1.506	1.00
94_N	111_L	1.494	1.00
43_T	46_Q	1.487	1.00
22_N	25_A	1.469	1.00
32_F	79_G	1.456	1.00
20_I	73_V	1.454	1.00
46_Q	131_Y	1.439	1.00
100_A	105_A	1.434	1.00
92_A	99_L	1.403	1.00
5_R	78_E	1.348	1.00
62_G	112_T	1.321	1.00
86_H	118_G	1.313	1.00
64_V	68_T	1.309	1.00
40_L	74_V	1.308	1.00
83_V	122_V	1.298	1.00
84_Q	88_D	1.298	1.00
49_G	52_A	1.295	1.00
124_S	127_R	1.282	1.00
30_A	89_L	1.280	1.00
126_A	130_A	1.280	1.00
125_A	129_I	1.263	1.00
85_R	88_D	1.250	1.00
61_D	65_E	1.233	1.00
13_N	66_F	1.222	1.00
47_A	68_T	1.217	1.00
36_G	76_V	1.201	1.00
44_V	64_V	1.156	1.00
81_N	85_R	1.131	1.00
27_F	77_L	1.114	1.00
53_E	124_S	1.113	1.00
14_A	23_I	1.113	1.00
42_L	47_A	1.111	1.00
27_F	90_L	1.101	1.00
122_V	126_A	1.100	1.00
130_A	135_E	1.079	1.00
16_A	113_E	1.078	1.00
24_F	37_T	1.077	1.00
9_I	72_I	1.058	1.00
5_R	35_V	1.053	1.00
86_H	90_L	1.035	0.99
56_G	61_D	1.021	0.99
14_A	115_G	1.013	0.99
39_M	73_V	1.012	0.99
80_E	110_S	1.010	0.99
33_K	78_E	1.003	0.99
15_V	20_I	0.998	0.99
17_K	115_G	0.990	0.99
48_R	60_F	0.988	0.99
24_F	73_V	0.970	0.99
69_S	113_E	0.957	0.99
15_V	39_M	0.937	0.99
92_A	97_N	0.932	0.99
37_T	75_S	0.927	0.99
44_V	61_D	0.924	0.99
42_L	67_M	0.921	0.99
6_T	86_H	0.894	0.98
117_H	128_E	0.880	0.98
95_P	111_L	0.880	0.98
48_R	64_V	0.877	0.98
23_I	115_G	0.873	0.98
40_L	46_Q	0.872	0.98
50_F	131_Y	0.871	0.98
54_H	63_L	0.863	0.98
101_G	106_D	0.862	0.98
66_F	69_S	0.859	0.98
109_D	113_E	0.856	0.98
86_H	116_T	0.852	0.98
95_P	110_S	0.846	0.98
19_V	22_N	0.845	0.98
85_R	89_L	0.835	0.98
19_V	115_G	0.834	0.98
42_L	72_I	0.834	0.98
17_K	109_D	0.833	0.98
26_R	103_L	0.824	0.97
127_R	131_Y	0.821	0.97
26_R	30_A	0.801	0.97
52_A	60_F	0.800	0.97
123_E	126_A	0.799	0.97
54_H	59_F	0.790	0.97
44_V	68_T	0.786	0.97
16_A	69_S	0.783	0.97
21_G	37_T	0.780	0.96
8_S	75_S	0.775	0.96
77_L	86_H	0.772	0.96
4_E	83_V	0.767	0.96
110_S	113_E	0.761	0.96
8_S	77_L	0.760	0.96
46_Q	49_G	0.760	0.96
32_F	86_H	0.760	0.96
8_S	27_F	0.758	0.96
20_I	39_M	0.751	0.96
45_E	48_R	0.746	0.95
92_A	98_A	0.743	0.95
54_H	57_K	0.742	0.95
99_L	102_T	0.741	0.95
52_A	55_D	0.724	0.95
103_L	116_T	0.721	0.94
34_I	37_T	0.712	0.94
30_A	85_R	0.704	0.94
50_F	132_F	0.693	0.93
47_A	64_V	0.688	0.93
79_G	82_A	0.680	0.93
91_G	104_R	0.679	0.93
21_G	24_F	0.659	0.91
56_G	62_G	0.654	0.91
5_R	129_I	0.650	0.91
10_I	23_I	0.649	0.91
95_P	108_A	0.645	0.91
59_F	63_L	0.644	0.90
58_P	62_G	0.644	0.90
25_A	28_E	0.644	0.90
18_N	33_K	0.642	0.90
62_G	65_E	0.630	0.89
6_T	77_L	0.629	0.89
83_V	121_S	0.621	0.89
66_F	109_D	0.618	0.89
130_A	134_G	0.616	0.88
3_I	78_E	0.616	0.88
119_S	128_E	0.615	0.88
55_D	61_D	0.615	0.88
87_R	117_H	0.614	0.88
105_A	115_G	0.614	0.88
55_D	64_V	0.612	0.88
5_R	126_A	0.608	0.88
63_L	67_M	0.607	0.88
21_G	39_M	0.605	0.88
108_A	115_G	0.605	0.88
20_I	28_E	0.604	0.87
121_S	127_R	0.604	0.87
39_M	71_P	0.603	0.87
42_L	46_Q	0.595	0.87
97_N	111_L	0.595	0.87
46_Q	50_F	0.594	0.87
52_A	127_R	0.593	0.86
35_V	76_V	0.593	0.86
104_R	114_N	0.592	0.86
4_E	81_N	0.592	0.86
96_A	109_D	0.584	0.86
15_V	73_V	0.583	0.86
87_R	93_T	0.582	0.85
60_F	64_V	0.580	0.85
92_A	95_P	0.578	0.85
26_R	29_A	0.572	0.84
22_N	107_Y	0.571	0.84
24_F	28_E	0.564	0.84
21_G	28_E	0.561	0.83
6_T	82_A	0.558	0.83
13_N	17_K	0.554	0.83
83_V	127_R	0.554	0.83
65_E	68_T	0.554	0.83
72_I	132_F	0.553	0.82
109_D	115_G	0.553	0.82
62_G	111_L	0.553	0.82
9_I	67_M	0.551	0.82
51_Y	117_H	0.545	0.82
15_V	70_G	0.544	0.81
4_E	84_Q	0.533	0.80
7_F	74_V	0.529	0.80
36_G	134_G	0.528	0.80
55_D	60_F	0.528	0.80
86_H	98_A	0.521	0.79
42_L	50_F	0.516	0.78
81_N	88_D	0.515	0.78
61_D	64_V	0.514	0.78
24_F	34_I	0.512	0.77
94_N	98_A	0.510	0.77
59_F	93_T	0.508	0.77
64_V	67_M	0.506	0.77
13_N	109_D	0.502	0.76
34_I	39_M	0.501	0.76
88_D	96_A	0.501	0.76
91_G	114_N	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
1w7wA	5	1	100	-0.011	Contact Map
4kpcA	4	0.986	100	-0.008	Contact Map
3r9lA	4	0.7832	100	-0.008	Contact Map
4c6aA	1	1	100	-0.004	Contact Map
2vu5A	5	0.986	100	-0.004	Contact Map
3l7uA	5	1	100	-0.004	Contact Map
1ehwA	4	0.986	100	-0.004	Contact Map
4w98A	2	1	100	-0.002	Contact Map
3q8uA	3	0.986	100	-0.001	Contact Map
3b54A	4	0.951	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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