YDEQ - BACSU - GREMLIN Contacts

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YDEQ - Uncharacterized NAD(P)H oxidoreductase YdeQ

UniProt:	P96674	Sequences: MDHMKTLVLVVHPNIESSRINKKWKEAVLSEPDVTVHDLYEKYRDQPIDVEFEQQQLLAHDRIVFQFPLYWYSSPPLLKQWFDEVFTFGWAHGPGGNKLKGKEWVTAMSIGSPEHSYQAGGYNLFSISELTKPFQASAHLVGMTYLPSFAEYRANTISDQEIAESANRYVKHITNIELNPKVRLQRYLKQLESVDLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	197 (169)
Sequences:	3743 (2729)
Seq/√Len:	209.9

ECOLI - KEFG KEFF YCAK MDAB AZOR
BACSU - YDEQ GS14 YRKL 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
35_T	59_A	3.664	1.00
80_Q	84_E	2.468	1.00
37_H	56_Q	2.402	1.00
38_D	41_E	2.369	1.00
11_V	77_L	2.328	1.00
5_K	33_D	2.247	1.00
54_Q	90_W	2.137	1.00
35_T	56_Q	2.085	1.00
69_L	108_M	2.027	1.00
103_E	144_T	2.011	1.00
10_V	21_N	2.006	1.00
55_Q	59_A	1.993	1.00
104_W	138_A	1.956	1.00
37_H	42_K	1.956	1.00
62_R	103_E	1.938	1.00
63_I	143_M	1.866	1.00
51_E	55_Q	1.857	1.00
5_K	59_A	1.850	1.00
25_K	29_L	1.825	1.00
46_Q	80_Q	1.805	1.00
159_D	163_A	1.789	1.00
6_T	62_R	1.770	1.00
55_Q	58_L	1.767	1.00
126_S	129_E	1.766	1.00
158_S	161_E	1.748	1.00
52_F	56_Q	1.746	1.00
7_L	56_Q	1.744	1.00
79_K	83_D	1.742	1.00
22_K	26_E	1.737	1.00
58_L	90_W	1.735	1.00
167_N	170_V	1.707	1.00
35_T	60_H	1.636	1.00
27_A	170_V	1.610	1.00
76_P	80_Q	1.589	1.00
161_E	164_E	1.586	1.00
11_V	40_Y	1.582	1.00
20_I	109_S	1.533	1.00
42_K	56_Q	1.527	1.00
66_Q	169_Y	1.520	1.00
53_E	81_W	1.508	1.00
107_A	169_Y	1.500	1.00
8_V	25_K	1.484	1.00
82_F	86_F	1.481	1.00
26_E	29_L	1.469	1.00
163_A	167_N	1.462	1.00
165_S	168_R	1.437	1.00
26_E	30_S	1.393	1.00
6_T	32_P	1.378	1.00
7_L	60_H	1.358	1.00
169_Y	173_I	1.356	1.00
100_K	142_G	1.356	1.00
54_Q	91_A	1.354	1.00
37_H	53_E	1.345	1.00
23_K	170_V	1.344	1.00
27_A	30_S	1.330	1.00
23_K	27_A	1.317	1.00
93_G	96_G	1.312	1.00
149_F	168_R	1.310	1.00
50_V	54_Q	1.291	1.00
42_K	52_F	1.288	1.00
104_W	143_M	1.250	1.00
21_N	36_V	1.235	1.00
97_N	100_K	1.226	1.00
157_I	162_I	1.225	1.00
52_F	55_Q	1.222	1.00
66_Q	107_A	1.217	1.00
127_I	150_A	1.214	1.00
17_S	109_S	1.158	1.00
138_A	143_M	1.152	1.00
69_L	127_I	1.148	1.00
24_W	28_V	1.144	1.00
27_A	31_E	1.138	1.00
11_V	78_L	1.125	1.00
93_G	98_K	1.124	1.00
23_K	26_E	1.119	1.00
114_E	152_Y	1.117	1.00
167_N	171_K	1.109	1.00
18_S	21_N	1.107	1.00
40_Y	77_L	1.101	1.00
171_K	175_N	1.095	1.00
169_Y	172_H	1.089	1.00
42_K	53_E	1.088	1.00
27_A	174_T	1.083	1.00
171_K	174_T	1.082	1.00
17_S	66_Q	1.075	1.00
25_K	36_V	1.065	1.00
129_E	132_K	1.062	1.00
162_I	166_A	1.059	1.00
49_D	52_F	1.057	1.00
164_E	168_R	1.053	1.00
64_V	105_V	1.050	1.00
136_A	139_H	1.040	1.00
99_L	143_M	1.037	1.00
151_E	157_I	1.036	1.00
74_S	78_L	1.036	1.00
86_F	141_V	1.032	1.00
44_R	47_P	1.030	1.00
107_A	149_F	1.023	1.00
170_V	174_T	1.009	1.00
30_S	170_V	1.005	1.00
114_E	118_Q	1.002	1.00
51_E	54_Q	1.002	1.00
151_E	165_S	0.998	1.00
101_G	144_T	0.997	1.00
67_F	106_T	0.994	1.00
56_Q	59_A	0.994	1.00
60_H	63_I	0.994	1.00
71_W	83_D	0.993	1.00
110_I	152_Y	0.988	1.00
61_D	102_K	0.958	1.00
58_L	98_K	0.957	1.00
54_Q	87_T	0.924	0.99
9_L	37_H	0.921	0.99
11_V	39_L	0.897	0.99
10_V	18_S	0.894	0.99
26_E	170_V	0.893	0.99
13_P	70_Y	0.886	0.99
31_E	174_T	0.881	0.99
44_R	80_Q	0.877	0.99
29_L	33_D	0.863	0.99
5_K	61_D	0.859	0.99
33_D	59_A	0.853	0.99
107_A	151_E	0.842	0.99
113_P	116_S	0.842	0.99
27_A	173_I	0.836	0.99
69_L	130_L	0.832	0.99
76_P	84_E	0.824	0.99
72_Y	140_L	0.820	0.99
105_V	172_H	0.812	0.98
137_S	141_V	0.805	0.98
19_R	162_I	0.802	0.98
37_H	81_W	0.801	0.98
162_I	165_S	0.798	0.98
108_M	150_A	0.796	0.98
82_F	137_S	0.795	0.98
88_F	92_H	0.794	0.98
57_L	63_I	0.793	0.98
112_S	123_N	0.792	0.98
67_F	131_T	0.790	0.98
132_K	135_Q	0.787	0.98
130_L	136_A	0.784	0.98
19_R	159_D	0.783	0.98
138_A	145_Y	0.781	0.98
24_W	169_Y	0.780	0.98
23_K	166_A	0.780	0.98
65_F	138_A	0.778	0.98
19_R	166_A	0.775	0.98
103_E	146_L	0.770	0.98
67_F	127_I	0.770	0.98
108_M	131_T	0.769	0.98
110_I	117_Y	0.766	0.98
110_I	127_I	0.765	0.98
43_Y	48_I	0.761	0.98
88_F	94_P	0.751	0.97
166_A	169_Y	0.744	0.97
8_V	64_V	0.742	0.97
24_W	107_A	0.742	0.97
15_I	41_E	0.729	0.97
164_E	167_N	0.720	0.97
71_W	92_H	0.716	0.97
105_V	149_F	0.713	0.96
110_I	150_A	0.711	0.96
158_S	162_I	0.704	0.96
21_N	66_Q	0.702	0.96
57_L	65_F	0.699	0.96
4_M	32_P	0.698	0.96
57_L	81_W	0.696	0.96
129_E	135_Q	0.691	0.96
23_K	163_A	0.687	0.96
53_E	56_Q	0.685	0.96
5_K	38_D	0.685	0.96
9_L	81_W	0.673	0.95
9_L	65_F	0.673	0.95
147_P	172_H	0.669	0.95
62_R	105_V	0.668	0.95
91_A	99_L	0.658	0.94
7_L	37_H	0.656	0.94
55_Q	171_K	0.656	0.94
104_W	145_Y	0.653	0.94
24_W	173_I	0.650	0.94
157_I	161_E	0.650	0.94
49_D	53_E	0.645	0.94
11_V	38_D	0.643	0.94
97_N	142_G	0.642	0.94
14_N	17_S	0.641	0.94
54_Q	85_V	0.638	0.93
46_Q	84_E	0.635	0.93
67_F	108_M	0.635	0.93
46_Q	77_L	0.633	0.93
24_W	151_E	0.614	0.92
44_R	84_E	0.609	0.92
69_L	117_Y	0.609	0.92
123_N	136_A	0.607	0.92
149_F	172_H	0.605	0.92
75_P	83_D	0.604	0.92
124_L	136_A	0.602	0.91
74_S	82_F	0.600	0.91
157_I	165_S	0.600	0.91
94_P	141_V	0.597	0.91
166_A	173_I	0.596	0.91
8_V	24_W	0.595	0.91
89_G	93_G	0.595	0.91
103_E	142_G	0.593	0.91
135_Q	148_S	0.587	0.90
159_D	162_I	0.587	0.90
154_A	157_I	0.584	0.90
47_P	80_Q	0.574	0.89
67_F	78_L	0.574	0.89
19_R	23_K	0.574	0.89
20_I	107_A	0.573	0.89
44_R	48_I	0.572	0.89
108_M	127_I	0.572	0.89
57_L	86_F	0.571	0.89
168_R	171_K	0.570	0.89
132_K	136_A	0.570	0.89
153_R	156_T	0.570	0.89
112_S	153_R	0.570	0.89
149_F	169_Y	0.569	0.89
30_S	174_T	0.569	0.89
77_L	81_W	0.567	0.89
84_E	87_T	0.563	0.88
67_F	74_S	0.561	0.88
51_E	164_E	0.560	0.88
28_V	169_Y	0.555	0.88
67_F	75_P	0.553	0.88
117_Y	152_Y	0.553	0.88
21_N	24_W	0.552	0.87
92_H	95_G	0.550	0.87
10_V	15_I	0.549	0.87
20_I	165_S	0.545	0.87
166_A	170_V	0.544	0.87
154_A	162_I	0.539	0.86
116_S	122_Y	0.538	0.86
5_K	35_T	0.537	0.86
54_Q	88_F	0.536	0.86
65_F	78_L	0.535	0.86
28_V	32_P	0.533	0.86
72_Y	112_S	0.533	0.86
4_M	62_R	0.532	0.85
51_E	87_T	0.530	0.85
111_G	155_N	0.527	0.85
32_P	62_R	0.526	0.85
131_T	148_S	0.525	0.85
72_Y	136_A	0.520	0.84
9_L	82_F	0.519	0.84
10_V	36_V	0.518	0.84
18_S	22_K	0.517	0.84
117_Y	121_G	0.516	0.84
14_N	84_E	0.512	0.83
10_V	25_K	0.511	0.83
90_W	99_L	0.509	0.83
69_L	110_I	0.506	0.83
135_Q	138_A	0.503	0.82
112_S	152_Y	0.500	0.82

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	0.377	Contact Map
4gi5A	2	0.9949	100	0.392	Contact Map
4fglA	2	0.9695	100	0.431	Contact Map
3l9wA	2	0.8883	100	0.462	Contact Map
2amjA	2	0.8426	100	0.466	Contact Map
3f2vA	2	0.8629	100	0.475	Contact Map
3rpeA	2	0.868	100	0.484	Contact Map
4r81A	4	0.9036	100	0.489	Contact Map
3ha2A	2	0.8376	100	0.49	Contact Map
3lcmA	2	0.8883	100	0.5	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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