YYAP - BACSU - GREMLIN Contacts

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YYAP - Uncharacterized protein YyaP

UniProt:	P37508	Sequences: MTNNLKQRRIILDLAVTLDGFIEGKNGEVDWCIMDPDMGFTDFLNQIDTILYGRKSFDLWGQYIPKNEDPDTEKELWKLVHSKKKYVFSRTQNEIDNQAIFINDNILEEVNKLKKNPGKDIWLYGGASLITTFINLGLVDEFRLSIHPVVLGEGKPLFIDVKQRINLKMVNTRTFSSGVVQIVYHWNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	188 (169)
Sequences:	5627 (3771)
Seq/√Len:	290.1

BACSU - YYAP YWJB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_I	182_I	4.038	1.00
54_R	58_D	3.518	1.00
168_K	185_H	3.206	1.00
134_I	142_F	3.012	1.00
12_L	130_I	2.952	1.00
170_V	185_H	2.653	1.00
105_N	108_E	2.609	1.00
84_K	100_I	2.412	1.00
22_I	127_A	2.343	1.00
141_E	183_V	2.320	1.00
128_S	132_T	2.293	1.00
112_K	116_N	2.280	1.00
88_F	129_L	2.261	1.00
8_R	118_G	2.258	1.00
49_T	86_Y	2.183	1.00
12_L	139_V	2.182	1.00
107_L	136_L	2.170	1.00
9_R	141_E	2.156	1.00
109_E	112_K	2.097	1.00
156_P	159_I	2.057	1.00
19_D	152_G	2.017	1.00
102_I	109_E	2.013	1.00
11_I	120_D	1.990	1.00
25_K	153_E	1.967	1.00
9_R	120_D	1.941	1.00
95_I	101_F	1.886	1.00
141_E	185_H	1.858	1.00
137_G	186_W	1.850	1.00
8_R	117_P	1.844	1.00
89_S	101_F	1.813	1.00
171_N	183_V	1.789	1.00
92_Q	101_F	1.773	1.00
112_K	115_K	1.648	1.00
46_Q	120_D	1.587	1.00
24_G	28_E	1.523	1.00
48_D	119_K	1.515	1.00
167_L	186_W	1.501	1.00
18_L	167_L	1.497	1.00
89_S	92_Q	1.420	1.00
143_R	183_V	1.413	1.00
147_H	179_V	1.402	1.00
139_V	142_F	1.386	1.00
107_L	111_N	1.367	1.00
23_E	155_K	1.364	1.00
86_Y	102_I	1.351	1.00
49_T	84_K	1.345	1.00
56_S	125_G	1.307	1.00
24_G	164_R	1.307	1.00
104_D	108_E	1.298	1.00
156_P	160_D	1.294	1.00
111_N	115_K	1.290	1.00
88_F	109_E	1.283	1.00
169_M	182_I	1.258	1.00
10_I	110_V	1.247	1.00
78_K	82_S	1.229	1.00
150_V	167_L	1.225	1.00
93_N	103_N	1.220	1.00
42_D	45_N	1.208	1.00
84_K	116_N	1.206	1.00
14_L	22_I	1.179	1.00
55_K	128_S	1.171	1.00
58_D	62_Q	1.169	1.00
41_T	45_N	1.150	1.00
95_I	99_A	1.134	1.00
88_F	102_I	1.130	1.00
9_R	185_H	1.120	1.00
36_P	39_G	1.115	1.00
169_M	172_T	1.100	1.00
49_T	121_I	1.089	1.00
21_F	156_P	1.072	1.00
143_R	181_Q	1.066	1.00
16_V	146_I	1.064	1.00
28_E	31_W	1.062	1.00
108_E	112_K	1.058	1.00
108_E	111_N	1.052	1.00
131_T	135_N	1.045	1.00
59_L	63_Y	1.040	1.00
142_F	167_L	1.037	1.00
169_M	180_V	1.036	1.00
54_R	90_R	1.032	1.00
15_A	147_H	1.021	1.00
145_S	181_Q	1.017	1.00
90_R	128_S	1.006	1.00
79_L	83_K	1.000	1.00
142_F	186_W	0.990	1.00
110_V	133_F	0.990	1.00
10_I	114_K	0.989	1.00
86_Y	116_N	0.977	1.00
35_D	39_G	0.976	1.00
16_V	22_I	0.973	1.00
104_D	112_K	0.972	1.00
17_T	151_L	0.964	1.00
35_D	38_M	0.962	1.00
171_N	174_T	0.962	1.00
135_N	161_V	0.951	1.00
170_V	183_V	0.947	1.00
145_S	179_V	0.945	1.00
134_I	139_V	0.934	1.00
16_V	144_L	0.933	1.00
153_E	160_D	0.931	1.00
27_G	55_K	0.929	1.00
14_L	127_A	0.915	1.00
135_N	162_K	0.913	1.00
42_D	46_Q	0.911	1.00
11_I	143_R	0.902	1.00
48_D	120_D	0.898	1.00
129_L	132_T	0.894	1.00
114_K	121_I	0.887	1.00
123_L	139_V	0.884	1.00
34_M	166_N	0.879	1.00
131_T	159_I	0.871	1.00
106_I	136_L	0.860	1.00
51_L	88_F	0.855	1.00
44_L	83_K	0.855	1.00
51_L	110_V	0.849	1.00
135_N	160_D	0.839	1.00
52_Y	60_W	0.837	1.00
12_L	126_G	0.835	1.00
173_R	181_Q	0.827	1.00
47_I	122_W	0.827	1.00
175_F	181_Q	0.825	1.00
57_F	61_G	0.823	1.00
132_T	136_L	0.820	1.00
137_G	165_I	0.819	1.00
54_R	92_Q	0.814	1.00
27_G	155_K	0.809	1.00
180_V	184_Y	0.807	1.00
86_Y	100_I	0.797	0.99
127_A	131_T	0.794	0.99
24_G	30_D	0.792	0.99
23_E	29_V	0.782	0.99
90_R	132_T	0.778	0.99
24_G	27_G	0.770	0.99
169_M	184_Y	0.770	0.99
8_R	48_D	0.766	0.99
13_D	143_R	0.765	0.99
52_Y	126_G	0.759	0.99
113_L	117_P	0.758	0.99
123_L	133_F	0.741	0.99
40_F	43_F	0.735	0.99
89_S	93_N	0.725	0.99
172_T	180_V	0.724	0.99
8_R	49_T	0.717	0.99
13_D	43_F	0.715	0.99
10_I	133_F	0.713	0.99
130_I	139_V	0.707	0.99
144_L	157_L	0.706	0.99
94_E	101_F	0.704	0.99
40_F	44_L	0.698	0.99
88_F	106_I	0.693	0.98
102_I	105_N	0.692	0.98
90_R	104_D	0.686	0.98
61_G	64_I	0.686	0.98
43_F	46_Q	0.684	0.98
86_Y	109_E	0.684	0.98
135_N	163_Q	0.684	0.98
50_I	83_K	0.681	0.98
55_K	58_D	0.674	0.98
10_I	123_L	0.674	0.98
43_F	143_R	0.673	0.98
166_N	169_M	0.672	0.98
51_L	133_F	0.672	0.98
150_V	165_I	0.671	0.98
109_E	113_L	0.666	0.98
62_Q	65_P	0.662	0.98
167_L	184_Y	0.661	0.98
132_T	135_N	0.661	0.98
141_E	170_V	0.660	0.98
42_D	173_R	0.658	0.98
48_D	117_P	0.647	0.98
14_L	130_I	0.647	0.98
54_R	91_T	0.644	0.98
100_I	109_E	0.636	0.97
14_L	126_G	0.631	0.97
38_M	179_V	0.631	0.97
91_T	95_I	0.630	0.97
103_N	109_E	0.629	0.97
102_I	106_I	0.627	0.97
45_N	79_L	0.627	0.97
134_I	186_W	0.620	0.97
59_L	62_Q	0.620	0.97
13_D	124_Y	0.616	0.97
172_T	182_I	0.615	0.97
161_V	164_R	0.611	0.97
49_T	118_G	0.610	0.97
15_A	32_C	0.608	0.97
29_V	59_L	0.607	0.97
14_L	157_L	0.605	0.96
85_K	98_Q	0.602	0.96
48_D	121_I	0.598	0.96
174_T	178_G	0.595	0.96
104_D	109_E	0.594	0.96
18_L	150_V	0.592	0.96
161_V	165_I	0.589	0.96
106_I	132_T	0.587	0.96
23_E	28_E	0.587	0.96
15_A	40_F	0.587	0.96
100_I	116_N	0.583	0.96
102_I	112_K	0.580	0.96
163_Q	166_N	0.580	0.96
23_E	27_G	0.578	0.95
58_D	61_G	0.576	0.95
13_D	122_W	0.569	0.95
111_N	136_L	0.569	0.95
48_D	118_G	0.569	0.95
21_F	155_K	0.568	0.95
175_F	178_G	0.568	0.95
52_Y	79_L	0.567	0.95
61_G	65_P	0.566	0.95
46_Q	143_R	0.566	0.95
123_L	126_G	0.565	0.95
174_T	180_V	0.562	0.95
58_D	92_Q	0.561	0.95
128_S	155_K	0.561	0.95
105_N	109_E	0.560	0.95
13_D	40_F	0.559	0.95
133_F	138_L	0.558	0.94
22_I	155_K	0.558	0.94
127_A	155_K	0.557	0.94
31_W	34_M	0.556	0.94
41_T	44_L	0.553	0.94
13_D	145_S	0.551	0.94
50_I	124_Y	0.550	0.94
105_N	111_N	0.548	0.94
85_K	99_A	0.546	0.94
85_K	97_N	0.545	0.94
21_F	153_E	0.545	0.94
13_D	32_C	0.544	0.94
50_I	122_W	0.542	0.94
43_F	47_I	0.541	0.94
60_W	85_K	0.541	0.94
78_K	81_H	0.540	0.93
128_S	131_T	0.540	0.93
35_D	177_S	0.540	0.93
121_I	125_G	0.538	0.93
91_T	94_E	0.536	0.93
35_D	176_S	0.532	0.93
56_S	126_G	0.529	0.93
64_I	97_N	0.520	0.92
146_I	180_V	0.516	0.92
86_Y	118_G	0.516	0.92
33_I	147_H	0.515	0.92
39_G	43_F	0.511	0.92
44_L	79_L	0.511	0.92
60_W	124_Y	0.510	0.91
15_A	126_G	0.508	0.91
120_D	123_L	0.506	0.91
36_P	176_S	0.505	0.91
30_D	34_M	0.505	0.91
106_I	133_F	0.503	0.91
131_T	134_I	0.501	0.91
53_G	56_S	0.500	0.91
23_E	127_A	0.500	0.91
11_I	122_W	0.500	0.91

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
2gd9A	2	0.9521	100	0.31	Contact Map
3jtwA	2	0.9096	100	0.374	Contact Map
3ky8A	2	0.9309	100	0.39	Contact Map
3kgyA	2	0.9255	100	0.391	Contact Map
2xw7A	2	0.8777	100	0.393	Contact Map
3nrrA	2	0.8883	100	0.408	Contact Map
3qg2A	2	0.9149	100	0.413	Contact Map
1cz3A	2	0.867	100	0.417	Contact Map
3ix9A	2	0.8511	100	0.421	Contact Map
3zpgA	2	0.9787	100	0.425	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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