T4_baseplate - PFAM28P - GREMLIN Contacts

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T4_baseplate - T4 bacteriophage base plate protein

PFAM:	PF12322	Sequences: YELTLPSTGKKIKYRPFLVKEEKILLMALESEDEKQIINAIKQIIKNCIVDKLPTFDIEYLFLNIRAKSVGETKVELNVTCPDCGEEVEVEINLDDIKVPEHTNKIKLTDDIGIKMKYPSLDDFDQIFDLIASCIDQIYDGEEVYDAKDFTKKELDEFIESLNSKQFKKIQKFFETPKLSHTIKVKCKCGVESEVVLEGLQSFFA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	205 (203)
Sequences:	5822 (4379)
Seq/√Len:	307.4
META:	0.986

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
186_K	192_E	3.412	1.00
76_E	91_E	3.171	1.00
93_N	96_D	3.031	1.00
184_K	194_E	3.007	1.00
2_E	11_K	2.775	1.00
78_N	89_E	2.697	1.00
73_T	91_E	2.692	1.00
182_T	194_E	2.674	1.00
163_N	166_Q	2.510	1.00
113_G	139_Y	2.458	1.00
178_K	198_E	2.361	1.00
80_T	87_E	2.357	1.00
3_L	61_L	2.357	1.00
184_K	192_E	2.247	1.00
42_K	51_D	2.240	1.00
115_K	137_Q	2.239	1.00
132_A	156_D	2.221	1.00
78_N	87_E	2.200	1.00
147_A	155_L	2.122	1.00
111_D	141_G	2.048	1.00
117_K	136_D	2.024	1.00
107_K	139_Y	2.017	1.00
56_F	118_Y	1.988	1.00
83_D	191_V	1.976	1.00
43_Q	47_N	1.971	1.00
86_E	188_K	1.952	1.00
105_K	115_K	1.934	1.00
33_D	36_Q	1.932	1.00
182_T	196_V	1.907	1.00
105_K	113_G	1.875	1.00
13_K	39_N	1.840	1.00
129_D	152_K	1.836	1.00
180_S	198_E	1.835	1.00
146_D	149_D	1.763	1.00
115_K	136_D	1.757	1.00
197_L	202_S	1.712	1.00
84_C	187_C	1.680	1.00
140_D	143_E	1.679	1.00
76_E	89_E	1.667	1.00
31_S	36_Q	1.665	1.00
104_N	115_K	1.664	1.00
107_K	113_G	1.611	1.00
140_D	145_Y	1.611	1.00
64_N	95_D	1.609	1.00
4_T	11_K	1.594	1.00
165_K	169_K	1.577	1.00
132_A	152_K	1.566	1.00
24_I	40_A	1.543	1.00
7_S	56_F	1.540	1.00
137_Q	144_V	1.524	1.00
2_E	13_K	1.521	1.00
171_Q	175_E	1.514	1.00
185_V	193_S	1.513	1.00
169_K	172_K	1.505	1.00
117_K	123_D	1.474	1.00
186_K	190_G	1.465	1.00
39_N	43_Q	1.454	1.00
84_C	189_C	1.450	1.00
7_S	57_D	1.430	1.00
180_S	196_V	1.426	1.00
4_T	9_G	1.387	1.00
147_A	150_F	1.383	1.00
107_K	110_D	1.360	1.00
153_K	157_E	1.347	1.00
156_D	160_E	1.304	1.00
64_N	67_A	1.292	1.00
133_S	152_K	1.280	1.00
88_V	185_V	1.277	1.00
2_E	39_N	1.277	1.00
45_I	49_I	1.276	1.00
172_K	175_E	1.268	1.00
135_I	159_I	1.245	1.00
60_Y	64_N	1.241	1.00
82_P	193_S	1.236	1.00
51_D	122_D	1.206	1.00
5_L	54_P	1.168	1.00
165_K	168_K	1.161	1.00
114_I	170_I	1.147	1.00
3_L	14_Y	1.145	1.00
67_A	95_D	1.143	1.00
75_V	94_L	1.126	1.00
168_K	171_Q	1.125	1.00
123_D	133_S	1.121	1.00
3_L	60_Y	1.109	1.00
46_K	50_V	1.094	1.00
64_N	98_K	1.088	1.00
72_E	95_D	1.076	1.00
44_I	48_C	1.060	1.00
164_S	168_K	1.041	1.00
46_K	51_D	1.034	1.00
68_K	72_E	1.028	1.00
107_K	111_D	1.025	1.00
158_F	161_S	1.023	1.00
15_R	21_E	1.022	1.00
5_L	8_T	1.019	1.00
112_I	140_D	1.017	1.00
1_Y	4_T	1.010	1.00
53_L	61_L	1.008	1.00
67_A	94_L	1.008	1.00
73_T	93_N	1.001	1.00
138_I	147_A	0.997	1.00
36_Q	39_N	0.995	1.00
80_T	85_G	0.994	1.00
117_K	120_S	0.993	1.00
137_Q	146_D	0.991	1.00
64_N	68_K	0.987	1.00
102_H	176_T	0.985	1.00
77_L	92_I	0.983	1.00
168_K	172_K	0.979	1.00
102_H	172_K	0.946	1.00
81_C	193_S	0.945	1.00
138_I	150_F	0.930	1.00
43_Q	46_K	0.925	1.00
14_Y	68_K	0.924	1.00
129_D	132_A	0.922	1.00
79_V	185_V	0.918	1.00
150_F	154_E	0.915	1.00
81_C	187_C	0.913	1.00
81_C	84_C	0.891	1.00
58_I	121_L	0.890	1.00
129_D	156_D	0.887	1.00
20_K	160_E	0.887	1.00
15_R	18_L	0.882	1.00
111_D	140_D	0.882	1.00
132_A	155_L	0.876	1.00
172_K	176_T	0.875	1.00
45_I	50_V	0.871	1.00
45_I	58_I	0.869	1.00
3_L	12_I	0.858	1.00
108_L	166_Q	0.858	1.00
134_C	174_F	0.858	1.00
79_V	90_V	0.850	1.00
45_I	65_I	0.847	1.00
97_I	181_H	0.845	1.00
106_I	116_M	0.842	1.00
6_P	60_Y	0.840	1.00
72_E	93_N	0.837	1.00
189_C	193_S	0.836	1.00
68_K	95_D	0.834	1.00
145_Y	150_F	0.831	1.00
187_C	193_S	0.812	1.00
81_C	189_C	0.809	1.00
32_E	36_Q	0.806	1.00
63_L	179_L	0.804	1.00
34_E	201_Q	0.802	1.00
96_D	181_H	0.797	1.00
146_D	150_F	0.796	1.00
151_T	154_E	0.796	1.00
59_E	199_G	0.794	1.00
34_E	38_I	0.793	1.00
2_E	35_K	0.793	1.00
60_Y	99_V	0.793	1.00
125_D	129_D	0.789	1.00
84_C	88_V	0.780	0.99
63_L	94_L	0.771	0.99
105_K	139_Y	0.770	0.99
187_C	191_V	0.769	0.99
147_A	152_K	0.768	0.99
128_F	160_E	0.767	0.99
40_A	48_C	0.760	0.99
3_L	64_N	0.751	0.99
152_K	156_D	0.746	0.99
115_K	139_Y	0.738	0.99
12_I	49_I	0.738	0.99
113_G	140_D	0.735	0.99
109_T	112_I	0.734	0.99
157_E	161_S	0.733	0.99
126_Q	129_D	0.732	0.99
38_I	42_K	0.727	0.99
152_K	155_L	0.726	0.99
127_I	131_I	0.725	0.99
5_L	61_L	0.723	0.99
17_F	26_L	0.715	0.99
198_E	202_S	0.712	0.99
157_E	160_E	0.710	0.99
81_C	88_V	0.706	0.99
17_F	70_V	0.706	0.99
36_Q	40_A	0.704	0.99
158_F	162_L	0.698	0.99
150_F	153_K	0.695	0.99
166_Q	169_K	0.694	0.99
81_C	185_V	0.692	0.99
150_F	155_L	0.691	0.99
5_L	12_I	0.688	0.99
136_D	146_D	0.687	0.99
173_F	176_T	0.685	0.99
6_P	99_V	0.683	0.99
103_T	176_T	0.682	0.99
118_Y	173_F	0.678	0.99
1_Y	81_C	0.675	0.99
45_I	53_L	0.675	0.99
81_C	191_V	0.674	0.99
120_S	123_D	0.673	0.98
8_T	11_K	0.672	0.98
103_T	108_L	0.672	0.98
63_L	97_I	0.669	0.98
153_K	156_D	0.666	0.98
77_L	197_L	0.659	0.98
119_P	134_C	0.655	0.98
82_P	195_V	0.650	0.98
83_D	187_C	0.650	0.98
73_T	76_E	0.648	0.98
125_D	156_D	0.648	0.98
24_I	47_N	0.646	0.98
185_V	191_V	0.646	0.98
185_V	189_C	0.644	0.98
141_G	145_Y	0.642	0.98
24_I	43_Q	0.640	0.98
28_A	40_A	0.640	0.98
112_I	138_I	0.639	0.98
82_P	191_V	0.639	0.98
24_I	27_M	0.638	0.98
119_P	177_P	0.631	0.98
151_T	155_L	0.631	0.98
164_S	167_F	0.627	0.98
135_I	138_I	0.627	0.98
135_I	147_A	0.626	0.98
138_I	145_Y	0.620	0.97
98_K	181_H	0.618	0.97
48_C	65_I	0.616	0.97
22_E	168_K	0.615	0.97
139_Y	145_Y	0.613	0.97
199_G	202_S	0.613	0.97
57_D	99_V	0.611	0.97
67_A	72_E	0.610	0.97
14_Y	65_I	0.610	0.97
66_R	70_V	0.610	0.97
11_K	35_K	0.608	0.97
162_L	166_Q	0.607	0.97
138_I	155_L	0.604	0.97
50_V	54_P	0.604	0.97
132_A	136_D	0.603	0.97
17_F	22_E	0.599	0.97
128_F	156_D	0.597	0.97
12_I	61_L	0.592	0.97
4_T	8_T	0.592	0.97
38_I	55_T	0.590	0.97
61_L	65_I	0.585	0.96
79_V	195_V	0.584	0.96
99_V	179_L	0.583	0.96
39_N	46_K	0.583	0.96
52_K	120_S	0.581	0.96
6_P	57_D	0.577	0.96
102_H	175_E	0.577	0.96
90_V	183_I	0.577	0.96
129_D	133_S	0.575	0.96
79_V	193_S	0.574	0.96
135_I	155_L	0.573	0.96
36_Q	43_Q	0.573	0.96
183_I	197_L	0.570	0.96
65_I	68_K	0.570	0.96
52_K	117_K	0.568	0.96
42_K	46_K	0.566	0.96
41_I	200_L	0.565	0.96
183_I	196_V	0.564	0.96
24_I	36_Q	0.562	0.95
46_K	49_I	0.562	0.95
44_I	47_N	0.559	0.95
113_G	137_Q	0.557	0.95
151_T	156_D	0.556	0.95
37_I	41_I	0.555	0.95
42_K	122_D	0.555	0.95
14_Y	64_N	0.553	0.95
84_C	193_S	0.552	0.95
165_K	172_K	0.552	0.95
170_I	174_F	0.550	0.95
167_F	170_I	0.549	0.95
6_P	9_G	0.549	0.95
81_C	85_G	0.546	0.95
130_L	134_C	0.546	0.95
86_E	187_C	0.545	0.95
5_L	56_F	0.544	0.95
53_L	58_I	0.544	0.95
92_I	181_H	0.543	0.95
116_M	173_F	0.542	0.95
114_I	158_F	0.541	0.94
113_G	144_V	0.540	0.94
6_P	11_K	0.536	0.94
66_R	71_G	0.536	0.94
132_A	147_A	0.535	0.94
106_I	169_K	0.531	0.94
28_A	31_S	0.530	0.94
29_L	38_I	0.526	0.94
52_K	122_D	0.525	0.94
103_T	106_I	0.523	0.93
141_G	144_V	0.523	0.93
55_T	124_F	0.522	0.93
93_N	181_H	0.522	0.93
40_A	44_I	0.521	0.93
59_E	121_L	0.521	0.93
133_S	136_D	0.520	0.93
25_L	44_I	0.519	0.93
118_Y	176_T	0.518	0.93
82_P	85_G	0.518	0.93
88_V	187_C	0.517	0.93
181_H	195_V	0.516	0.93
108_L	112_I	0.515	0.93
136_D	139_Y	0.513	0.93
103_T	107_K	0.513	0.93
35_K	39_N	0.512	0.93
16_P	19_V	0.510	0.93
179_L	202_S	0.502	0.92
50_V	61_L	0.501	0.92
27_M	31_S	0.500	0.92

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
3wwlA	1	0.2488	10.1	0.94	Contact Map
1wiiA	1	0.3756	9	0.942	Contact Map
2p14A	1	0.3122	8.5	0.942	Contact Map
3f6nA	3	0.3561	6.8	0.945	Contact Map
2k2dA	1	0.2049	6	0.946	Contact Map
3lywA	1	0.1268	4.5	0.949	Contact Map
2jnsA	1	0.4293	4.4	0.949	Contact Map
4aybP	1	0.2098	4.3	0.95	Contact Map
4aboI	1	0.2634	4.2	0.95	Contact Map
1pqvS	1	0.4195	4.2	0.95	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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