YPBD - BACSU - GREMLIN Contacts

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YPBD - Uncharacterized protein YpbD

UniProt:	P50730	Sequences: MTQLLIIFAAAAAGLFFFEDVRDVLKLWDIRDMRIIWYGVSIAVIVILADMAVMKWFPSHLYDDGGINKKIFSKRSIPHIIFLTLLIAFAEEMLFRGVLQTHIGLWTASLIFAALHFRYLSKWLLFIMVTAISFLLGLMYEWTGNLFVPMTAHFIIDAVFACQIRFEHVRRDKHDEHVESREKKSPESL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	189 (157)
Sequences:	2348 (2073)
Seq/√Len:	165.4

BACSU - YPBD YDIL YYAK
HALSA - Q9HMZ0 Q9HS87 Q9HNQ5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
145_N	148_V	3.915	1.00
84_T	158_A	3.802	1.00
100_Q	141_E	3.340	1.00
88_A	154_F	3.338	1.00
139_M	152_A	3.304	1.00
109_S	134_F	3.277	1.00
113_A	130_T	3.264	1.00
105_L	137_G	3.032	1.00
100_Q	137_G	2.949	1.00
105_L	141_E	2.800	1.00
156_I	160_F	2.764	1.00
110_L	130_T	2.749	1.00
122_K	125_L	2.589	1.00
113_A	129_V	2.521	1.00
125_L	129_V	2.517	1.00
147_F	150_M	2.441	1.00
87_I	154_F	2.394	1.00
140_Y	149_P	2.143	1.00
95_F	115_L	2.126	1.00
105_L	134_F	2.124	1.00
138_L	142_W	2.116	1.00
109_S	130_T	2.111	1.00
38_Y	42_I	1.855	1.00
89_F	150_M	1.839	1.00
140_Y	143_T	1.766	1.00
108_A	137_G	1.744	1.00
69_K	73_S	1.690	1.00
106_W	134_F	1.640	1.00
100_Q	108_A	1.594	1.00
139_M	148_V	1.492	1.00
113_A	133_S	1.477	1.00
136_L	152_A	1.456	1.00
122_K	129_V	1.440	1.00
109_S	137_G	1.433	1.00
84_T	87_I	1.427	1.00
125_L	128_M	1.402	1.00
88_A	157_D	1.372	1.00
128_M	156_I	1.359	1.00
43_A	47_I	1.310	1.00
145_N	149_P	1.301	1.00
108_A	133_S	1.290	1.00
98_V	102_H	1.286	1.00
136_L	149_P	1.275	1.00
25_L	28_W	1.269	1.00
155_I	158_A	1.268	1.00
84_T	88_A	1.247	1.00
35_I	39_G	1.207	1.00
130_T	134_F	1.206	1.00
134_F	138_L	1.193	1.00
19_E	22_R	1.189	1.00
139_M	149_P	1.177	1.00
83_L	87_I	1.174	1.00
97_G	101_T	1.126	1.00
39_G	43_A	1.111	1.00
36_I	40_V	1.108	1.00
126_F	129_V	1.107	1.00
84_T	161_A	1.107	1.00
103_I	107_T	1.087	1.00
64_D	68_N	1.070	0.99
99_L	111_I	1.069	0.99
58_P	67_I	1.068	0.99
25_L	29_D	1.053	0.99
132_I	136_L	1.051	0.99
79_H	83_L	1.041	0.99
59_S	62_Y	1.037	0.99
27_L	30_I	1.017	0.99
87_I	150_M	1.016	0.99
57_F	60_H	0.990	0.99
100_Q	105_L	0.990	0.99
50_D	53_V	0.972	0.99
104_G	108_A	0.969	0.99
122_K	126_F	0.966	0.99
65_G	68_N	0.960	0.99
14_G	18_F	0.956	0.99
30_I	41_S	0.956	0.99
97_G	145_N	0.953	0.99
58_P	61_L	0.947	0.99
138_L	148_V	0.946	0.99
66_G	69_K	0.944	0.99
6_I	9_A	0.940	0.99
85_L	154_F	0.924	0.98
41_S	45_I	0.908	0.98
97_G	146_L	0.906	0.98
108_A	140_Y	0.895	0.98
132_I	152_A	0.889	0.98
109_S	133_S	0.888	0.98
37_W	41_S	0.885	0.98
57_F	62_Y	0.883	0.98
85_L	89_F	0.882	0.98
113_A	125_L	0.866	0.98
37_W	51_M	0.855	0.97
47_I	54_M	0.855	0.97
55_K	58_P	0.847	0.97
51_M	58_P	0.844	0.97
66_G	70_K	0.842	0.97
103_I	145_N	0.841	0.97
115_L	122_K	0.839	0.97
6_I	10_A	0.837	0.97
9_A	12_A	0.834	0.97
65_G	69_K	0.822	0.97
25_L	144_G	0.818	0.97
154_F	158_A	0.817	0.97
77_I	81_I	0.809	0.97
69_K	110_L	0.801	0.96
51_M	54_M	0.798	0.96
29_D	32_D	0.786	0.96
51_M	55_K	0.784	0.96
128_M	160_F	0.784	0.96
137_G	141_E	0.782	0.96
109_S	113_A	0.781	0.96
36_I	43_A	0.778	0.96
24_V	31_R	0.776	0.96
117_F	122_K	0.770	0.95
65_G	70_K	0.769	0.95
67_I	75_R	0.760	0.95
15_L	19_E	0.757	0.95
137_G	149_P	0.755	0.95
44_V	48_L	0.751	0.95
67_I	71_I	0.747	0.95
94_L	98_V	0.744	0.94
52_A	55_K	0.743	0.94
47_I	50_D	0.741	0.94
101_T	104_G	0.740	0.94
113_A	126_F	0.736	0.94
50_D	54_M	0.732	0.94
57_F	61_L	0.732	0.94
104_G	129_V	0.732	0.94
39_G	46_V	0.731	0.94
102_H	128_M	0.729	0.94
7_I	13_A	0.728	0.94
80_I	154_F	0.726	0.94
108_A	126_F	0.724	0.94
63_D	70_K	0.724	0.94
58_P	62_Y	0.723	0.94
151_T	154_F	0.722	0.94
117_F	126_F	0.722	0.94
144_G	149_P	0.716	0.93
90_A	132_I	0.714	0.93
10_A	13_A	0.712	0.93
40_V	151_T	0.706	0.93
80_I	161_A	0.689	0.92
34_R	40_V	0.688	0.92
129_V	145_N	0.685	0.92
33_M	36_I	0.684	0.92
150_M	154_F	0.684	0.92
101_T	140_Y	0.683	0.92
86_L	90_A	0.679	0.91
99_L	108_A	0.677	0.91
9_A	13_A	0.663	0.90
69_K	72_F	0.659	0.90
31_R	44_V	0.658	0.90
98_V	115_L	0.657	0.90
133_S	137_G	0.656	0.90
20_D	23_D	0.654	0.90
126_F	130_T	0.650	0.89
33_M	44_V	0.643	0.89
28_W	31_R	0.642	0.89
13_A	17_F	0.641	0.89
104_G	132_I	0.638	0.89
93_M	150_M	0.632	0.88
101_T	142_W	0.629	0.88
36_I	39_G	0.627	0.88
100_Q	140_Y	0.624	0.87
82_F	86_L	0.623	0.87
151_T	155_I	0.623	0.87
48_L	51_M	0.621	0.87
10_A	16_F	0.620	0.87
81_I	85_L	0.615	0.87
28_W	40_V	0.615	0.87
74_K	126_F	0.615	0.87
88_A	165_R	0.612	0.86
99_L	109_S	0.607	0.86
159_V	163_Q	0.607	0.86
15_L	21_V	0.606	0.86
114_A	144_G	0.599	0.85
18_F	23_D	0.598	0.85
72_F	76_S	0.595	0.85
124_L	128_M	0.593	0.85
102_H	148_V	0.591	0.84
9_A	17_F	0.589	0.84
7_I	11_A	0.588	0.84
87_I	157_D	0.587	0.84
129_V	156_I	0.587	0.84
23_D	27_L	0.586	0.84
125_L	145_N	0.581	0.83
110_L	151_T	0.580	0.83
21_V	24_V	0.580	0.83
46_V	50_D	0.576	0.83
10_A	14_G	0.575	0.83
132_I	156_I	0.574	0.83
157_D	161_A	0.571	0.82
34_R	39_G	0.570	0.82
40_V	43_A	0.568	0.82
147_F	151_T	0.567	0.82
48_L	52_A	0.567	0.82
146_L	149_P	0.563	0.82
11_A	106_W	0.563	0.82
104_G	125_L	0.561	0.81
140_Y	145_N	0.560	0.81
74_K	159_V	0.558	0.81
45_I	49_A	0.555	0.81
148_V	151_T	0.553	0.80
105_L	109_S	0.552	0.80
128_M	143_T	0.551	0.80
20_D	24_V	0.551	0.80
93_M	98_V	0.551	0.80
98_V	146_L	0.550	0.80
88_A	108_A	0.548	0.80
13_A	18_F	0.544	0.79
70_K	73_S	0.541	0.79
7_I	20_D	0.538	0.79
24_V	37_W	0.538	0.79
33_M	47_I	0.536	0.78
94_L	99_L	0.533	0.78
36_I	73_S	0.532	0.78
39_G	47_I	0.531	0.78
78_P	83_L	0.531	0.78
88_A	113_A	0.530	0.78
114_A	129_V	0.530	0.78
66_G	72_F	0.529	0.77
83_L	88_A	0.529	0.77
122_K	128_M	0.528	0.77
33_M	42_I	0.525	0.77
7_I	93_M	0.524	0.77
59_S	63_D	0.524	0.77
17_F	46_V	0.523	0.77
100_Q	129_V	0.515	0.75
11_A	35_I	0.515	0.75
44_V	162_C	0.515	0.75
65_G	76_S	0.513	0.75
97_G	156_I	0.513	0.75
100_Q	104_G	0.510	0.75
12_A	134_F	0.508	0.75
33_M	38_Y	0.505	0.74
105_L	156_I	0.502	0.74
42_I	46_V	0.500	0.73

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
4cadC	1	0.8942	99.8	0.545	Contact Map
4n7wA	2	0.8571	16.9	0.933	Contact Map
4w6vA	1	0.7619	12.8	0.936	Contact Map
3zuxA	1	0.8466	11.4	0.937	Contact Map
3w4tA	1	0.8201	7.7	0.942	Contact Map
4rp9A	2	0.9788	4.7	0.948	Contact Map
4j05A	3	0.7884	4.6	0.948	Contact Map
2wswA	3	0.8042	3.8	0.95	Contact Map
4c7rA	3	0.8571	3.8	0.95	Contact Map
4eneA	2	0.9418	3.5	0.951	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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