TMP_2 - PFAM28P - GREMLIN Contacts

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TMP_2 - Prophage tail length tape measure protein

PFAM:	PF06791	Sequences: QALNKAGISAKQTAAALRQLPAQFTDIVTSLASGQSPLTVLLQQGGQLKDMFGGVGPAAKALGGYLLGLINPLTLAAAAVGALAAAAYQGSKEARAFNKALILTGNAAGVTAGQLADLARALAAATGSQGAAREALAALAATGKIAGDQFERAAQAALDMAAATGQDVDEAAKQLAKALDDPVKAALALNRQYHFLTAAQYEQIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	205 (200)
Sequences:	1805 (1582)
Seq/√Len:	111.9
META:	0.735

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_N	74_T	3.420	1.00
186_A	195_F	3.250	1.00
170_E	173_K	2.802	1.00
181_D	184_K	2.717	1.00
190_N	195_F	2.491	1.00
121_A	151_E	2.383	1.00
8_I	12_Q	2.366	1.00
30_S	40_V	2.320	1.00
161_A	171_A	2.279	1.00
88_Y	92_K	2.204	1.00
27_I	40_V	2.139	1.00
31_L	40_V	2.123	1.00
166_Q	174_Q	2.109	1.00
188_A	191_R	2.105	1.00
198_A	202_E	2.060	1.00
184_K	188_A	2.038	1.00
30_S	35_Q	2.036	1.00
85_A	89_Q	1.940	1.00
81_G	84_A	1.928	1.00
20_L	48_L	1.927	1.00
6_A	13_T	1.909	1.00
98_N	107_A	1.902	1.00
167_D	170_E	1.863	1.00
80_V	87_A	1.862	1.00
155_Q	159_D	1.846	1.00
30_S	33_S	1.827	1.00
177_K	188_A	1.827	1.00
197_T	200_Q	1.786	1.00
32_A	39_T	1.783	1.00
25_T	50_D	1.770	1.00
166_Q	171_A	1.622	1.00
89_Q	92_K	1.620	1.00
25_T	29_T	1.612	1.00
81_G	85_A	1.607	1.00
25_T	46_G	1.589	1.00
136_L	154_A	1.586	1.00
186_A	204_I	1.586	1.00
200_Q	203_Q	1.570	1.00
173_K	177_K	1.566	1.00
182_P	189_L	1.554	1.00
199_A	202_E	1.547	1.00
23_Q	26_D	1.541	1.00
139_L	153_A	1.492	1.00
160_M	164_T	1.485	1.00
177_K	180_D	1.448	1.00
38_L	41_L	1.448	1.00
29_T	32_A	1.434	1.00
157_A	171_A	1.420	1.00
115_L	136_L	1.413	1.00
100_A	137_A	1.411	1.00
59_A	62_L	1.404	1.00
19_Q	51_M	1.403	1.00
187_L	191_R	1.396	1.00
37_P	41_L	1.378	1.00
107_A	194_H	1.377	1.00
142_T	145_I	1.371	1.00
26_D	47_Q	1.366	1.00
116_A	121_A	1.327	1.00
166_Q	170_E	1.317	1.00
44_Q	47_Q	1.310	0.99
190_N	201_Y	1.305	0.99
91_S	95_R	1.301	0.99
116_A	133_R	1.289	0.99
96_A	99_K	1.274	0.99
160_M	171_A	1.266	0.99
22_A	25_T	1.265	0.99
55_V	62_L	1.247	0.99
18_R	22_A	1.238	0.99
84_A	88_Y	1.234	0.99
9_S	12_Q	1.228	0.99
8_I	11_K	1.224	0.99
138_A	169_D	1.214	0.99
23_Q	29_T	1.205	0.99
12_Q	15_A	1.197	0.99
193_Y	200_Q	1.191	0.99
73_L	76_A	1.181	0.99
27_I	31_L	1.179	0.99
187_L	192_Q	1.148	0.99
184_K	187_L	1.146	0.99
138_A	141_A	1.135	0.99
79_A	82_A	1.112	0.98
26_D	29_T	1.103	0.98
123_A	129_Q	1.100	0.98
72_P	75_L	1.098	0.98
188_A	192_Q	1.093	0.98
24_F	28_V	1.089	0.98
56_G	60_K	1.081	0.98
23_Q	47_Q	1.079	0.98
113_G	117_D	1.071	0.98
98_N	112_A	1.062	0.98
134_E	138_A	1.060	0.98
12_Q	16_A	1.059	0.98
16_A	21_P	1.051	0.98
97_F	137_A	1.050	0.98
110_V	114_Q	1.047	0.98
66_L	73_L	1.047	0.98
159_D	162_A	1.045	0.97
131_A	134_E	1.045	0.97
174_Q	192_Q	1.040	0.97
97_F	115_L	1.033	0.97
80_V	83_L	1.026	0.97
185_A	189_L	1.023	0.97
153_A	179_L	1.021	0.97
123_A	128_S	1.015	0.97
87_A	94_A	1.011	0.97
19_Q	22_A	1.010	0.97
135_A	138_A	1.004	0.97
90_G	94_A	1.004	0.97
29_T	46_G	1.002	0.97
7_G	13_T	0.995	0.97
27_I	48_L	0.991	0.97
90_G	93_E	0.982	0.96
95_R	98_N	0.980	0.96
46_G	49_K	0.977	0.96
118_L	136_L	0.977	0.96
78_A	81_G	0.976	0.96
26_D	43_Q	0.959	0.96
112_A	121_A	0.944	0.95
92_K	96_A	0.941	0.95
149_Q	152_R	0.939	0.95
26_D	30_S	0.936	0.95
123_A	127_G	0.935	0.95
130_G	134_E	0.928	0.95
190_N	199_A	0.922	0.95
14_A	18_R	0.918	0.95
118_L	151_E	0.918	0.95
68_G	72_P	0.917	0.95
23_Q	43_Q	0.915	0.95
153_A	160_M	0.914	0.95
168_V	175_L	0.912	0.95
186_A	196_L	0.910	0.94
36_S	39_T	0.906	0.94
10_A	13_T	0.902	0.94
22_A	39_T	0.885	0.94
30_S	39_T	0.880	0.93
114_Q	117_D	0.874	0.93
23_Q	30_S	0.868	0.93
23_Q	44_Q	0.867	0.93
27_I	30_S	0.866	0.93
95_R	100_A	0.865	0.93
11_K	14_A	0.863	0.93
153_A	156_A	0.862	0.93
19_Q	23_Q	0.858	0.93
20_L	62_L	0.857	0.92
105_G	114_Q	0.855	0.92
112_A	116_A	0.854	0.92
71_N	75_L	0.854	0.92
174_Q	177_K	0.852	0.92
16_A	22_A	0.851	0.92
179_L	185_A	0.850	0.92
197_T	203_Q	0.849	0.92
183_V	187_L	0.845	0.92
78_A	82_A	0.842	0.92
97_F	133_R	0.827	0.91
25_T	49_K	0.823	0.91
106_N	110_V	0.819	0.91
83_L	87_A	0.812	0.90
26_D	44_Q	0.811	0.90
78_A	85_A	0.810	0.90
16_A	19_Q	0.809	0.90
48_L	51_M	0.807	0.90
35_Q	38_L	0.805	0.90
151_E	155_Q	0.793	0.89
142_T	176_A	0.793	0.89
15_A	19_Q	0.791	0.89
135_A	168_V	0.790	0.89
33_S	39_T	0.790	0.89
103_L	143_G	0.787	0.89
24_F	65_Y	0.786	0.89
135_A	158_L	0.783	0.89
116_A	120_R	0.778	0.88
7_G	10_A	0.778	0.88
95_R	99_K	0.775	0.88
21_P	25_T	0.774	0.88
12_Q	19_Q	0.772	0.88
147_G	151_E	0.766	0.88
56_G	62_L	0.766	0.88
46_G	50_D	0.763	0.87
91_S	96_A	0.758	0.87
22_A	50_D	0.758	0.87
29_T	42_L	0.757	0.87
77_A	83_L	0.753	0.87
169_D	173_K	0.753	0.87
168_V	172_A	0.748	0.86
133_R	137_A	0.748	0.86
181_D	185_A	0.740	0.86
99_K	103_L	0.740	0.86
77_A	81_G	0.739	0.86
56_G	65_Y	0.738	0.86
146_A	149_Q	0.736	0.85
182_P	185_A	0.735	0.85
22_A	26_D	0.732	0.85
29_T	33_S	0.732	0.85
194_H	202_E	0.726	0.85
122_L	125_A	0.724	0.84
6_A	9_S	0.713	0.84
9_S	16_A	0.713	0.84
128_S	131_A	0.712	0.83
28_V	42_L	0.711	0.83
190_N	194_H	0.710	0.83
49_K	57_P	0.710	0.83
157_A	161_A	0.709	0.83
67_L	71_N	0.709	0.83
132_A	136_L	0.706	0.83
10_A	14_A	0.704	0.83
180_D	184_K	0.702	0.83
110_V	151_E	0.701	0.83
121_A	124_A	0.699	0.82
117_D	120_R	0.697	0.82
17_L	20_L	0.693	0.82
18_R	25_T	0.692	0.82
17_L	21_P	0.692	0.82
65_Y	69_L	0.690	0.82
151_E	159_D	0.689	0.81
145_I	149_Q	0.688	0.81
79_A	83_L	0.685	0.81
139_L	145_I	0.684	0.81
33_S	40_V	0.682	0.81
106_N	109_G	0.680	0.81
87_A	97_F	0.677	0.80
15_A	18_R	0.670	0.80
30_S	43_Q	0.670	0.80
6_A	10_A	0.669	0.79
137_A	141_A	0.669	0.79
136_L	140_A	0.663	0.79
187_L	190_N	0.661	0.79
43_Q	47_Q	0.659	0.78
122_L	158_L	0.654	0.78
96_A	100_A	0.652	0.78
154_A	158_L	0.648	0.77
85_A	88_Y	0.646	0.77
80_V	84_A	0.643	0.77
187_L	201_Y	0.633	0.76
77_A	82_A	0.632	0.76
109_G	114_Q	0.632	0.76
55_V	58_A	0.629	0.75
31_L	35_Q	0.627	0.75
35_Q	43_Q	0.625	0.75
149_Q	153_A	0.625	0.75
30_S	36_S	0.621	0.74
68_G	71_N	0.617	0.74
157_A	164_T	0.614	0.73
37_P	40_V	0.611	0.73
69_L	74_T	0.610	0.73
20_L	27_I	0.605	0.72
69_L	72_P	0.605	0.72
81_G	88_Y	0.604	0.72
13_T	17_L	0.601	0.72
121_A	125_A	0.599	0.72
18_R	23_Q	0.592	0.71
161_A	164_T	0.589	0.70
164_T	167_D	0.586	0.70
115_L	118_L	0.585	0.70
123_A	130_G	0.580	0.69
8_I	13_T	0.579	0.69
61_A	64_G	0.579	0.69
139_L	142_T	0.579	0.69
19_Q	36_S	0.578	0.69
48_L	61_A	0.577	0.69
189_L	196_L	0.577	0.69
5_K	8_I	0.567	0.67
70_I	74_T	0.563	0.67
93_E	96_A	0.563	0.67
82_A	85_A	0.558	0.66
37_P	42_L	0.558	0.66
168_V	178_A	0.558	0.66
22_A	29_T	0.555	0.66
120_R	124_A	0.554	0.66
49_K	55_V	0.553	0.66
195_F	201_Y	0.547	0.65
17_L	24_F	0.547	0.65
87_A	91_S	0.546	0.65
175_L	179_L	0.545	0.64
11_K	20_L	0.545	0.64
98_N	104_T	0.545	0.64
22_A	28_V	0.542	0.64
23_Q	27_I	0.541	0.64
29_T	40_V	0.541	0.64
8_I	15_A	0.539	0.64
21_P	24_F	0.539	0.64
36_S	40_V	0.539	0.64
178_A	181_D	0.534	0.63
122_L	154_A	0.534	0.63
122_L	126_T	0.533	0.63
178_A	185_A	0.529	0.62
147_G	152_R	0.528	0.62
174_Q	193_Y	0.527	0.62
140_A	150_F	0.526	0.62
35_Q	40_V	0.526	0.62
157_A	172_A	0.520	0.61
39_T	42_L	0.518	0.61
198_A	201_Y	0.514	0.60
135_A	157_A	0.514	0.60
58_A	61_A	0.511	0.60
156_A	159_D	0.510	0.59
173_K	192_Q	0.506	0.59
49_K	54_G	0.505	0.59
24_F	30_S	0.502	0.58
196_L	201_Y	0.501	0.58
29_T	36_S	0.500	0.58

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
3zx6A	2	0.9366	30	0.913	Contact Map
2ch7A	2	0.961	12.2	0.927	Contact Map
1qu7A	2	0.9463	9.7	0.93	Contact Map
4j42A	2	0.4049	9.1	0.931	Contact Map
4q4gX	1	0	7.8	0.933	Contact Map
2nrjA	1	0.7951	7.4	0.934	Contact Map
2wssS	1	0.6439	7.2	0.934	Contact Map
4cgkA	3	0.5073	6.6	0.935	Contact Map
1ciiA	1	0.4634	4.2	0.941	Contact Map
3gwkC	2	0.4732	3.5	0.943	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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