Kdo_hydroxy - PFAM28P - GREMLIN Contacts

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Kdo_hydroxy - 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase

PFAM:	PF11004	Sequences: PERQRAACAALEAGKVLFFPRLPFALPEEERRFLSPQLLDGKAKNISYDPATGRLRGAAGDGADAERLRAMMRRFSAQATALVARLLPPYAGHLRLDRTSFRPVEEAGRDLSWRKDDDRLHVDAFPSRPTRGRRILRVFTNVNPSGEPRVWRVGEPFEALARRFAPRAGLPLPGSAALLRALGITKSRRSPYDHLMLQLHDRMKADADYQRNAPQQRVEFPPGSTWIVFTDQVSHAALSGQYALEQTFLLPVEAMVDPERSPLRILERLAGRPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	274 (271)
Sequences:	2152 (1493)
Seq/√Len:	90.7
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_T	225_T	4.266	1.00
18_F	221_P	4.083	1.00
208_D	212_N	3.634	1.00
150_V	217_R	3.026	1.00
105_E	147_E	2.902	1.00
203_M	234_S	2.856	1.00
251_P	254_A	2.804	1.00
75_F	140_T	2.737	1.00
53_G	73_R	2.732	1.00
95_R	133_R	2.724	1.00
97_D	249_L	2.620	1.00
152_R	215_Q	2.566	1.00
152_R	238_L	2.435	1.00
221_P	224_S	2.392	1.00
160_L	234_S	2.378	1.00
160_L	203_M	2.335	1.00
155_E	209_Y	2.322	1.00
158_E	162_R	2.310	1.00
209_Y	213_A	2.267	1.00
180_R	188_R	2.263	1.00
142_V	244_L	2.245	1.00
49_D	98_R	2.234	1.00
80_T	96_L	2.180	1.00
28_E	31_R	2.111	1.00
197_L	201_D	2.103	1.00
66_E	69_R	1.991	1.00
215_Q	238_L	1.976	1.00
113_W	205_A	1.971	1.00
80_T	248_F	1.961	1.00
131_R	190_S	1.948	1.00
150_V	219_E	1.931	1.00
83_V	138_V	1.919	1.00
18_F	224_S	1.912	1.00
33_F	67_R	1.908	1.00
177_A	181_A	1.903	1.00
39_L	104_V	1.899	1.00
159_A	162_R	1.898	1.00
80_T	84_A	1.896	1.00
177_A	183_G	1.880	1.00
138_V	225_T	1.874	1.00
70_A	74_R	1.844	1.00
13_A	260_R	1.839	1.00
270_A	273_P	1.838	1.00
264_R	267_E	1.833	1.00
148_P	219_E	1.833	1.00
47_S	56_R	1.779	1.00
89_P	256_V	1.758	1.00
58_A	62_G	1.739	1.00
169_G	198_Q	1.732	1.00
161_A	269_L	1.706	1.00
76_S	99_T	1.697	1.00
155_E	163_R	1.676	1.00
114_R	205_A	1.670	1.00
167_R	202_R	1.658	1.00
257_D	260_R	1.628	1.00
230_T	243_A	1.626	1.00
150_V	239_S	1.618	1.00
48_Y	53_G	1.594	1.00
158_E	268_R	1.593	1.00
84_A	91_A	1.560	1.00
112_S	115_K	1.548	1.00
10_A	15_K	1.526	1.00
61_D	64_D	1.516	1.00
83_V	94_L	1.509	1.00
49_D	52_T	1.489	1.00
29_E	67_R	1.487	1.00
105_E	109_R	1.474	1.00
79_A	138_V	1.462	1.00
108_G	118_D	1.432	0.99
119_R	207_A	1.417	0.99
26_L	34_L	1.411	0.99
84_A	92_G	1.402	0.99
198_Q	202_R	1.392	0.99
107_A	147_E	1.383	0.99
168_A	171_P	1.381	0.99
153_V	218_V	1.370	0.99
195_L	270_A	1.350	0.99
97_D	128_R	1.346	0.99
252_V	264_R	1.338	0.99
76_S	96_L	1.299	0.99
75_F	79_A	1.296	0.99
101_F	242_Y	1.289	0.99
83_V	227_I	1.287	0.99
73_R	77_A	1.280	0.99
8_C	89_P	1.280	0.99
71_M	101_F	1.278	0.99
154_G	213_A	1.258	0.98
58_A	68_L	1.253	0.98
168_A	202_R	1.248	0.98
39_L	42_K	1.228	0.98
19_F	82_L	1.225	0.98
58_A	65_A	1.215	0.98
178_L	182_L	1.211	0.98
32_R	64_D	1.204	0.98
213_A	234_S	1.198	0.98
161_A	265_I	1.185	0.98
175_S	183_G	1.183	0.98
167_R	206_D	1.182	0.98
93_H	253_E	1.177	0.98
106_E	118_D	1.175	0.98
78_Q	81_A	1.170	0.98
32_R	67_R	1.166	0.98
93_H	254_A	1.164	0.97
69_R	73_R	1.151	0.97
156_P	159_A	1.144	0.97
202_R	206_D	1.136	0.97
147_E	241_Q	1.134	0.97
143_N	147_E	1.126	0.97
155_E	159_A	1.123	0.97
7_A	10_A	1.113	0.97
24_F	138_V	1.112	0.97
261_S	265_I	1.107	0.97
207_A	211_R	1.106	0.97
177_A	188_R	1.104	0.97
81_A	85_R	1.100	0.96
168_A	199_L	1.098	0.96
98_R	128_R	1.089	0.96
252_V	263_L	1.088	0.96
258_P	264_R	1.076	0.96
252_V	255_M	1.076	0.96
6_A	10_A	1.074	0.96
199_L	206_D	1.064	0.96
28_E	32_R	1.063	0.96
169_G	175_S	1.059	0.96
130_T	133_R	1.056	0.96
143_N	242_Y	1.053	0.95
124_A	190_S	1.051	0.95
47_S	100_S	1.045	0.95
19_F	227_I	1.033	0.95
199_L	203_M	1.023	0.95
49_D	54_R	1.013	0.94
164_F	202_R	1.012	0.94
84_A	94_L	1.003	0.94
229_F	232_Q	0.999	0.94
165_A	168_A	0.997	0.94
77_A	96_L	0.992	0.94
232_Q	255_M	0.982	0.93
128_R	228_V	0.981	0.93
101_F	142_V	0.973	0.93
60_G	65_A	0.972	0.93
4_Q	7_A	0.959	0.93
263_L	267_E	0.952	0.92
155_E	213_A	0.950	0.92
100_S	135_I	0.948	0.92
143_N	241_Q	0.947	0.92
29_E	32_R	0.947	0.92
208_D	211_R	0.943	0.92
33_F	38_L	0.938	0.92
39_L	43_A	0.936	0.92
63_A	67_R	0.929	0.91
53_G	69_R	0.926	0.91
133_R	251_P	0.923	0.91
113_W	207_A	0.921	0.91
171_P	175_S	0.917	0.91
6_A	9_A	0.917	0.91
155_E	214_P	0.917	0.91
22_L	225_T	0.913	0.91
232_Q	265_I	0.913	0.91
65_A	69_R	0.908	0.90
75_F	225_T	0.904	0.90
271_G	274_L	0.903	0.90
66_E	70_A	0.900	0.90
139_F	230_T	0.894	0.90
255_M	260_R	0.893	0.90
5_R	9_A	0.891	0.90
114_R	201_D	0.887	0.89
170_L	195_L	0.883	0.89
4_Q	8_C	0.881	0.89
30_E	74_R	0.879	0.89
20_P	23_P	0.878	0.89
31_R	35_S	0.874	0.89
128_R	135_I	0.873	0.89
77_A	85_R	0.872	0.89
9_A	257_D	0.871	0.89
254_A	267_E	0.870	0.88
9_A	13_A	0.867	0.88
44_K	115_K	0.866	0.88
120_L	255_M	0.865	0.88
101_F	230_T	0.863	0.88
33_F	68_L	0.860	0.88
34_L	142_V	0.857	0.88
180_R	187_S	0.854	0.88
33_F	64_D	0.850	0.87
165_A	270_A	0.849	0.87
260_R	265_I	0.849	0.87
177_A	180_R	0.846	0.87
11_L	87_L	0.839	0.87
106_E	111_L	0.835	0.86
134_R	232_Q	0.830	0.86
152_R	217_R	0.829	0.86
122_V	237_A	0.821	0.85
165_A	170_L	0.819	0.85
172_L	175_S	0.818	0.85
67_R	70_A	0.814	0.85
103_P	237_A	0.813	0.85
15_K	18_F	0.812	0.85
156_P	232_Q	0.808	0.85
120_L	236_A	0.805	0.84
178_L	181_A	0.802	0.84
130_T	228_V	0.801	0.84
111_L	115_K	0.801	0.84
16_V	153_V	0.800	0.84
163_R	208_D	0.796	0.84
231_D	235_H	0.796	0.84
8_C	256_V	0.796	0.84
138_V	227_I	0.794	0.83
154_G	209_Y	0.791	0.83
220_F	224_S	0.788	0.83
86_L	227_I	0.786	0.83
47_S	98_R	0.778	0.82
200_H	204_K	0.777	0.82
106_E	243_A	0.776	0.82
171_P	174_G	0.775	0.82
163_R	167_R	0.775	0.82
38_L	43_A	0.771	0.82
44_K	200_H	0.771	0.82
38_L	41_G	0.766	0.81
115_K	201_D	0.765	0.81
115_K	130_T	0.764	0.81
140_T	222_P	0.761	0.81
260_R	264_R	0.758	0.81
217_R	238_L	0.757	0.80
161_A	165_A	0.757	0.80
104_V	108_G	0.753	0.80
191_P	195_L	0.750	0.80
261_S	264_R	0.750	0.80
170_L	191_P	0.746	0.79
162_R	269_L	0.745	0.79
74_R	78_Q	0.743	0.79
101_F	122_V	0.742	0.79
49_D	128_R	0.733	0.78
64_D	68_L	0.731	0.78
232_Q	260_R	0.731	0.78
56_R	60_G	0.727	0.78
154_G	215_Q	0.724	0.77
105_E	108_G	0.722	0.77
140_T	161_A	0.720	0.77
177_A	182_L	0.720	0.77
45_N	100_S	0.719	0.77
63_A	66_E	0.718	0.77
19_F	22_L	0.714	0.76
168_A	194_H	0.714	0.76
30_E	37_Q	0.711	0.76
105_E	111_L	0.706	0.76
249_L	252_V	0.704	0.75
252_V	261_S	0.704	0.75
72_M	219_E	0.698	0.75
67_R	71_M	0.697	0.75
104_V	111_L	0.697	0.75
127_S	184_I	0.696	0.75
188_R	191_P	0.695	0.75
11_L	14_G	0.695	0.75
168_A	195_L	0.685	0.73
153_V	222_P	0.683	0.73
118_D	195_L	0.678	0.73
168_A	180_R	0.678	0.73
131_R	188_R	0.674	0.72
228_V	233_V	0.672	0.72
24_F	30_E	0.670	0.72
165_A	191_P	0.669	0.72
82_L	86_L	0.669	0.72
38_L	42_K	0.666	0.71
48_Y	72_M	0.665	0.71
81_A	208_D	0.663	0.71
172_L	176_A	0.661	0.71
156_P	209_Y	0.659	0.71
63_A	73_R	0.656	0.70
112_S	218_V	0.656	0.70
45_N	200_H	0.654	0.70
30_E	33_F	0.649	0.69
94_L	250_L	0.649	0.69
203_M	255_M	0.649	0.69
158_E	260_R	0.647	0.69
77_A	81_A	0.646	0.69
74_R	77_A	0.644	0.69
237_A	246_Q	0.643	0.69
259_E	268_R	0.641	0.68
237_A	251_P	0.638	0.68
189_R	194_H	0.636	0.68
153_V	216_Q	0.636	0.68
48_Y	73_R	0.634	0.68
58_A	61_D	0.632	0.67
221_P	230_T	0.632	0.67
227_I	255_M	0.631	0.67
175_S	178_L	0.631	0.67
133_R	249_L	0.631	0.67
49_D	97_D	0.630	0.67
125_F	245_E	0.630	0.67
168_A	198_Q	0.630	0.67
33_F	37_Q	0.630	0.67
263_L	274_L	0.628	0.67
89_P	92_G	0.624	0.66
87_L	120_L	0.623	0.66
79_A	83_V	0.621	0.66
242_Y	270_A	0.620	0.66
130_T	227_I	0.618	0.66
8_C	88_P	0.616	0.65
96_L	237_A	0.615	0.65
131_R	187_S	0.615	0.65
127_S	197_L	0.615	0.65
111_L	203_M	0.611	0.65
33_F	71_M	0.608	0.64
33_F	41_G	0.607	0.64
115_K	143_N	0.606	0.64
176_A	188_R	0.605	0.64
167_R	173_P	0.602	0.64
111_L	118_D	0.599	0.63
112_S	134_R	0.596	0.63
44_K	47_S	0.596	0.63
114_R	232_Q	0.595	0.63
109_R	160_L	0.595	0.63
225_T	243_A	0.594	0.63
49_D	56_R	0.593	0.62
112_S	234_S	0.593	0.62
72_M	147_E	0.592	0.62
162_R	268_R	0.591	0.62
160_L	164_F	0.589	0.62
113_W	119_R	0.588	0.62
115_K	197_L	0.583	0.61
189_R	197_L	0.579	0.61
35_S	38_L	0.577	0.60
199_L	202_R	0.577	0.60
83_V	248_F	0.575	0.60
180_R	183_G	0.574	0.60
176_A	179_L	0.573	0.60
9_A	256_V	0.573	0.60
148_P	222_P	0.572	0.60
25_A	31_R	0.572	0.60
44_K	50_P	0.570	0.59
269_L	274_L	0.568	0.59
120_L	213_A	0.567	0.59
191_P	272_R	0.566	0.59
106_E	117_D	0.566	0.59
74_R	120_L	0.565	0.59
5_R	8_C	0.564	0.59
217_R	239_S	0.562	0.58
39_L	203_M	0.562	0.58
160_L	199_L	0.561	0.58
203_M	206_D	0.558	0.58
135_I	251_P	0.556	0.58
109_R	234_S	0.556	0.58
24_F	74_R	0.555	0.57
25_A	110_D	0.554	0.57
199_L	232_Q	0.553	0.57
179_L	183_G	0.552	0.57
127_S	189_R	0.552	0.57
125_F	200_H	0.550	0.57
155_E	216_Q	0.549	0.57
166_P	172_L	0.549	0.57
164_F	167_R	0.548	0.56
106_E	230_T	0.547	0.56
30_E	35_S	0.547	0.56
159_A	214_P	0.544	0.56
22_L	75_F	0.544	0.56
55_L	69_R	0.543	0.56
168_A	203_M	0.541	0.56
125_F	189_R	0.540	0.55
23_P	32_R	0.537	0.55
130_T	190_S	0.537	0.55
113_W	228_V	0.536	0.55
226_W	231_D	0.535	0.55
94_L	227_I	0.533	0.54
105_E	118_D	0.532	0.54
20_P	36_P	0.532	0.54
154_G	218_V	0.531	0.54
80_T	242_Y	0.531	0.54
178_L	250_L	0.530	0.54
58_A	64_D	0.527	0.54
76_S	80_T	0.527	0.54
48_Y	106_E	0.527	0.54
78_Q	85_R	0.525	0.53
113_W	118_D	0.523	0.53
198_Q	228_V	0.522	0.53
225_T	228_V	0.521	0.53
16_V	220_F	0.521	0.53
98_R	126_P	0.520	0.53
64_D	67_R	0.518	0.52
125_F	196_M	0.518	0.52
102_R	125_F	0.518	0.52
165_A	269_L	0.516	0.52
112_S	127_S	0.515	0.52
265_I	269_L	0.515	0.52
97_D	116_D	0.515	0.52
36_P	39_L	0.515	0.52
134_R	262_P	0.514	0.52
115_K	174_G	0.512	0.52
218_V	221_P	0.511	0.51
15_K	221_P	0.510	0.51
103_P	230_T	0.508	0.51
12_E	16_V	0.508	0.51
173_P	183_G	0.508	0.51
266_L	274_L	0.508	0.51
257_D	261_S	0.508	0.51
48_Y	130_T	0.506	0.51
158_E	232_Q	0.505	0.51
16_V	218_V	0.505	0.51
119_R	209_Y	0.504	0.50
262_P	266_L	0.504	0.50
219_E	243_A	0.504	0.50
45_N	109_R	0.504	0.50
176_A	191_P	0.503	0.50
47_S	218_V	0.503	0.50
169_G	172_L	0.501	0.50
257_D	265_I	0.501	0.50
79_A	99_T	0.501	0.50
205_A	222_P	0.500	0.50

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
3zytA	3	0.5584	22.6	0.973	Contact Map
4j25A	2	0.6606	18	0.974	Contact Map
4qu7A	1	0.2956	17.5	0.974	Contact Map
3d8cA	2	0.3248	15.6	0.975	Contact Map
2kxnB	1	0.3321	14.7	0.975	Contact Map
2qz6A	1	0.6058	14.5	0.975	Contact Map
1vrbA	2	0.3613	13.5	0.976	Contact Map
3fedA	2	0.3139	12.7	0.976	Contact Map
2mpuA	1	0.3212	12	0.976	Contact Map
4wkrA	1	0.2774	11.8	0.976	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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