YDEN - BACSU - GREMLIN Contacts

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YDEN - Putative hydrolase YdeN

UniProt:	P96671	Sequences: MTKQVYIIHGYRASSTNHWFPWLKKRLLADGVQADILNMPNPLQPRLEDWLDTLSLYQHTLHENTYLVAHSLGCPAILRFLEHLQLRKQLGGIILVSGFAKSLPTLQMLDEFTQGSFDHQKIIESAKHRAVIASKDDQIVPFSFSKDLAQQIDAALYEVQHGGHFLEDEGFTSLPIVYDVLTSYFSKETR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	190 (170)
Sequences:	1387 (998)
Seq/√Len:	76.6

BACSU - YDEN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
129_R	154_A	4.891	1.00
135_K	158_E	3.920	1.00
54_L	76_A	3.682	1.00
69_A	77_I	3.421	1.00
24_K	36_I	3.159	1.00
135_K	142_F	2.674	1.00
8_I	73_G	2.391	1.00
135_K	161_H	2.320	1.00
166_L	169_E	2.161	1.00
40_P	53_T	2.117	1.00
136_D	161_H	2.113	1.00
94_I	184_Y	2.066	1.00
174_L	177_V	1.974	1.00
21_P	36_I	1.932	1.00
47_L	79_R	1.893	1.00
4_Q	63_E	1.779	1.00
72_L	112_F	1.771	1.00
23_L	177_V	1.753	1.00
140_V	145_S	1.730	1.00
155_A	183_S	1.716	1.00
142_F	158_E	1.664	1.00
133_A	156_L	1.650	1.00
40_P	49_D	1.641	1.00
100_A	144_F	1.623	1.00
81_L	127_K	1.605	1.00
47_L	51_L	1.601	1.00
69_A	74_C	1.592	1.00
8_I	76_A	1.578	0.99
162_G	171_F	1.551	0.99
134_S	162_G	1.516	0.99
67_L	77_I	1.514	0.99
75_P	101_K	1.494	0.99
46_R	49_D	1.463	0.99
27_L	34_A	1.458	0.99
71_S	164_H	1.452	0.99
14_S	20_F	1.450	0.99
112_F	116_S	1.441	0.99
6_Y	37_L	1.441	0.99
27_L	178_Y	1.438	0.99
66_Y	92_G	1.427	0.99
53_T	56_L	1.413	0.99
55_S	80_F	1.396	0.99
133_A	142_F	1.389	0.99
55_S	59_H	1.388	0.99
142_F	156_L	1.377	0.99
131_V	154_A	1.352	0.98
5_V	68_V	1.349	0.98
139_I	166_L	1.341	0.98
135_K	160_Q	1.331	0.98
51_L	76_A	1.329	0.98
146_K	158_E	1.324	0.98
22_W	173_S	1.320	0.98
99_F	140_V	1.320	0.98
26_R	178_Y	1.306	0.98
41_N	44_Q	1.270	0.98
53_T	57_Y	1.270	0.98
98_G	148_L	1.267	0.97
162_G	165_F	1.266	0.97
140_V	148_L	1.266	0.97
142_F	146_K	1.259	0.97
39_M	53_T	1.258	0.97
130_A	157_Y	1.248	0.97
58_Q	65_T	1.218	0.97
77_I	93_I	1.199	0.96
64_N	91_G	1.193	0.96
162_G	176_I	1.177	0.96
159_V	162_G	1.165	0.96
125_S	129_R	1.160	0.96
7_I	34_A	1.144	0.95
93_I	127_K	1.129	0.95
167_E	171_F	1.114	0.95
94_I	181_L	1.113	0.95
6_Y	57_Y	1.111	0.95
133_A	145_S	1.105	0.94
146_K	150_Q	1.100	0.94
162_G	170_G	1.097	0.94
146_K	156_L	1.092	0.94
80_F	84_L	1.089	0.94
28_L	34_A	1.085	0.94
23_L	27_L	1.081	0.94
22_W	26_R	1.072	0.93
52_D	56_L	1.064	0.93
61_L	65_T	1.053	0.93
7_I	24_K	1.050	0.93
15_S	21_P	1.048	0.93
92_G	128_H	1.047	0.93
92_G	130_A	1.043	0.93
55_S	83_H	1.032	0.92
13_A	38_N	1.025	0.92
11_Y	109_L	1.020	0.92
94_I	130_A	1.008	0.91
8_I	77_I	1.004	0.91
4_Q	61_L	0.989	0.90
4_Q	62_H	0.989	0.90
94_I	177_V	0.989	0.90
75_P	99_F	0.983	0.90
99_F	139_I	0.972	0.90
140_V	144_F	0.966	0.89
178_Y	183_S	0.962	0.89
24_K	28_L	0.946	0.88
23_L	181_L	0.945	0.88
55_S	84_L	0.926	0.87
45_P	72_L	0.920	0.87
144_F	147_D	0.914	0.87
4_Q	35_D	0.911	0.86
132_I	165_F	0.911	0.86
8_I	54_L	0.902	0.86
93_I	126_A	0.900	0.86
37_L	54_L	0.894	0.85
12_R	43_L	0.890	0.85
90_L	136_D	0.869	0.84
117_F	151_Q	0.858	0.83
89_Q	151_Q	0.858	0.83
75_P	115_G	0.857	0.83
47_L	83_H	0.857	0.83
148_L	151_Q	0.856	0.83
34_A	37_L	0.850	0.82
23_L	171_F	0.848	0.82
166_L	170_G	0.844	0.82
14_S	42_P	0.841	0.82
131_V	149_A	0.838	0.81
134_S	163_G	0.833	0.81
10_G	19_W	0.832	0.81
34_A	178_Y	0.832	0.81
99_F	144_F	0.830	0.81
4_Q	94_I	0.827	0.80
129_R	153_D	0.827	0.80
9_H	39_M	0.824	0.80
5_V	27_L	0.823	0.80
130_A	184_Y	0.822	0.80
4_Q	65_T	0.818	0.80
11_Y	106_L	0.816	0.80
171_F	174_L	0.813	0.79
13_A	166_L	0.812	0.79
60_T	88_K	0.810	0.79
144_F	148_L	0.807	0.79
147_D	150_Q	0.806	0.79
7_I	27_L	0.806	0.79
22_W	25_K	0.802	0.78
21_P	24_K	0.801	0.78
110_D	113_T	0.800	0.78
149_A	156_L	0.790	0.77
48_E	83_H	0.789	0.77
132_I	180_V	0.784	0.77
17_N	22_W	0.782	0.77
94_I	180_V	0.774	0.76
15_S	167_E	0.769	0.75
106_L	109_L	0.766	0.75
5_V	34_A	0.759	0.74
81_L	95_L	0.758	0.74
157_Y	180_V	0.752	0.74
71_S	166_L	0.750	0.74
102_S	144_F	0.747	0.73
7_I	68_V	0.741	0.73
58_Q	61_L	0.739	0.73
50_W	72_L	0.738	0.72
50_W	96_V	0.734	0.72
12_R	109_L	0.734	0.72
130_A	155_A	0.730	0.72
79_R	116_S	0.728	0.71
103_L	141_P	0.724	0.71
101_K	144_F	0.718	0.70
10_G	20_F	0.716	0.70
35_D	57_Y	0.705	0.69
14_S	166_L	0.703	0.69
51_L	79_R	0.702	0.69
10_G	71_S	0.697	0.68
20_F	71_S	0.693	0.68
98_G	131_V	0.690	0.67
93_I	131_V	0.687	0.67
74_C	140_V	0.686	0.67
20_F	98_G	0.680	0.66
124_E	153_D	0.675	0.66
60_T	179_D	0.674	0.65
5_V	181_L	0.673	0.65
72_L	75_P	0.671	0.65
13_A	42_P	0.667	0.65
147_D	151_Q	0.663	0.64
131_V	156_L	0.660	0.64
36_I	42_P	0.653	0.63
180_V	183_S	0.652	0.63
17_N	167_E	0.651	0.63
45_P	50_W	0.648	0.62
20_F	99_F	0.641	0.62
52_D	82_E	0.634	0.61
73_G	77_I	0.634	0.61
175_P	178_Y	0.633	0.61
48_E	52_D	0.623	0.59
15_S	36_I	0.621	0.59
41_N	49_D	0.619	0.59
74_C	78_L	0.618	0.59
24_K	34_A	0.616	0.59
26_R	63_E	0.611	0.58
42_P	50_W	0.607	0.57
99_F	103_L	0.600	0.57
39_M	45_P	0.600	0.57
8_I	67_L	0.598	0.56
66_Y	181_L	0.595	0.56
80_F	173_S	0.592	0.56
23_L	139_I	0.590	0.55
111_E	115_G	0.589	0.55
9_H	37_L	0.587	0.55
173_S	178_Y	0.586	0.55
98_G	140_V	0.585	0.55
133_A	158_E	0.583	0.54
176_I	180_V	0.581	0.54
83_H	150_Q	0.580	0.54
7_I	178_Y	0.580	0.54
138_Q	166_L	0.574	0.53
10_G	149_A	0.573	0.53
22_W	159_V	0.573	0.53
136_D	163_G	0.571	0.53
66_Y	91_G	0.571	0.53
163_G	166_L	0.570	0.53
96_V	165_F	0.570	0.53
39_M	42_P	0.566	0.52
163_G	169_E	0.564	0.52
40_P	46_R	0.559	0.51
52_D	58_Q	0.559	0.51
54_L	67_L	0.558	0.51
143_S	150_Q	0.557	0.51
177_V	181_L	0.556	0.51
68_V	128_H	0.555	0.51
5_V	179_D	0.549	0.50
100_A	132_I	0.546	0.50
72_L	99_F	0.545	0.50
90_L	175_P	0.543	0.49
10_G	96_V	0.542	0.49
160_Q	163_G	0.542	0.49
47_L	72_L	0.541	0.49
93_I	154_A	0.539	0.49
46_R	111_E	0.538	0.49
178_Y	182_T	0.536	0.48
49_D	88_K	0.535	0.48
179_D	182_T	0.534	0.48
10_G	18_H	0.533	0.48
79_R	112_F	0.527	0.47
113_T	118_D	0.527	0.47
16_T	25_K	0.526	0.47
69_A	99_F	0.520	0.46
42_P	177_V	0.519	0.46
159_V	165_F	0.519	0.46
72_L	139_I	0.518	0.46
49_D	53_T	0.518	0.46
45_P	76_A	0.515	0.46
103_L	109_L	0.513	0.46
10_G	14_S	0.513	0.46
100_A	152_I	0.512	0.45
155_A	180_V	0.512	0.45
152_I	163_G	0.511	0.45
98_G	144_F	0.510	0.45
97_S	139_I	0.509	0.45
63_E	89_Q	0.507	0.45
111_E	114_Q	0.501	0.44
58_Q	80_F	0.500	0.44

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
1uxoA	1	0.9684	100	0.477	Contact Map
2qs9A	1	0.9526	100	0.515	Contact Map
3bdvA	1	0.9158	99.9	0.553	Contact Map
2wtmA	2	0.9684	99.8	0.652	Contact Map
2qjwA	2	0.8684	99.8	0.655	Contact Map
1xklA	3	0.9474	99.8	0.663	Contact Map
4k5qA	1	0.9737	99.8	0.665	Contact Map
4fleA	1	0.8895	99.8	0.666	Contact Map
3hjuA	2	0.9789	99.8	0.666	Contact Map
3pfbA	2	0.9474	99.8	0.666	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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