Phage_T7_tail - PFAM28P - GREMLIN Contacts

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Phage_T7_tail - Phage T7 tail fibre protein

PFAM:	PF03906	Sequences: MANTPNSYVTYTGDGSTTTFSFTFPYLDTSDVKVTVDGVVKTLTTDYTFANATTITFTTAPANGAAIRIRRDTPTDTRLVDFQDGSVLTESDLDTNFLQNLYLAQEAIDLAADSLGLDADGNWDAQNKRITNVADPTDAQDAVTKNYVDTTITSQLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	157 (144)
Sequences:	1379 (1110)
Seq/√Len:	92.5
META:	0.909

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_P	147_Y	3.700	1.00
36_V	65_A	3.133	1.00
143_V	148_V	2.928	1.00
81_D	94_D	2.922	1.00
33_K	72_D	2.894	1.00
135_D	140_Q	2.832	1.00
19_T	56_T	2.670	1.00
140_Q	144_T	2.662	1.00
145_K	149_D	2.564	1.00
31_D	102_Y	2.496	1.00
62_A	65_A	2.203	1.00
133_V	142_A	2.106	1.00
90_E	94_D	2.016	1.00
127_N	134_A	1.940	1.00
14_D	17_T	1.921	1.00
120_D	131_T	1.919	1.00
31_D	74_P	1.913	1.00
135_D	146_N	1.886	1.00
29_T	49_F	1.867	1.00
140_Q	146_N	1.828	1.00
25_P	102_Y	1.769	1.00
18_T	60_A	1.735	1.00
125_A	130_I	1.705	1.00
20_F	67_I	1.652	1.00
98_L	102_Y	1.634	1.00
101_L	105_Q	1.623	1.00
139_A	146_N	1.594	1.00
41_K	46_D	1.592	1.00
122_N	129_R	1.585	1.00
29_T	52_A	1.549	1.00
22_F	26_Y	1.534	1.00
41_K	47_Y	1.526	1.00
10_T	68_R	1.523	1.00
124_D	132_N	1.517	1.00
139_A	149_D	1.478	1.00
57_F	61_P	1.473	1.00
75_T	103_L	1.470	1.00
147_Y	150_T	1.466	1.00
78_R	101_L	1.450	1.00
22_F	49_F	1.422	0.99
136_P	145_K	1.407	0.99
37_D	65_A	1.361	0.99
34_V	55_I	1.304	0.99
78_R	97_F	1.280	0.99
118_D	131_T	1.273	0.99
49_F	52_A	1.260	0.99
129_R	141_D	1.224	0.98
130_I	133_V	1.199	0.98
18_T	56_T	1.192	0.98
107_A	111_A	1.174	0.98
89_T	92_D	1.171	0.98
35_T	68_R	1.162	0.98
78_R	96_N	1.158	0.98
117_L	128_K	1.142	0.97
81_D	90_E	1.138	0.97
21_S	54_T	1.136	0.97
28_D	31_D	1.118	0.97
123_W	128_K	1.105	0.97
35_T	70_R	1.089	0.96
125_A	133_V	1.088	0.96
115_L	123_W	1.082	0.96
35_T	40_V	1.080	0.96
9_V	23_T	1.076	0.96
97_F	100_N	1.072	0.96
79_L	95_T	1.067	0.96
146_N	150_T	1.066	0.96
123_W	130_I	1.066	0.96
84_D	89_T	1.054	0.96
84_D	88_L	1.049	0.96
41_K	44_T	1.049	0.96
50_A	56_T	1.046	0.96
49_F	55_I	1.040	0.95
15_G	63_N	1.038	0.95
13_G	20_F	1.035	0.95
13_G	60_A	1.030	0.95
129_R	137_T	1.029	0.95
33_K	70_R	1.019	0.95
73_T	106_E	1.013	0.95
78_R	98_L	1.011	0.95
123_W	126_Q	1.007	0.95
31_D	79_L	1.005	0.94
19_T	50_A	0.999	0.94
136_P	148_V	0.970	0.93
137_T	147_Y	0.965	0.93
146_N	149_D	0.963	0.93
122_N	131_T	0.960	0.93
32_V	49_F	0.953	0.93
80_V	95_T	0.929	0.92
82_F	96_N	0.917	0.91
130_I	142_A	0.910	0.91
99_Q	106_E	0.908	0.91
128_K	132_N	0.899	0.90
73_T	99_Q	0.883	0.90
57_F	60_A	0.870	0.89
36_V	67_I	0.865	0.89
19_T	54_T	0.861	0.88
135_D	148_V	0.860	0.88
88_L	93_L	0.856	0.88
141_D	145_K	0.850	0.88
57_F	67_I	0.829	0.87
100_N	105_Q	0.820	0.86
26_Y	29_T	0.817	0.86
118_D	122_N	0.816	0.86
42_T	46_D	0.810	0.85
61_P	65_A	0.805	0.85
137_T	149_D	0.799	0.84
135_D	147_Y	0.788	0.84
141_D	144_T	0.784	0.83
34_V	47_Y	0.782	0.83
13_G	61_P	0.780	0.83
138_D	141_D	0.765	0.82
89_T	94_D	0.759	0.81
122_N	125_A	0.759	0.81
128_K	134_A	0.758	0.81
51_N	54_T	0.754	0.81
73_T	102_Y	0.751	0.81
139_A	144_T	0.745	0.80
124_D	131_T	0.743	0.80
134_A	137_T	0.742	0.80
110_L	114_S	0.742	0.80
136_P	143_V	0.741	0.80
80_V	97_F	0.739	0.80
43_L	47_Y	0.732	0.79
125_A	142_A	0.724	0.78
110_L	113_D	0.721	0.78
7_S	11_Y	0.719	0.78
135_D	142_A	0.712	0.77
136_P	141_D	0.711	0.77
104_A	107_A	0.709	0.77
24_F	32_V	0.709	0.77
82_F	97_F	0.707	0.76
117_L	121_G	0.704	0.76
36_V	41_K	0.702	0.76
130_I	141_D	0.698	0.76
143_V	149_D	0.692	0.75
121_G	128_K	0.686	0.74
41_K	57_F	0.685	0.74
7_S	10_T	0.684	0.74
13_G	63_N	0.680	0.74
93_L	106_E	0.679	0.74
92_D	96_N	0.676	0.73
140_Q	143_V	0.674	0.73
133_V	136_P	0.673	0.73
139_A	150_T	0.666	0.72
27_L	31_D	0.650	0.70
8_Y	68_R	0.645	0.70
103_L	108_I	0.641	0.69
97_F	101_L	0.641	0.69
40_V	43_L	0.636	0.69
129_R	138_D	0.634	0.68
40_V	47_Y	0.634	0.68
112_A	126_Q	0.632	0.68
15_G	61_P	0.627	0.68
43_L	46_D	0.626	0.67
134_A	141_D	0.626	0.67
57_F	69_I	0.624	0.67
137_T	141_D	0.623	0.67
17_T	20_F	0.621	0.67
96_N	103_L	0.619	0.67
125_A	128_K	0.616	0.66
73_T	92_D	0.609	0.65
110_L	116_G	0.606	0.65
84_D	87_V	0.599	0.64
37_D	41_K	0.599	0.64
91_S	95_T	0.598	0.64
140_Q	149_D	0.598	0.64
135_D	149_D	0.597	0.64
13_G	67_I	0.595	0.64
38_G	41_K	0.588	0.63
111_A	114_S	0.588	0.63
43_L	48_T	0.588	0.63
74_P	100_N	0.587	0.62
127_N	132_N	0.583	0.62
34_V	69_I	0.582	0.62
51_N	56_T	0.572	0.60
125_A	132_N	0.572	0.60
18_T	59_T	0.570	0.60
129_R	136_P	0.569	0.60
112_A	116_G	0.566	0.60
22_F	25_P	0.566	0.60
130_I	135_D	0.565	0.60
82_F	100_N	0.562	0.59
74_P	79_L	0.561	0.59
132_N	139_A	0.556	0.58
117_L	120_D	0.555	0.58
36_V	61_P	0.554	0.58
134_A	140_Q	0.551	0.58
13_G	62_A	0.546	0.57
87_V	90_E	0.544	0.57
41_K	48_T	0.541	0.56
115_L	130_I	0.538	0.56
144_T	148_V	0.536	0.56
82_F	94_D	0.535	0.55
84_D	91_S	0.534	0.55
22_F	97_F	0.531	0.55
115_L	118_D	0.530	0.55
31_D	73_T	0.523	0.54
13_G	66_A	0.519	0.53
135_D	139_A	0.518	0.53
139_A	147_Y	0.518	0.53
143_V	147_Y	0.516	0.53
86_S	92_D	0.516	0.53
92_D	95_T	0.515	0.53
138_D	143_V	0.515	0.53
16_S	21_S	0.515	0.53
144_T	147_Y	0.511	0.52
119_A	125_A	0.510	0.52
84_D	92_D	0.510	0.52
11_Y	22_F	0.509	0.52
75_T	108_I	0.509	0.52
48_T	58_T	0.507	0.52
133_V	143_V	0.506	0.51
130_I	137_T	0.505	0.51
22_F	75_T	0.503	0.51
143_V	146_N	0.503	0.51
71_R	106_E	0.500	0.51

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
4lgoA	3	0.7197	80	0.892	Contact Map
3d9xA	3	0.4968	66.6	0.903	Contact Map
3emoC	3	0.1847	60.6	0.907	Contact Map
3wprA	3	0.9172	34.9	0.92	Contact Map
4usxA	3	0.1975	26.3	0.925	Contact Map
2yo2A	3	0.6879	17.5	0.931	Contact Map
3s6lA	4	0.5987	16.3	0.932	Contact Map
2d73A	2	0.535	14.6	0.933	Contact Map
2xqhA	3	0.5796	11.5	0.936	Contact Map
3wpaA	3	0.7898	11.5	0.936	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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