YKVQ - BACSU - GREMLIN Contacts

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YKVQ - Putative glycosylase YkvQ

UniProt:	O31682	Sequences: MFQMSYYYSGLGWDFIQHVDQTNGVLNVVSPDFFYIRKDGSLLLRSANPDVIKALHRRKLKVVPFLSNHWDQDLGRFALMNRVLLAKQISHAIEELDLDGVNIDIENLTEKDRNLFTDFIRLVRKSIPRHKEVSVAVAANPFGWTKGWHGSYDYEYLAKYADYLMVMAYDESRLAGPTASVGWVEKSIQYVLTQKISPQKLVLGLPFYGRCWMEGQSASQAIPLYLVVSKKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	232 (208)
Sequences:	5426 (3955)
Seq/√Len:	274.2

BACSU - YKVQ YAAH YDHD YVBX
HALSA - Q9HR84 Q9HR83

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_R	122_L	3.329	1.00
124_R	128_P	3.234	1.00
185_E	189_Q	3.174	1.00
153_D	156_Y	3.081	1.00
87_K	126_S	2.916	1.00
137_V	161_A	2.762	1.00
91_H	95_E	2.680	1.00
86_A	122_L	2.592	1.00
34_F	64_P	2.485	1.00
121_R	160_Y	2.340	1.00
182_G	185_E	2.266	1.00
89_I	101_V	2.192	1.00
83_V	87_K	2.174	1.00
158_A	197_S	2.167	1.00
112_D	115_L	2.130	1.00
120_I	157_L	2.074	1.00
179_A	206_P	2.064	1.00
103_I	120_I	2.045	1.00
192_L	198_P	2.013	1.00
184_V	203_L	2.009	1.00
76_R	112_D	1.980	1.00
166_V	188_I	1.929	1.00
158_A	164_L	1.906	1.00
94_E	131_K	1.869	1.00
124_R	135_V	1.834	1.00
83_V	122_L	1.831	1.00
139_A	191_V	1.797	1.00
117_T	156_Y	1.724	1.00
47_A	50_D	1.723	1.00
117_T	153_D	1.722	1.00
93_I	133_V	1.716	1.00
83_V	126_S	1.705	1.00
86_A	123_V	1.702	1.00
90_S	126_S	1.648	1.00
190_Y	194_Q	1.634	1.00
86_A	126_S	1.624	1.00
37_R	41_S	1.614	1.00
61_K	99_D	1.608	1.00
188_I	203_L	1.562	1.00
63_V	134_S	1.530	1.00
121_R	156_Y	1.502	1.00
79_L	119_F	1.495	1.00
120_I	161_A	1.492	1.00
158_A	200_K	1.492	1.00
9_S	12_G	1.466	1.00
168_A	203_L	1.445	1.00
161_A	164_L	1.442	1.00
114_N	153_D	1.403	1.00
122_L	126_S	1.384	1.00
171_E	180_S	1.378	1.00
17_Q	20_D	1.370	1.00
127_I	133_V	1.359	1.00
118_D	121_R	1.355	1.00
163_Y	202_V	1.337	1.00
50_D	62_V	1.336	1.00
189_Q	193_T	1.336	1.00
137_V	157_L	1.323	1.00
156_Y	159_K	1.321	1.00
30_S	65_F	1.317	1.00
158_A	196_I	1.285	1.00
63_V	136_A	1.284	1.00
139_A	164_L	1.279	1.00
64_P	92_A	1.275	1.00
86_A	90_S	1.270	1.00
35_Y	71_D	1.261	1.00
103_I	123_V	1.258	1.00
117_T	160_Y	1.252	1.00
94_E	133_V	1.236	1.00
121_R	125_K	1.236	1.00
28_V	63_V	1.212	1.00
106_E	167_M	1.211	1.00
93_I	101_V	1.209	1.00
104_D	167_M	1.199	1.00
63_V	100_G	1.191	1.00
120_I	160_Y	1.188	1.00
138_A	167_M	1.185	1.00
54_A	58_R	1.183	1.00
78_A	81_N	1.179	1.00
30_S	165_M	1.163	1.00
196_I	201_L	1.152	1.00
171_E	187_S	1.148	1.00
80_M	115_L	1.138	1.00
77_F	80_M	1.137	1.00
113_R	153_D	1.131	1.00
114_N	118_D	1.131	1.00
164_L	196_I	1.131	1.00
102_N	138_A	1.130	1.00
87_K	91_H	1.123	1.00
169_Y	204_G	1.116	1.00
102_N	136_A	1.116	1.00
48_N	52_I	1.113	1.00
28_V	134_S	1.112	1.00
47_A	51_V	1.096	1.00
171_E	184_V	1.095	1.00
154_Y	196_I	1.093	1.00
82_R	118_D	1.088	1.00
113_R	151_S	1.087	1.00
40_G	43_L	1.087	1.00
142_F	147_G	1.085	1.00
52_I	55_L	1.081	1.00
19_V	49_P	1.068	1.00
122_L	125_K	1.062	1.00
90_S	94_E	1.061	1.00
125_K	160_Y	1.059	1.00
116_F	137_V	1.052	1.00
79_L	105_I	1.023	1.00
75_G	79_L	1.015	1.00
23_N	57_R	1.015	1.00
165_M	202_V	1.009	1.00
128_P	132_E	1.003	1.00
188_I	192_L	1.002	1.00
102_N	165_M	0.997	1.00
170_D	210_R	0.996	1.00
154_Y	191_V	0.996	1.00
181_V	185_E	0.992	1.00
197_S	200_K	0.984	1.00
62_V	99_D	0.982	1.00
52_I	56_H	0.979	1.00
178_T	210_R	0.979	1.00
38_K	42_L	0.979	1.00
37_R	44_L	0.975	1.00
155_E	159_K	0.973	1.00
92_A	96_L	0.973	1.00
167_M	208_Y	0.969	1.00
22_T	25_V	0.954	1.00
30_S	63_V	0.951	1.00
136_A	165_M	0.949	1.00
53_K	57_R	0.949	1.00
48_N	51_V	0.949	1.00
189_Q	192_L	0.943	1.00
41_S	45_R	0.942	1.00
50_D	53_K	0.939	1.00
113_R	117_T	0.931	1.00
109_T	112_D	0.929	1.00
51_V	62_V	0.923	1.00
118_D	122_L	0.922	1.00
123_V	127_I	0.921	1.00
188_I	201_L	0.918	1.00
124_R	160_Y	0.915	1.00
106_E	138_A	0.905	1.00
134_S	163_Y	0.903	1.00
28_V	61_K	0.887	1.00
126_S	129_R	0.879	1.00
56_H	99_D	0.877	1.00
71_D	74_L	0.873	1.00
190_Y	193_T	0.856	1.00
64_P	98_L	0.851	1.00
141_P	187_S	0.850	1.00
78_A	85_L	0.849	1.00
85_L	89_I	0.847	1.00
37_R	42_L	0.841	1.00
79_L	115_L	0.834	1.00
39_D	42_L	0.833	1.00
116_F	120_I	0.832	1.00
53_K	60_L	0.828	0.99
23_N	60_L	0.821	0.99
16_I	22_T	0.820	0.99
23_N	26_L	0.820	0.99
75_G	78_A	0.818	0.99
157_L	161_A	0.816	0.99
154_Y	194_Q	0.809	0.99
101_V	135_V	0.809	0.99
28_V	163_Y	0.803	0.99
78_A	86_A	0.788	0.99
54_A	57_R	0.787	0.99
84_L	88_Q	0.782	0.99
38_K	41_S	0.781	0.99
106_E	169_Y	0.781	0.99
33_F	106_E	0.781	0.99
34_F	66_L	0.779	0.99
82_R	86_A	0.774	0.99
84_L	87_K	0.773	0.99
32_D	65_F	0.768	0.99
120_I	137_V	0.764	0.99
69_H	107_N	0.762	0.99
33_F	65_F	0.762	0.99
61_K	134_S	0.759	0.99
76_R	80_M	0.759	0.99
57_R	60_L	0.757	0.99
140_N	151_S	0.756	0.99
164_L	191_V	0.748	0.99
119_F	123_V	0.746	0.99
111_K	115_L	0.746	0.99
172_S	176_G	0.744	0.99
155_E	158_A	0.742	0.99
157_L	164_L	0.741	0.99
89_I	123_V	0.736	0.99
93_I	97_D	0.728	0.99
129_R	132_E	0.727	0.99
77_F	81_N	0.726	0.99
24_G	57_R	0.726	0.99
80_M	111_K	0.724	0.99
176_G	212_W	0.722	0.99
91_H	94_E	0.719	0.99
127_I	135_V	0.714	0.98
71_D	75_G	0.712	0.98
76_R	79_L	0.711	0.98
53_K	58_R	0.711	0.98
90_S	133_V	0.710	0.98
134_S	162_D	0.710	0.98
66_L	85_L	0.709	0.98
117_T	121_R	0.704	0.98
148_W	151_S	0.703	0.98
37_R	40_G	0.703	0.98
40_G	44_L	0.699	0.98
186_K	190_Y	0.695	0.98
82_R	115_L	0.693	0.98
36_I	78_A	0.692	0.98
168_A	202_V	0.691	0.98
34_F	96_L	0.690	0.98
139_A	154_Y	0.688	0.98
136_A	163_Y	0.687	0.98
76_R	115_L	0.686	0.98
166_V	191_V	0.686	0.98
38_K	45_R	0.685	0.98
202_V	206_P	0.682	0.98
39_D	43_L	0.676	0.98
54_A	60_L	0.676	0.98
216_Q	219_S	0.674	0.98
18_H	21_Q	0.673	0.98
141_P	171_E	0.672	0.98
120_I	124_R	0.672	0.98
170_D	208_Y	0.670	0.98
147_G	151_S	0.665	0.98
138_A	169_Y	0.664	0.98
152_Y	157_L	0.663	0.98
13_W	17_Q	0.663	0.98
146_K	150_G	0.660	0.97
115_L	118_D	0.654	0.97
156_Y	160_Y	0.653	0.97
191_V	201_L	0.653	0.97
55_L	59_K	0.651	0.97
90_S	127_I	0.649	0.97
33_F	138_A	0.645	0.97
50_D	54_A	0.644	0.97
54_A	62_V	0.643	0.97
37_R	43_L	0.638	0.97
40_G	84_L	0.637	0.97
49_P	53_K	0.636	0.97
31_P	98_L	0.633	0.97
41_S	84_L	0.627	0.97
104_D	138_A	0.627	0.97
104_D	208_Y	0.624	0.97
89_I	93_I	0.620	0.96
83_V	125_K	0.610	0.96
16_I	20_D	0.610	0.96
74_L	78_A	0.609	0.96
76_R	109_T	0.608	0.96
65_F	68_N	0.607	0.96
90_S	93_I	0.603	0.96
140_N	149_H	0.599	0.96
47_A	52_I	0.598	0.96
140_N	152_Y	0.597	0.96
90_S	128_P	0.596	0.95
87_K	90_S	0.591	0.95
48_N	53_K	0.591	0.95
73_D	77_F	0.590	0.95
128_P	131_K	0.590	0.95
29_V	60_L	0.586	0.95
167_M	170_D	0.586	0.95
177_P	180_S	0.586	0.95
101_V	123_V	0.583	0.95
187_S	191_V	0.582	0.95
55_L	58_R	0.579	0.95
34_F	92_A	0.578	0.95
101_V	127_I	0.575	0.95
26_L	29_V	0.572	0.94
114_N	156_Y	0.569	0.94
86_A	118_D	0.569	0.94
121_R	159_K	0.567	0.94
102_N	106_E	0.567	0.94
68_N	75_G	0.561	0.94
75_G	103_I	0.560	0.94
72_Q	76_R	0.559	0.94
56_H	62_V	0.557	0.94
183_W	186_K	0.555	0.93
30_S	163_Y	0.554	0.93
63_V	165_M	0.553	0.93
192_L	201_L	0.553	0.93
155_E	195_K	0.552	0.93
157_L	160_Y	0.552	0.93
103_I	119_F	0.550	0.93
114_N	121_R	0.549	0.93
107_N	148_W	0.545	0.93
80_M	112_D	0.540	0.92
175_A	215_G	0.535	0.92
113_R	157_L	0.535	0.92
10_G	14_D	0.532	0.92
9_S	17_Q	0.532	0.92
135_V	161_A	0.532	0.92
94_E	132_E	0.531	0.92
34_F	98_L	0.531	0.92
93_I	98_L	0.531	0.92
69_H	72_Q	0.530	0.92
35_Y	43_L	0.528	0.92
65_F	102_N	0.528	0.92
105_I	119_F	0.527	0.92
179_A	184_V	0.527	0.92
104_D	169_Y	0.523	0.91
12_G	15_F	0.522	0.91
36_I	85_L	0.519	0.91
172_S	177_P	0.515	0.91
199_Q	202_V	0.512	0.90
100_G	205_L	0.511	0.90
63_V	209_G	0.509	0.90
132_E	162_D	0.506	0.90
125_K	129_R	0.505	0.90
51_V	98_L	0.504	0.90
107_N	167_M	0.503	0.90
50_D	60_L	0.501	0.89
125_K	128_P	0.501	0.89
92_A	95_E	0.500	0.89

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
3w4rA	1	0.9914	100	0.156	Contact Map
1itxA	1	0.9871	100	0.158	Contact Map
1vf8A	1	0.9828	100	0.162	Contact Map
1wb0A	2	0.9828	100	0.163	Contact Map
3fy1A	1	0.9828	100	0.163	Contact Map
4wkaA	1	0.9828	100	0.17	Contact Map
3arxA	1	0.9871	100	0.177	Contact Map
1ll7A	1	0.9698	100	0.177	Contact Map
1edqA	1	0.9784	100	0.179	Contact Map
1w9pA	1	0.9698	100	0.179	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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