Phage_gp53 - PFAM28P - GREMLIN Contacts

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Phage_gp53 - Base plate wedge protein 53

PFAM:	PF11246	Sequences: MYFSYFPKIEYDSVTVKNIFRRVKLRLDDILNAFTFYKYTIKDGERPDTVAEKLYGDPELDWVVLLTNNIINPQYDWPLSQYDLYKYIEDKYGSEEGANTIHHYETEEGRDYYNLIEVPDNPTVIYDKGDVSNTYPDVGTDDYTTVLYNGIVIPVTNYEYETELNEKKRNIYLLKPEYLQQFINDFRRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	189 (173)
Sequences:	1237 (1096)
Seq/√Len:	83.4
META:	0.96

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
164_L	167_K	3.969	1.00
101_I	104_Y	3.530	1.00
45_E	53_K	3.366	1.00
50_V	64_V	2.927	1.00
52_E	58_P	2.925	1.00
63_V	179_L	2.533	1.00
54_L	173_L	2.501	1.00
47_P	65_L	2.314	1.00
102_H	105_E	2.194	1.00
38_K	172_Y	2.063	1.00
159_E	163_E	1.942	1.00
101_I	105_E	1.877	1.00
25_L	29_D	1.874	1.00
27_L	31_L	1.865	1.00
64_V	173_L	1.844	1.00
122_P	125_I	1.842	1.00
155_V	158_Y	1.796	1.00
84_L	88_I	1.758	1.00
51_A	57_D	1.752	1.00
47_P	77_W	1.749	1.00
105_E	108_E	1.729	1.00
57_D	60_L	1.698	1.00
46_R	61_D	1.685	1.00
18_N	22_R	1.670	1.00
121_N	124_V	1.665	1.00
80_S	83_D	1.632	1.00
48_D	61_D	1.623	1.00
27_L	30_I	1.617	1.00
134_T	137_D	1.582	1.00
106_T	109_G	1.576	1.00
158_Y	162_T	1.572	1.00
130_D	133_N	1.523	0.99
30_I	34_F	1.517	0.99
29_D	35_T	1.501	0.99
110_R	113_Y	1.495	0.99
100_T	103_H	1.472	0.99
124_V	127_D	1.456	0.99
92_Y	161_E	1.452	0.99
40_T	170_N	1.444	0.99
103_H	106_T	1.423	0.99
25_L	28_D	1.421	0.99
46_R	49_T	1.401	0.99
29_D	32_N	1.396	0.99
125_I	128_K	1.372	0.99
29_D	36_F	1.370	0.99
115_L	118_V	1.359	0.99
29_D	34_F	1.354	0.99
27_L	34_F	1.353	0.99
25_L	31_L	1.346	0.99
110_R	114_N	1.343	0.99
94_S	97_G	1.333	0.99
132_S	135_Y	1.311	0.98
174_L	182_F	1.307	0.98
111_D	114_N	1.294	0.98
17_K	20_F	1.283	0.98
67_T	174_L	1.268	0.98
54_L	176_P	1.256	0.98
31_L	34_F	1.251	0.98
82_Y	86_K	1.241	0.98
51_A	60_L	1.234	0.98
27_L	32_N	1.228	0.98
128_K	131_V	1.227	0.98
166_E	169_R	1.217	0.98
105_E	109_G	1.213	0.97
45_E	49_T	1.212	0.97
118_V	121_N	1.209	0.97
132_S	136_P	1.191	0.97
127_D	130_D	1.191	0.97
25_L	32_N	1.190	0.97
28_D	31_L	1.185	0.97
65_L	73_P	1.184	0.97
26_R	29_D	1.181	0.97
148_Y	151_I	1.181	0.97
32_N	35_T	1.178	0.97
93_G	97_G	1.178	0.97
106_T	111_D	1.171	0.97
29_D	33_A	1.167	0.97
71_I	76_D	1.142	0.96
129_G	132_S	1.142	0.96
70_I	77_W	1.117	0.96
128_K	132_S	1.112	0.96
156_T	159_E	1.111	0.96
127_D	131_V	1.099	0.95
31_L	35_T	1.094	0.95
133_N	136_P	1.077	0.95
159_E	162_T	1.071	0.95
42_K	45_E	1.070	0.95
126_Y	129_G	1.067	0.95
119_P	122_P	1.060	0.94
25_L	34_F	1.058	0.94
30_I	33_A	1.056	0.94
79_L	83_D	1.049	0.94
93_G	96_E	1.046	0.94
133_N	137_D	1.028	0.94
155_V	159_E	1.027	0.93
87_Y	91_K	1.019	0.93
147_L	150_G	1.019	0.93
125_I	129_G	1.005	0.93
30_I	35_T	1.001	0.93
42_K	53_K	0.993	0.92
43_D	81_Q	0.985	0.92
86_K	89_E	0.983	0.92
102_H	106_T	0.982	0.92
139_G	142_D	0.980	0.92
107_E	110_R	0.979	0.92
85_Y	88_I	0.966	0.91
38_K	170_N	0.963	0.91
109_G	112_Y	0.962	0.91
64_V	67_T	0.939	0.90
109_G	113_Y	0.939	0.90
143_Y	146_V	0.939	0.90
26_R	32_N	0.928	0.89
19_I	23_V	0.927	0.89
27_L	36_F	0.925	0.89
26_R	30_I	0.922	0.89
182_F	186_F	0.914	0.89
131_V	134_T	0.912	0.89
122_P	127_D	0.911	0.89
98_A	101_I	0.902	0.88
100_T	104_Y	0.901	0.88
63_V	174_L	0.899	0.88
51_A	64_V	0.891	0.87
79_L	84_L	0.890	0.87
44_G	49_T	0.885	0.87
84_L	87_Y	0.872	0.86
31_L	36_F	0.868	0.86
99_N	104_Y	0.868	0.86
131_V	137_D	0.864	0.86
70_I	76_D	0.860	0.86
60_L	179_L	0.852	0.85
150_G	153_I	0.849	0.85
60_L	183_I	0.844	0.85
24_K	27_L	0.840	0.84
65_L	77_W	0.826	0.83
131_V	135_Y	0.823	0.83
164_L	168_K	0.820	0.83
108_E	111_D	0.814	0.82
76_D	168_K	0.803	0.81
84_L	165_N	0.798	0.81
130_D	134_T	0.793	0.81
119_P	123_T	0.787	0.80
60_L	63_V	0.783	0.80
112_Y	117_E	0.777	0.79
81_Q	84_L	0.775	0.79
89_E	93_G	0.773	0.79
120_D	123_T	0.769	0.79
124_V	128_K	0.769	0.79
106_T	113_Y	0.767	0.78
139_G	143_Y	0.765	0.78
114_N	117_E	0.760	0.78
16_V	22_R	0.759	0.78
163_E	167_K	0.756	0.77
98_A	103_H	0.753	0.77
117_E	120_D	0.745	0.76
118_V	122_P	0.736	0.75
79_L	87_Y	0.733	0.75
148_Y	152_V	0.732	0.75
27_L	33_A	0.730	0.75
89_E	94_S	0.728	0.75
52_E	56_G	0.724	0.74
14_V	17_K	0.724	0.74
87_Y	92_Y	0.721	0.74
25_L	30_I	0.713	0.73
65_L	76_D	0.711	0.73
111_D	116_I	0.708	0.73
180_Q	185_D	0.698	0.72
62_W	68_N	0.697	0.71
141_D	144_T	0.691	0.71
99_N	103_H	0.691	0.71
27_L	35_T	0.689	0.71
121_N	125_I	0.689	0.71
46_R	60_L	0.685	0.70
16_V	19_I	0.683	0.70
129_G	135_Y	0.681	0.70
143_Y	148_Y	0.681	0.70
154_P	158_Y	0.679	0.69
126_Y	132_S	0.679	0.69
101_I	106_T	0.678	0.69
39_Y	45_E	0.676	0.69
111_D	117_E	0.674	0.69
61_D	66_L	0.664	0.68
30_I	36_F	0.662	0.68
50_V	54_L	0.662	0.68
154_P	157_N	0.662	0.68
150_G	157_N	0.661	0.67
23_V	26_R	0.658	0.67
106_T	112_Y	0.658	0.67
106_T	110_R	0.654	0.67
167_K	170_N	0.648	0.66
89_E	95_E	0.645	0.66
97_G	100_T	0.645	0.66
119_P	124_V	0.641	0.65
54_L	75_Y	0.636	0.64
117_E	122_P	0.631	0.64
126_Y	131_V	0.627	0.63
94_S	98_A	0.625	0.63
107_E	112_Y	0.618	0.62
165_N	168_K	0.618	0.62
113_Y	117_E	0.618	0.62
151_I	154_P	0.611	0.61
41_I	77_W	0.610	0.61
91_K	161_E	0.607	0.61
26_R	34_F	0.606	0.61
50_V	53_K	0.604	0.60
127_D	133_N	0.604	0.60
48_D	72_N	0.603	0.60
28_D	33_A	0.596	0.59
133_N	138_V	0.595	0.59
66_L	72_N	0.594	0.59
138_V	143_Y	0.593	0.59
121_N	127_D	0.593	0.59
20_F	61_D	0.592	0.59
42_K	50_V	0.591	0.59
100_T	105_E	0.590	0.59
71_I	170_N	0.585	0.58
88_I	158_Y	0.585	0.58
63_V	67_T	0.584	0.58
115_L	119_P	0.584	0.58
114_N	118_V	0.582	0.58
25_L	36_F	0.574	0.57
107_E	114_N	0.574	0.57
102_H	107_E	0.571	0.56
81_Q	162_T	0.569	0.56
22_R	25_L	0.566	0.56
102_H	157_N	0.564	0.55
142_D	146_V	0.563	0.55
127_D	132_S	0.562	0.55
120_D	125_I	0.560	0.55
103_H	107_E	0.554	0.54
88_I	157_N	0.552	0.54
89_E	98_A	0.552	0.54
65_L	70_I	0.551	0.54
128_K	133_N	0.549	0.53
110_R	116_I	0.549	0.53
28_D	34_F	0.541	0.52
21_R	24_K	0.540	0.52
104_Y	107_E	0.538	0.52
122_P	128_K	0.534	0.51
155_V	163_E	0.530	0.51
146_V	150_G	0.528	0.51
145_T	148_Y	0.527	0.50
72_N	172_Y	0.526	0.50
108_E	114_N	0.526	0.50
112_Y	115_L	0.526	0.50
105_E	110_R	0.520	0.50
91_K	157_N	0.518	0.49
144_T	149_N	0.518	0.49
127_D	135_Y	0.513	0.49
108_E	112_Y	0.512	0.48
98_A	104_Y	0.508	0.48
72_N	75_Y	0.507	0.48
45_E	80_S	0.506	0.48
157_N	163_E	0.505	0.48
43_D	169_R	0.505	0.48
19_I	22_R	0.505	0.48
180_Q	184_N	0.505	0.48
132_S	137_D	0.504	0.47
20_F	24_K	0.502	0.47
136_P	144_T	0.501	0.47
104_Y	108_E	0.500	0.47

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
2ltfA	1	0.3545	90.2	0.909	Contact Map
4pxvA	1	0.254	12.1	0.953	Contact Map
3mujA	2	0.2593	4.5	0.961	Contact Map
3otdA	4	0.2593	3.2	0.964	Contact Map
1e0gA	1	0.254	3	0.965	Contact Map
3fwbB	1	0.1481	2.4	0.966	Contact Map
3hvzA	2	0.328	2.4	0.966	Contact Map
1ujlA	1	0.2222	2.2	0.967	Contact Map
2fgcA	2	0.3386	2.2	0.967	Contact Map
2mkxA	1	0.2698	2	0.968	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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