YCAK - ECOLI - GREMLIN Contacts

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YCAK - Uncharacterized NAD(P)H oxidoreductase YcaK

UniProt:	P43340	Sequences: MQSERIYLVWAHPRHDSLTAHIADAIHQRAMERKIQVTELDLYRRNFNPVMTPEDEPDWKNMDKRYSPEVHQLYSELLEHDTLVVVFPLWWYSFPAMLKGYIDRVWNNGLAYGDGHKLPFNKVRWVALVGGDKESFVQMGWEKNISDYLKNMCSYLGIEDADVTFLCNTVVFDGEELHASYYQSLLSQVRDMVDAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12702
Length:	196 (179)
Sequences:	3132 (2263)
Seq/√Len:	169.1

ECOLI - YCAK KEFG KEFF MDAB AZOR
BACSU - YDEQ YRKL GS14 AZOR2 AZOR1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_T	79_E	4.682	1.00
5_R	36_Q	3.276	1.00
11_A	97_M	2.946	1.00
48_N	52_T	2.842	1.00
41_D	44_R	2.832	1.00
38_T	76_E	2.720	1.00
74_Y	110_L	2.685	1.00
40_L	76_E	2.518	1.00
10_W	23_A	2.171	1.00
40_L	45_R	2.142	1.00
27_H	31_M	2.135	1.00
123_V	153_C	2.101	1.00
75_S	79_E	2.052	1.00
78_L	110_L	2.014	1.00
24_D	28_Q	1.990	1.00
75_S	78_L	1.988	1.00
20_A	23_A	1.971	1.00
82_T	122_K	1.942	1.00
174_G	179_A	1.891	1.00
83_L	158_I	1.854	1.00
144_N	147_D	1.836	1.00
122_K	159_E	1.834	1.00
100_G	104_R	1.833	1.00
6_I	82_T	1.827	1.00
6_I	35_I	1.824	1.00
71_H	75_S	1.822	1.00
25_A	186_L	1.807	1.00
89_L	127_A	1.802	1.00
72_Q	76_E	1.800	1.00
23_A	39_E	1.784	1.00
11_A	43_Y	1.767	1.00
173_D	176_E	1.761	1.00
74_Y	111_A	1.728	1.00
73_L	101_Y	1.714	1.00
18_L	178_H	1.667	1.00
5_R	79_E	1.626	1.00
183_Q	186_L	1.620	1.00
40_L	73_L	1.612	1.00
45_R	76_E	1.606	1.00
99_K	103_D	1.568	1.00
29_R	186_L	1.532	1.00
38_T	80_H	1.521	1.00
179_A	183_Q	1.513	1.00
19_T	128_L	1.511	1.00
113_G	117_K	1.487	1.00
28_Q	32_E	1.476	1.00
8_L	27_H	1.473	1.00
7_Y	76_E	1.470	1.00
102_I	106_W	1.466	1.00
28_Q	31_M	1.428	1.00
172_F	178_H	1.421	1.00
86_V	185_L	1.417	1.00
96_A	100_G	1.411	1.00
45_R	72_Q	1.391	1.00
126_V	185_L	1.390	1.00
106_W	156_L	1.380	1.00
25_A	29_R	1.373	1.00
7_Y	80_H	1.343	1.00
19_T	86_V	1.307	1.00
153_C	158_I	1.295	1.00
166_L	172_F	1.268	1.00
185_L	189_V	1.256	1.00
94_F	98_L	1.232	1.00
20_A	24_D	1.229	1.00
28_Q	186_L	1.218	1.00
119_P	157_G	1.207	1.00
86_V	126_V	1.199	1.00
15_H	44_R	1.193	1.00
21_H	24_D	1.186	1.00
89_L	145_I	1.177	1.00
123_V	158_I	1.169	1.00
43_Y	97_M	1.167	1.00
66_Y	100_G	1.158	1.00
72_Q	75_S	1.149	1.00
25_A	28_Q	1.146	1.00
70_V	74_Y	1.142	1.00
24_D	27_H	1.137	1.00
118_L	158_I	1.120	1.00
45_R	73_L	1.116	1.00
14_R	56_E	1.115	1.00
129_V	167_C	1.111	1.00
18_L	169_T	1.108	1.00
180_S	183_Q	1.095	1.00
76_E	79_E	1.089	1.00
145_I	165_F	1.082	1.00
111_A	118_L	1.053	0.99
92_Y	151_N	1.041	0.99
126_V	164_T	1.030	0.99
164_T	184_S	1.020	0.99
29_R	33_R	1.019	0.99
185_L	188_Q	1.018	0.99
21_H	182_Y	1.018	0.99
181_Y	184_S	1.009	0.99
172_F	176_E	1.005	0.99
51_M	55_D	1.001	0.99
74_Y	107_N	0.996	0.99
178_H	182_Y	0.995	0.99
36_Q	79_E	0.995	0.99
91_W	112_Y	0.976	0.99
49_P	100_G	0.976	0.99
27_H	39_E	0.961	0.99
81_D	121_N	0.952	0.99
91_W	103_D	0.934	0.99
183_Q	187_S	0.933	0.99
18_L	166_L	0.920	0.99
21_H	25_A	0.910	0.98
40_L	101_Y	0.905	0.98
9_V	40_L	0.897	0.98
80_H	83_L	0.896	0.98
87_F	125_W	0.888	0.98
166_L	181_Y	0.886	0.98
10_W	20_A	0.877	0.98
108_N	112_Y	0.871	0.98
18_L	22_I	0.867	0.98
71_H	74_Y	0.864	0.98
5_R	81_D	0.853	0.98
176_E	180_S	0.849	0.98
21_H	178_H	0.844	0.97
16_D	24_D	0.844	0.97
53_P	57_P	0.842	0.97
78_L	117_K	0.835	0.97
31_M	36_Q	0.834	0.97
84_V	124_R	0.832	0.97
102_I	152_M	0.818	0.97
17_S	20_A	0.817	0.97
23_A	26_I	0.811	0.97
29_R	32_E	0.811	0.97
125_W	153_C	0.800	0.97
108_N	114_D	0.798	0.96
132_D	135_S	0.797	0.96
8_L	84_V	0.795	0.96
11_A	98_L	0.792	0.96
145_I	149_L	0.791	0.96
26_I	185_L	0.785	0.96
9_V	85_V	0.785	0.96
122_K	161_A	0.784	0.96
18_L	182_Y	0.776	0.96
109_G	113_G	0.760	0.95
53_P	58_D	0.754	0.95
69_E	72_Q	0.752	0.95
141_W	151_N	0.745	0.95
77_L	83_L	0.745	0.95
92_Y	155_Y	0.745	0.95
184_S	187_S	0.742	0.95
174_G	178_H	0.741	0.95
52_T	55_D	0.740	0.95
120_F	159_E	0.738	0.95
64_K	68_P	0.737	0.95
137_V	142_E	0.733	0.94
133_K	167_C	0.730	0.94
92_Y	141_W	0.729	0.94
97_M	101_Y	0.729	0.94
19_T	22_I	0.729	0.94
180_S	184_S	0.729	0.94
21_H	26_I	0.728	0.94
31_M	34_K	0.728	0.94
129_V	165_F	0.723	0.94
25_A	182_Y	0.714	0.94
7_Y	40_L	0.713	0.93
94_F	152_M	0.707	0.93
89_L	136_F	0.705	0.93
46_N	52_T	0.704	0.93
8_L	26_I	0.701	0.93
16_D	20_A	0.692	0.92
32_E	186_L	0.688	0.92
26_I	30_A	0.686	0.92
69_E	73_L	0.685	0.92
122_K	160_D	0.678	0.92
49_P	97_M	0.672	0.91
131_G	142_E	0.671	0.91
182_Y	185_L	0.670	0.91
126_V	166_L	0.670	0.91
139_M	146_S	0.670	0.91
146_S	149_L	0.668	0.91
10_W	39_E	0.665	0.91
75_S	187_S	0.660	0.91
110_L	118_L	0.659	0.91
66_Y	107_N	0.657	0.90
74_Y	105_V	0.655	0.90
89_L	148_Y	0.649	0.90
29_R	189_V	0.648	0.90
133_K	137_V	0.648	0.90
87_F	156_L	0.643	0.89
18_L	21_H	0.642	0.89
172_F	181_Y	0.641	0.89
129_V	145_I	0.637	0.89
49_P	52_T	0.637	0.89
124_R	164_T	0.636	0.89
51_M	54_E	0.635	0.89
9_V	101_Y	0.634	0.89
113_G	116_H	0.626	0.88
96_A	104_R	0.626	0.88
26_I	84_V	0.622	0.88
77_L	85_V	0.621	0.88
152_M	156_L	0.618	0.88
95_P	103_D	0.613	0.87
68_P	72_Q	0.612	0.87
85_V	123_V	0.612	0.87
121_N	130_G	0.611	0.87
6_I	30_A	0.610	0.87
90_W	99_K	0.609	0.87
22_I	26_I	0.607	0.87
83_L	123_V	0.604	0.86
148_Y	151_N	0.601	0.86
47_F	100_G	0.598	0.86
35_I	82_T	0.596	0.86
92_Y	131_G	0.595	0.85
12_H	17_S	0.593	0.85
11_A	42_L	0.589	0.85
75_S	179_A	0.588	0.85
169_T	178_H	0.588	0.85
26_I	189_V	0.585	0.85
173_D	178_H	0.584	0.84
149_L	163_V	0.581	0.84
142_E	154_S	0.580	0.84
77_L	106_W	0.569	0.83
46_N	50_V	0.565	0.82
11_A	41_D	0.563	0.82
87_F	145_I	0.563	0.82
77_L	110_L	0.561	0.82
64_K	67_S	0.559	0.82
26_I	29_R	0.558	0.82
26_I	126_V	0.558	0.82
58_D	64_K	0.557	0.82
127_A	165_F	0.557	0.82
67_S	104_R	0.556	0.81
127_A	145_I	0.555	0.81
50_V	97_M	0.554	0.81
182_Y	189_V	0.550	0.81
91_W	151_N	0.550	0.81
178_H	181_Y	0.550	0.81
51_M	56_E	0.548	0.81
153_C	160_D	0.548	0.81
154_S	158_I	0.547	0.80
13_P	90_W	0.543	0.80
129_V	169_T	0.539	0.79
57_P	116_H	0.539	0.79
164_T	181_Y	0.539	0.79
14_R	104_R	0.538	0.79
123_V	160_D	0.536	0.79
140_G	147_D	0.535	0.79
87_F	95_P	0.534	0.79
122_K	157_G	0.533	0.79
124_R	188_Q	0.532	0.79
10_W	41_D	0.531	0.78
142_E	147_D	0.529	0.78
80_H	121_N	0.528	0.78
118_L	156_L	0.524	0.78
82_T	124_R	0.523	0.77
98_L	102_I	0.522	0.77
94_F	148_Y	0.521	0.77
52_T	56_E	0.517	0.77
14_R	53_P	0.516	0.76
108_N	113_G	0.516	0.76
54_E	57_P	0.515	0.76
8_L	37_V	0.514	0.76
71_H	180_S	0.510	0.76
25_A	183_Q	0.509	0.75
131_G	168_N	0.509	0.75
104_R	107_N	0.508	0.75
85_V	98_L	0.507	0.75
24_D	39_E	0.507	0.75
74_Y	112_Y	0.507	0.75
6_I	84_V	0.506	0.75
87_F	101_Y	0.505	0.75
87_F	127_A	0.503	0.75
22_I	181_Y	0.501	0.74
48_N	54_E	0.500	0.74

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
1d4aA	2	0.9898	100	0.37	Contact Map
4gi5A	2	0.9949	100	0.38	Contact Map
4fglA	2	0.9949	100	0.426	Contact Map
4r81A	4	0.9898	100	0.438	Contact Map
3lcmA	2	0.9541	100	0.44	Contact Map
2amjA	2	0.8469	100	0.451	Contact Map
3rpeA	2	0.8622	100	0.485	Contact Map
3l9wA	2	0.8776	100	0.489	Contact Map
4n65A	2	0.949	100	0.501	Contact Map
3w7aA	2	0.9541	100	0.503	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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