UDPK - BACSU - GREMLIN Contacts

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UDPK - Undecaprenol kinase

UniProt:	P19638	Sequences: MDSKDHRNELNRFFKSFVHAGRGIWETARTERNFQFHAAAACAVLICGFLVELSIIEWMIIFLLIGGMFSLELLNTAIEHTVDLITDKHHPLAKAAKDAAAGAVCVFAVISCIIGLLIFLPKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	123 (111)
Sequences:	2393 (1738)
Seq/√Len:	165.0

ECOLI - KDGL
BACSU - UDPK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_V	93_A	3.364	1.00
22_R	94_K	3.270	1.00
27_T	73_L	2.852	1.00
28_A	38_A	2.588	1.00
71_L	74_L	2.526	1.00
66_G	110_I	2.324	1.00
25_W	29_R	2.080	1.00
41_A	65_I	2.050	1.00
71_L	107_F	1.991	1.00
84_L	93_A	1.901	1.00
48_G	58_W	1.862	1.00
28_A	39_A	1.834	1.00
53_L	118_I	1.788	1.00
24_I	102_G	1.735	1.00
80_H	95_A	1.716	1.00
67_G	107_F	1.713	1.00
70_S	107_F	1.708	1.00
81_T	96_A	1.674	1.00
52_E	58_W	1.656	1.00
54_S	57_E	1.516	1.00
27_T	34_F	1.468	1.00
73_L	99_A	1.463	1.00
56_I	60_I	1.440	1.00
81_T	85_I	1.403	1.00
92_L	96_A	1.400	1.00
34_F	37_H	1.379	1.00
57_E	118_I	1.377	1.00
60_I	64_L	1.377	1.00
68_M	111_S	1.373	1.00
34_F	69_F	1.351	1.00
76_T	99_A	1.345	1.00
15_K	18_V	1.344	1.00
69_F	106_V	1.286	1.00
27_T	99_A	1.279	1.00
13_F	17_F	1.275	1.00
116_L	120_L	1.269	1.00
30_T	95_A	1.257	1.00
63_L	110_I	1.256	1.00
20_A	101_A	1.249	1.00
73_L	102_G	1.243	1.00
45_L	65_I	1.242	1.00
71_L	103_A	1.230	1.00
68_M	104_V	1.219	1.00
19_H	22_R	1.213	1.00
46_I	50_L	1.204	1.00
44_V	65_I	1.201	1.00
62_F	110_I	1.196	1.00
13_F	32_R	1.181	1.00
13_F	36_F	1.174	1.00
26_E	95_A	1.154	1.00
16_S	33_N	1.137	1.00
112_C	116_L	1.101	1.00
55_I	59_M	1.087	1.00
64_L	114_I	1.082	1.00
37_H	104_V	1.064	0.99
53_L	61_I	1.063	0.99
17_F	105_C	1.057	0.99
68_M	107_F	1.042	0.99
59_M	117_L	1.009	0.99
70_S	74_L	0.994	0.99
86_T	93_A	0.993	0.99
31_E	80_H	0.986	0.99
73_L	106_V	0.985	0.99
59_M	114_I	0.974	0.99
55_I	117_L	0.974	0.99
66_G	106_V	0.972	0.99
33_N	36_F	0.965	0.99
51_V	119_F	0.958	0.99
76_T	80_H	0.941	0.99
61_I	64_L	0.927	0.99
77_A	96_A	0.921	0.98
36_F	40_A	0.913	0.98
76_T	95_A	0.912	0.98
11_N	15_K	0.908	0.98
15_K	19_H	0.907	0.98
67_G	70_S	0.894	0.98
85_I	93_A	0.891	0.98
21_G	25_W	0.882	0.98
33_N	37_H	0.881	0.98
80_H	83_D	0.870	0.98
12_R	32_R	0.867	0.98
26_E	31_E	0.864	0.98
64_L	111_S	0.847	0.97
16_S	20_A	0.836	0.97
100_A	103_A	0.836	0.97
30_T	76_T	0.835	0.97
86_T	90_H	0.824	0.97
105_C	109_V	0.822	0.97
48_G	61_I	0.816	0.97
34_F	73_L	0.813	0.97
26_E	30_T	0.790	0.96
74_L	103_A	0.789	0.96
14_F	18_V	0.781	0.96
17_F	36_F	0.780	0.96
82_V	96_A	0.780	0.96
84_L	90_H	0.777	0.96
38_A	69_F	0.777	0.96
56_I	59_M	0.774	0.95
113_I	116_L	0.766	0.95
84_L	96_A	0.763	0.95
17_F	21_G	0.761	0.95
37_H	68_M	0.747	0.95
108_A	112_C	0.736	0.94
37_H	108_A	0.734	0.94
55_I	118_I	0.729	0.94
84_L	92_L	0.709	0.93
59_M	113_I	0.704	0.93
48_G	62_F	0.703	0.93
41_A	44_V	0.699	0.92
66_G	113_I	0.691	0.92
96_A	100_A	0.688	0.92
113_I	117_L	0.686	0.92
83_D	97_K	0.677	0.91
109_V	113_I	0.673	0.91
37_H	41_A	0.671	0.91
61_I	119_F	0.664	0.90
104_V	111_S	0.661	0.90
18_V	22_R	0.656	0.90
22_R	26_E	0.654	0.90
40_A	108_A	0.647	0.89
95_A	99_A	0.642	0.89
26_E	94_K	0.640	0.89
91_P	95_A	0.637	0.88
60_I	110_I	0.636	0.88
68_M	108_A	0.635	0.88
45_L	49_F	0.630	0.88
30_T	80_H	0.626	0.88
77_A	103_A	0.624	0.87
86_T	94_K	0.610	0.86
53_L	58_W	0.596	0.85
64_L	107_F	0.594	0.85
49_F	58_W	0.592	0.84
77_A	81_T	0.579	0.83
32_R	35_Q	0.578	0.83
85_I	89_H	0.577	0.83
28_A	34_F	0.575	0.83
80_H	96_A	0.570	0.82
19_H	26_E	0.562	0.81
32_R	36_F	0.560	0.81
44_V	111_S	0.554	0.80
21_G	105_C	0.552	0.80
18_V	21_G	0.551	0.80
81_T	93_A	0.550	0.80
80_H	99_A	0.549	0.80
31_E	98_D	0.548	0.80
46_I	49_F	0.544	0.79
82_V	86_T	0.543	0.79
62_F	117_L	0.542	0.79
64_L	68_M	0.541	0.79
43_A	47_C	0.529	0.77
19_H	33_N	0.528	0.77
63_L	67_G	0.528	0.77
85_I	96_A	0.524	0.77
65_I	111_S	0.522	0.76
47_C	51_V	0.521	0.76
26_E	99_A	0.518	0.76
12_R	36_F	0.517	0.76
43_A	50_L	0.515	0.75
49_F	117_L	0.512	0.75
85_I	92_L	0.510	0.75
10_L	13_F	0.510	0.75
115_G	119_F	0.508	0.74
73_L	103_A	0.504	0.74
36_F	39_A	0.503	0.74
111_S	114_I	0.501	0.73
16_S	19_H	0.500	0.73

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
3ze3A	4	0.9268	100	0.104	Contact Map
4k1cA	4	0.8455	12.7	0.934	Contact Map
4w252	1	0.3821	12.5	0.934	Contact Map
4tq3A	1	0.7805	7.8	0.94	Contact Map
1rh5B	1	0.3252	6.5	0.942	Contact Map
4wrtC	1	0	5.1	0.945	Contact Map
1pi7A	1	0.1545	3.5	0.949	Contact Map
4rp9A	2	0.878	2.8	0.951	Contact Map
1m56D	1	0.2927	2.7	0.952	Contact Map
2lzrA	1	0.3171	2.5	0.952	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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