YPDP - BACSU - GREMLIN Contacts

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YPDP - Uncharacterized protein YpdP

UniProt:	P54163	Sequences: MFNNSFWIFFAIIHFIIVLLFYKGFGKMGLFVWIGFATVCANLQVVKTVELFGLTATLGNVMYGTIFFATDVLNEKYGPAEARKAVWLGFSTLLTLTFVMQGVLLFEPASSDISQTALETIFGFLPRVALGSLLAFIFSQTLDVYVYSAIRRIFPSDRLLWLRNGGSTAVSQLFDTFIFTAVAFLGIYPADVWLHIFISTYLIKFAVSLISLPYAYAAKKMIPNDERSS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	229 (200)
Sequences:	1637 (1016)
Seq/√Len:	71.8

ECOLI - YHHQ
BACSU - YPDP
HALSA - Q9HN39

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_L	174_F	5.081	1.00
134_L	182_V	4.303	1.00
161_W	216_Y	3.472	1.00
73_L	85_A	2.950	1.00
149_A	152_R	2.900	1.00
131_G	182_V	2.811	1.00
178_I	182_V	2.688	1.00
117_A	120_T	2.568	1.00
127_R	186_G	2.361	1.00
134_L	178_I	2.336	1.00
31_F	85_A	2.264	1.00
71_D	167_S	2.232	1.00
87_W	141_T	2.198	1.00
176_T	204_K	2.193	1.00
49_V	106_F	2.142	1.00
173_L	201_Y	2.118	1.00
189_P	192_V	2.107	1.00
116_T	119_E	2.096	1.00
127_R	184_F	2.064	1.00
177_F	197_F	2.011	1.00
89_G	136_F	1.997	1.00
115_Q	119_E	1.976	1.00
149_A	153_I	1.927	1.00
74_N	148_S	1.919	1.00
80_A	83_R	1.894	1.00
173_L	177_F	1.839	1.00
87_W	91_S	1.825	1.00
146_V	150_I	1.803	1.00
37_A	66_I	1.799	1.00
169_A	201_Y	1.793	1.00
142_L	170_V	1.781	1.00
42_N	132_S	1.774	1.00
165_G	212_L	1.768	1.00
138_F	174_F	1.693	1.00
139_S	171_S	1.676	1.00
179_F	183_A	1.673	1.00
35_G	39_V	1.641	0.99
138_F	178_I	1.626	0.99
39_V	96_L	1.602	0.99
142_L	146_V	1.547	0.99
104_L	119_E	1.540	0.99
57_T	200_T	1.529	0.99
70_T	143_D	1.499	0.99
143_D	171_S	1.487	0.99
169_A	205_F	1.481	0.99
159_L	162_L	1.469	0.99
63_Y	139_S	1.465	0.99
45_V	57_T	1.434	0.99
193_W	197_F	1.418	0.98
164_N	212_L	1.416	0.98
140_Q	144_V	1.390	0.98
68_F	215_A	1.389	0.98
32_V	88_L	1.364	0.98
57_T	180_T	1.350	0.98
58_L	106_F	1.340	0.98
192_V	195_H	1.335	0.98
150_I	157_D	1.328	0.98
145_Y	149_A	1.316	0.98
75_E	163_R	1.311	0.97
212_L	216_Y	1.293	0.97
45_V	60_N	1.287	0.97
143_D	147_Y	1.264	0.97
50_E	53_G	1.257	0.97
195_H	199_S	1.254	0.97
51_L	56_A	1.247	0.97
164_N	211_S	1.243	0.97
128_V	183_A	1.242	0.97
132_S	175_D	1.241	0.96
72_V	218_A	1.213	0.96
161_W	212_L	1.202	0.96
94_L	133_L	1.197	0.96
172_Q	208_S	1.188	0.95
33_W	95_T	1.181	0.95
60_N	200_T	1.181	0.95
27_K	81_E	1.177	0.95
217_A	221_M	1.164	0.95
211_S	214_Y	1.142	0.94
71_D	168_T	1.142	0.94
97_T	129_A	1.135	0.94
181_A	193_W	1.123	0.94
90_F	182_V	1.122	0.94
40_C	96_L	1.122	0.94
30_L	69_A	1.121	0.94
185_L	190_A	1.119	0.94
103_V	118_L	1.091	0.93
94_L	98_F	1.089	0.93
55_T	109_A	1.089	0.93
112_D	118_L	1.083	0.93
153_I	158_R	1.074	0.92
25_F	29_G	1.073	0.92
93_L	97_T	1.067	0.92
160_L	215_A	1.054	0.92
181_A	185_L	1.036	0.91
140_Q	147_Y	1.036	0.91
45_V	200_T	1.036	0.91
79_P	83_R	1.036	0.91
47_K	115_Q	1.036	0.91
175_D	179_F	1.034	0.91
44_Q	59_G	1.026	0.91
202_L	206_A	1.025	0.90
152_R	214_Y	1.016	0.90
208_S	211_S	0.994	0.89
104_L	118_L	0.991	0.89
29_G	33_W	0.980	0.88
56_A	203_I	0.971	0.88
68_F	211_S	0.968	0.88
63_Y	67_F	0.967	0.88
70_T	208_S	0.966	0.88
190_A	194_L	0.947	0.87
44_Q	100_M	0.944	0.86
34_I	89_G	0.941	0.86
160_L	164_N	0.940	0.86
188_Y	196_I	0.936	0.86
36_F	39_V	0.935	0.86
58_L	103_V	0.926	0.85
36_F	92_T	0.915	0.85
102_G	138_F	0.910	0.84
114_S	120_T	0.908	0.84
112_D	115_Q	0.906	0.84
104_L	122_F	0.905	0.84
176_T	201_Y	0.898	0.84
143_D	167_S	0.895	0.83
80_A	152_R	0.893	0.83
80_A	84_K	0.891	0.83
146_V	149_A	0.891	0.83
155_P	160_L	0.883	0.83
71_D	216_Y	0.882	0.82
79_P	144_V	0.872	0.82
140_Q	143_D	0.871	0.82
104_L	123_G	0.868	0.81
90_F	133_L	0.867	0.81
43_L	122_F	0.857	0.81
177_F	181_A	0.853	0.80
168_T	216_Y	0.851	0.80
153_I	156_S	0.849	0.80
118_L	121_I	0.847	0.80
206_A	209_L	0.845	0.80
111_S	192_V	0.844	0.80
191_D	194_L	0.838	0.79
71_D	143_D	0.832	0.79
128_V	179_F	0.831	0.79
98_F	102_G	0.827	0.78
63_Y	164_N	0.823	0.78
42_N	175_D	0.818	0.77
153_I	198_I	0.818	0.77
160_L	219_K	0.812	0.77
140_Q	176_T	0.807	0.77
101_Q	105_L	0.804	0.76
135_A	175_D	0.802	0.76
100_M	122_F	0.799	0.76
90_F	137_I	0.794	0.75
103_V	174_F	0.793	0.75
134_L	138_F	0.790	0.75
207_V	211_S	0.789	0.75
101_Q	104_L	0.789	0.75
112_D	121_I	0.786	0.75
79_P	148_S	0.784	0.74
136_F	175_D	0.783	0.74
63_Y	143_D	0.774	0.73
63_Y	204_K	0.770	0.73
146_V	170_V	0.766	0.73
76_K	222_I	0.763	0.72
30_L	73_L	0.756	0.72
68_F	214_Y	0.754	0.72
95_T	99_V	0.754	0.72
48_T	184_F	0.750	0.71
75_E	151_R	0.741	0.70
196_I	200_T	0.740	0.70
75_E	160_L	0.735	0.70
83_R	87_W	0.733	0.69
63_Y	132_S	0.723	0.68
175_D	204_K	0.720	0.68
150_I	166_G	0.716	0.68
167_S	208_S	0.713	0.67
48_T	111_S	0.712	0.67
151_R	223_P	0.712	0.67
97_T	125_L	0.710	0.67
38_T	66_I	0.705	0.66
147_Y	164_N	0.701	0.66
126_P	129_A	0.699	0.66
71_D	183_A	0.693	0.65
58_L	200_T	0.691	0.65
59_G	93_L	0.688	0.64
35_G	144_V	0.688	0.64
143_D	208_S	0.685	0.64
142_L	145_Y	0.684	0.64
55_T	111_S	0.683	0.64
160_L	212_L	0.680	0.64
165_G	211_S	0.680	0.64
124_F	178_I	0.674	0.63
155_P	216_Y	0.673	0.63
96_L	100_M	0.665	0.62
148_S	211_S	0.663	0.62
157_D	223_P	0.661	0.61
60_N	199_S	0.661	0.61
79_P	152_R	0.658	0.61
151_R	163_R	0.657	0.61
172_Q	211_S	0.656	0.61
90_F	136_F	0.655	0.61
54_L	92_T	0.654	0.61
217_A	220_K	0.653	0.60
180_T	200_T	0.650	0.60
142_L	150_I	0.649	0.60
173_L	197_F	0.648	0.60
81_E	84_K	0.648	0.60
57_T	196_I	0.647	0.60
39_V	121_I	0.644	0.59
59_G	141_T	0.642	0.59
128_V	132_S	0.641	0.59
144_V	147_Y	0.641	0.59
63_Y	205_F	0.639	0.59
51_L	106_F	0.638	0.59
168_T	208_S	0.637	0.59
40_C	95_T	0.636	0.58
110_S	131_G	0.634	0.58
53_G	196_I	0.631	0.58
45_V	51_L	0.631	0.58
104_L	115_Q	0.627	0.57
214_Y	218_A	0.624	0.57
92_T	118_L	0.624	0.57
121_I	130_L	0.623	0.57
127_R	193_W	0.621	0.57
188_Y	192_V	0.619	0.56
62_M	99_V	0.618	0.56
135_A	178_I	0.617	0.56
128_V	131_G	0.614	0.56
59_G	170_V	0.612	0.56
108_P	125_L	0.612	0.56
143_D	165_G	0.612	0.56
41_A	63_Y	0.608	0.55
82_A	140_Q	0.607	0.55
33_W	37_A	0.605	0.55
179_F	184_F	0.601	0.54
98_F	152_R	0.601	0.54
34_I	38_T	0.598	0.54
160_L	163_R	0.594	0.53
29_G	88_L	0.593	0.53
188_Y	193_W	0.593	0.53
34_I	61_V	0.589	0.53
83_R	151_R	0.587	0.52
165_G	169_A	0.585	0.52
48_T	196_I	0.583	0.52
215_A	219_K	0.582	0.52
88_L	92_T	0.582	0.52
91_S	177_F	0.582	0.52
33_W	65_T	0.577	0.51
125_L	156_S	0.575	0.51
38_T	136_F	0.573	0.51
125_L	129_A	0.573	0.51
86_V	144_V	0.573	0.51
79_P	151_R	0.571	0.51
67_F	71_D	0.570	0.50
89_G	172_Q	0.567	0.50
186_G	189_P	0.565	0.50
148_S	152_R	0.564	0.50
176_T	200_T	0.564	0.50
132_S	179_F	0.563	0.50
151_R	204_K	0.563	0.50
50_E	110_S	0.563	0.50
122_F	136_F	0.559	0.49
35_G	182_V	0.558	0.49
63_Y	211_S	0.555	0.49
73_L	222_I	0.554	0.48
79_P	145_Y	0.554	0.48
206_A	210_I	0.553	0.48
76_K	223_P	0.551	0.48
57_T	100_M	0.551	0.48
46_V	100_M	0.549	0.48
27_K	73_L	0.549	0.48
50_E	220_K	0.547	0.48
95_T	178_I	0.547	0.48
187_I	191_D	0.545	0.47
55_T	93_L	0.545	0.47
128_V	184_F	0.545	0.47
142_L	149_A	0.543	0.47
144_V	208_S	0.543	0.47
198_I	202_L	0.541	0.47
85_A	219_K	0.537	0.46
136_F	203_I	0.535	0.46
180_T	197_F	0.534	0.46
63_Y	175_D	0.532	0.46
109_A	112_D	0.530	0.45
60_N	203_I	0.529	0.45
153_I	159_L	0.529	0.45
68_F	139_S	0.528	0.45
156_S	221_M	0.528	0.45
46_V	124_F	0.525	0.45
82_A	86_V	0.522	0.45
188_Y	199_S	0.521	0.44
34_I	168_T	0.520	0.44
79_P	147_Y	0.516	0.44
155_P	159_L	0.512	0.43
201_Y	205_F	0.510	0.43
26_G	77_Y	0.509	0.43
40_C	103_V	0.507	0.43
70_T	147_Y	0.505	0.42
48_T	112_D	0.503	0.42
72_V	122_F	0.502	0.42
138_F	198_I	0.501	0.42
65_T	105_L	0.500	0.42

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
4rfsS	1	0.7598	40.6	0.942	Contact Map
4huqS	1	0.6332	21	0.95	Contact Map
3o7qA	1	0.5764	8.6	0.958	Contact Map
4pypA	1	0.5808	8.5	0.958	Contact Map
2gfpA	2	0.5415	6.3	0.96	Contact Map
4ldsA	2	0.5415	4.6	0.963	Contact Map
4xnjA	1	0.5983	4.3	0.963	Contact Map
2k1eA	3	0.4192	3.9	0.964	Contact Map
3p5nA	2	0.5852	3.4	0.965	Contact Map
3mktA	1	0.9039	3.3	0.965	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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