Phage_Gp15 - PFAM28P - GREMLIN Contacts

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Phage_Gp15 - Bacteriophage Gp15 protein

PFAM:	PF06854	Sequences: LTDELPTSVEVDGKEYPINTDFRNVLRIFEALEDPELSDEEKILIALELLYPEPPEDLEEAIEKLLWFYNCGKEEEDKKSKGDEKGNPMPRLYDFEQDAEYIYAAFLQVYGIDLREEGYLHWWKFLALFNGLPEDTKFSKIIGIRSKKLKGKLDKEEREFYRKLKELYAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	170 (166)
Sequences:	1829 (1646)
Seq/√Len:	127.7
META:	0.86

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_D	124_K	4.660	1.00
109_V	133_P	4.268	1.00
101_Y	141_I	3.280	1.00
10_E	13_G	2.477	1.00
138_F	142_I	2.447	1.00
71_C	126_L	2.380	1.00
93_Y	138_F	2.373	1.00
20_T	119_Y	2.283	1.00
110_Y	128_L	2.250	1.00
108_Q	136_T	2.194	1.00
107_L	124_K	2.175	1.00
64_K	67_W	2.112	1.00
92_L	146_S	2.111	1.00
116_E	124_K	2.056	1.00
30_E	96_E	2.043	1.00
10_E	15_E	2.000	1.00
25_V	50_L	1.986	1.00
137_K	140_K	1.985	1.00
8_S	15_E	1.975	1.00
12_D	57_D	1.968	1.00
160_F	164_L	1.962	1.00
60_E	64_K	1.837	1.00
157_E	160_F	1.802	1.00
129_F	138_F	1.799	1.00
25_V	69_Y	1.778	1.00
59_E	63_E	1.750	1.00
159_E	163_K	1.689	1.00
117_E	120_L	1.682	1.00
147_K	161_Y	1.677	1.00
19_N	24_N	1.670	1.00
95_F	129_F	1.669	1.00
31_A	37_L	1.609	1.00
112_I	128_L	1.588	1.00
93_Y	129_F	1.584	1.00
23_R	118_G	1.579	1.00
31_A	45_I	1.486	1.00
25_V	28_I	1.420	1.00
108_Q	133_P	1.415	1.00
91_R	94_D	1.409	1.00
134_E	140_K	1.390	1.00
67_W	72_G	1.386	1.00
24_N	49_L	1.382	1.00
38_S	41_E	1.372	1.00
20_T	25_V	1.332	1.00
46_A	65_L	1.328	1.00
27_R	30_E	1.323	1.00
164_L	168_Y	1.322	1.00
94_D	97_Q	1.319	1.00
166_E	169_A	1.315	1.00
54_P	57_D	1.311	1.00
105_A	109_V	1.301	1.00
153_L	157_E	1.278	1.00
57_D	60_E	1.272	1.00
101_Y	137_K	1.266	1.00
31_A	49_L	1.259	1.00
105_A	108_Q	1.243	1.00
21_D	119_Y	1.230	1.00
144_I	164_L	1.219	0.99
120_L	128_L	1.218	0.99
137_K	141_I	1.216	0.99
50_L	65_L	1.214	0.99
141_I	144_I	1.206	0.99
6_P	123_W	1.202	0.99
61_A	68_F	1.201	0.99
100_E	130_N	1.196	0.99
144_I	147_K	1.193	0.99
37_L	41_E	1.155	0.99
107_L	111_G	1.142	0.99
115_R	124_K	1.138	0.99
147_K	157_E	1.135	0.99
104_A	131_G	1.133	0.99
60_E	63_E	1.127	0.99
105_A	137_K	1.120	0.99
139_S	142_I	1.118	0.99
23_R	119_Y	1.107	0.99
9_V	67_W	1.092	0.99
150_K	153_L	1.089	0.99
120_L	124_K	1.080	0.99
95_F	126_L	1.078	0.99
20_T	24_N	1.073	0.99
105_A	136_T	1.068	0.99
135_D	140_K	1.059	0.99
112_I	117_E	1.050	0.98
143_G	147_K	1.033	0.98
154_D	157_E	1.033	0.98
57_D	61_A	1.026	0.98
161_Y	165_K	1.007	0.98
106_F	114_L	1.000	0.98
16_Y	55_P	0.993	0.98
103_Y	107_L	0.983	0.98
149_L	153_L	0.983	0.98
131_G	137_K	0.981	0.98
28_I	50_L	0.973	0.97
149_L	162_R	0.953	0.97
32_L	46_A	0.943	0.97
142_I	146_S	0.939	0.97
99_A	103_Y	0.933	0.97
34_D	42_K	0.924	0.97
51_Y	61_A	0.911	0.96
110_Y	113_D	0.904	0.96
109_V	136_T	0.903	0.96
144_I	160_F	0.901	0.96
68_F	72_G	0.895	0.96
47_L	51_Y	0.893	0.96
154_D	158_R	0.892	0.96
157_E	161_Y	0.890	0.96
92_L	142_I	0.872	0.95
110_Y	131_G	0.871	0.95
112_I	120_L	0.870	0.95
9_V	51_Y	0.868	0.95
110_Y	114_L	0.857	0.95
106_F	110_Y	0.854	0.95
105_A	132_L	0.849	0.94
97_Q	101_Y	0.847	0.94
106_F	125_F	0.847	0.94
27_R	31_A	0.845	0.94
24_N	27_R	0.840	0.94
27_R	34_D	0.835	0.94
107_L	113_D	0.831	0.94
64_K	68_F	0.827	0.94
104_A	127_A	0.823	0.93
155_K	159_E	0.822	0.93
12_D	60_E	0.819	0.93
73_K	100_E	0.813	0.93
106_F	112_I	0.811	0.93
29_F	69_Y	0.808	0.93
143_G	146_S	0.806	0.93
140_K	143_G	0.804	0.93
98_D	145_R	0.802	0.93
149_L	152_K	0.798	0.92
19_N	52_P	0.788	0.92
103_Y	114_L	0.779	0.91
134_E	139_S	0.778	0.91
6_P	121_H	0.774	0.91
27_R	49_L	0.772	0.91
26_L	30_E	0.770	0.91
106_F	128_L	0.759	0.90
100_E	127_A	0.751	0.90
156_E	159_E	0.745	0.90
104_A	130_N	0.740	0.89
97_Q	169_A	0.735	0.89
45_I	48_E	0.735	0.89
59_E	62_I	0.732	0.89
114_L	128_L	0.728	0.88
156_E	160_F	0.728	0.88
33_E	96_E	0.726	0.88
25_V	29_F	0.722	0.88
136_T	139_S	0.718	0.88
137_K	144_I	0.710	0.87
103_Y	115_R	0.707	0.87
62_I	66_L	0.704	0.87
149_L	165_K	0.702	0.87
65_L	68_F	0.701	0.86
99_A	105_A	0.700	0.86
160_F	163_K	0.694	0.86
134_E	143_G	0.689	0.86
103_Y	127_A	0.687	0.85
148_K	152_K	0.684	0.85
106_F	132_L	0.682	0.85
14_K	17_P	0.682	0.85
31_A	46_A	0.681	0.85
101_Y	131_G	0.678	0.85
31_A	42_K	0.676	0.84
146_S	150_K	0.671	0.84
159_E	162_R	0.671	0.84
17_P	52_P	0.669	0.84
31_A	34_D	0.668	0.84
68_F	121_H	0.667	0.84
150_K	154_D	0.664	0.83
107_L	112_I	0.663	0.83
83_D	86_G	0.661	0.83
153_L	160_F	0.657	0.83
55_P	61_A	0.653	0.82
149_L	158_R	0.648	0.82
101_Y	105_A	0.648	0.82
34_D	37_L	0.647	0.82
164_L	167_L	0.644	0.82
37_L	45_I	0.643	0.81
84_E	87_N	0.641	0.81
148_K	154_D	0.636	0.81
148_K	161_Y	0.636	0.81
148_K	151_G	0.635	0.81
28_I	46_A	0.634	0.80
28_I	32_L	0.631	0.80
33_E	91_R	0.630	0.80
7_T	119_Y	0.621	0.79
109_V	132_L	0.618	0.79
141_I	168_Y	0.613	0.78
11_V	57_D	0.609	0.78
133_P	142_I	0.607	0.78
22_F	114_L	0.603	0.77
39_D	42_K	0.602	0.77
45_I	49_L	0.598	0.77
139_S	143_G	0.592	0.76
132_L	139_S	0.587	0.75
161_Y	164_L	0.587	0.75
99_A	127_A	0.586	0.75
103_Y	129_F	0.585	0.75
149_L	161_Y	0.584	0.75
66_L	69_Y	0.580	0.74
165_K	168_Y	0.578	0.74
28_I	69_Y	0.577	0.74
39_D	43_I	0.577	0.74
162_R	165_K	0.572	0.73
153_L	161_Y	0.572	0.73
161_Y	169_A	0.571	0.73
94_D	151_G	0.571	0.73
105_A	141_I	0.569	0.73
107_L	117_E	0.569	0.73
66_L	70_N	0.562	0.72
114_L	132_L	0.560	0.72
20_T	28_I	0.558	0.71
29_F	33_E	0.557	0.71
153_L	165_K	0.553	0.71
152_K	157_E	0.552	0.71
32_L	42_K	0.545	0.70
141_I	164_L	0.543	0.69
40_E	44_L	0.542	0.69
47_L	58_L	0.539	0.69
133_P	140_K	0.538	0.69
106_F	129_F	0.538	0.69
29_F	93_Y	0.535	0.68
153_L	158_R	0.534	0.68
78_K	87_N	0.532	0.68
43_I	46_A	0.530	0.68
158_R	162_R	0.529	0.67
11_V	64_K	0.529	0.67
53_E	154_D	0.528	0.67
83_D	90_P	0.528	0.67
47_L	61_A	0.525	0.67
102_I	129_F	0.523	0.67
26_L	29_F	0.523	0.67
22_F	125_F	0.522	0.66
6_P	11_V	0.521	0.66
47_L	72_G	0.519	0.66
125_F	129_F	0.516	0.66
16_Y	97_Q	0.515	0.65
23_R	117_E	0.514	0.65
147_K	152_K	0.514	0.65
22_F	106_F	0.514	0.65
67_W	71_C	0.513	0.65
61_A	64_K	0.512	0.65
71_C	123_W	0.510	0.65
147_K	165_K	0.508	0.64
22_F	117_E	0.505	0.64
22_F	31_A	0.503	0.64
114_L	156_E	0.502	0.63
93_Y	130_N	0.501	0.63
105_A	131_G	0.500	0.63

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
4oh8B	1	0.2059	6	0.95	Contact Map
2ii2A	1	0.6	5.6	0.95	Contact Map
1x4rA	1	0.2353	5.1	0.951	Contact Map
2h2kA	2	0.5529	4.9	0.952	Contact Map
2qipA	2	0.4294	4.4	0.953	Contact Map
3lijA	1	0.7118	3.1	0.956	Contact Map
1xl3C	1	0.2176	2.7	0.957	Contact Map
4un4B	1	0.8824	2.6	0.958	Contact Map
2kouA	1	0.4412	2.4	0.959	Contact Map
4qnuA	2	0.4412	2.1	0.96	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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