Phage_GPL - PFAM28P - GREMLIN Contacts

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Phage_GPL - Phage head completion protein (GPL)

PFAM:	PF05926	Sequences: ITNDGFWPDIDLADFREAMRLDGTVTPERLRDALIAAMAEVNRELAAWRAAQQAAGYATLADVPAEQIDGESVLVHLYRRAVYARAKADLLERYRDYDATASGEKRAEELEETIDDLRRDARWAIRDILGRPRTTVELI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (139)
Sequences:	1114 (827)
Seq/√Len:	70.1
META:	0.489

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_Q	55_A	3.414	1.00
15_F	34_L	3.061	1.00
42_N	78_Y	2.995	1.00
31_R	69_D	2.887	1.00
3_N	42_N	2.780	1.00
71_E	79_R	2.657	1.00
48_W	52_Q	2.561	1.00
85_R	121_A	2.468	1.00
17_E	28_E	2.466	1.00
127_D	133_R	2.463	1.00
87_K	96_D	2.456	1.00
41_V	125_I	2.418	1.00
49_R	53_Q	2.352	1.00
59_T	62_D	2.340	1.00
117_L	120_D	2.322	1.00
4_D	49_R	2.288	1.00
65_A	72_S	2.202	1.00
12_L	34_L	2.142	1.00
5_G	9_D	2.072	1.00
49_R	66_E	2.041	1.00
57_Y	64_P	2.036	1.00
6_F	59_T	2.026	1.00
34_L	86_A	2.019	1.00
35_I	69_D	1.993	1.00
14_D	79_R	1.836	1.00
74_L	128_I	1.833	1.00
39_A	73_V	1.738	1.00
87_K	91_L	1.732	1.00
93_R	120_D	1.707	1.00
3_N	78_Y	1.700	1.00
3_N	9_D	1.693	1.00
89_D	120_D	1.676	1.00
103_G	107_A	1.572	0.99
73_V	77_L	1.548	0.99
15_F	86_A	1.532	0.99
36_A	77_L	1.461	0.99
35_I	68_I	1.416	0.98
48_W	128_I	1.355	0.98
15_F	83_Y	1.346	0.98
44_E	122_R	1.345	0.98
41_V	81_A	1.302	0.97
31_R	35_I	1.299	0.97
19_M	87_K	1.284	0.97
104_E	108_E	1.284	0.97
4_D	7_W	1.231	0.96
44_E	126_R	1.182	0.95
79_R	83_Y	1.181	0.95
35_I	76_H	1.150	0.94
126_R	129_L	1.144	0.94
11_D	14_D	1.143	0.94
18_A	83_Y	1.123	0.93
52_Q	128_I	1.113	0.93
80_R	124_A	1.108	0.93
84_A	120_D	1.107	0.93
71_E	75_V	1.095	0.93
86_A	121_A	1.086	0.92
15_F	30_L	1.051	0.91
2_T	9_D	1.034	0.90
40_E	127_D	1.032	0.90
4_D	66_E	1.032	0.90
80_R	84_A	0.976	0.88
125_I	129_L	0.968	0.87
116_D	119_R	0.959	0.87
41_V	121_A	0.953	0.86
14_D	83_Y	0.946	0.86
3_N	38_M	0.946	0.86
123_W	126_R	0.944	0.86
104_E	107_A	0.943	0.86
52_Q	63_V	0.942	0.86
39_A	77_L	0.921	0.84
19_M	117_L	0.920	0.84
104_E	109_E	0.918	0.84
126_R	131_R	0.918	0.84
16_R	20_R	0.910	0.84
72_S	75_V	0.900	0.83
99_A	110_L	0.897	0.83
60_L	65_A	0.896	0.83
134_T	139_I	0.892	0.82
87_K	99_A	0.889	0.82
60_L	63_V	0.884	0.82
92_E	119_R	0.881	0.82
107_A	113_T	0.880	0.82
44_E	135_T	0.879	0.81
122_R	126_R	0.851	0.79
95_R	116_D	0.848	0.79
89_D	117_L	0.843	0.79
53_Q	56_G	0.838	0.78
101_A	105_K	0.832	0.78
77_L	133_R	0.831	0.78
108_E	112_E	0.826	0.77
64_P	72_S	0.820	0.77
25_V	29_R	0.799	0.75
63_V	74_L	0.795	0.75
43_R	73_V	0.793	0.74
131_R	135_T	0.784	0.73
136_V	139_I	0.781	0.73
80_R	89_D	0.777	0.73
110_L	114_I	0.773	0.72
77_L	127_D	0.771	0.72
22_D	97_Y	0.769	0.72
16_R	29_R	0.758	0.71
36_A	40_E	0.757	0.71
18_A	32_D	0.749	0.70
32_D	79_R	0.748	0.70
10_I	38_M	0.744	0.70
96_D	110_L	0.741	0.69
98_D	110_L	0.738	0.69
37_A	85_R	0.738	0.69
16_R	92_E	0.737	0.69
91_L	110_L	0.733	0.68
33_A	89_D	0.732	0.68
121_A	128_I	0.732	0.68
15_F	19_M	0.728	0.68
12_L	27_P	0.726	0.68
42_N	94_Y	0.726	0.68
32_D	80_R	0.726	0.68
1_I	125_I	0.720	0.67
99_A	105_K	0.716	0.67
1_I	15_F	0.713	0.66
13_A	17_E	0.712	0.66
133_R	139_I	0.711	0.66
46_A	50_A	0.705	0.65
19_M	86_A	0.703	0.65
92_E	114_I	0.702	0.65
93_R	117_L	0.691	0.64
44_E	85_R	0.691	0.64
85_R	118_R	0.689	0.64
77_L	124_A	0.688	0.63
77_L	128_I	0.681	0.63
14_D	18_A	0.671	0.62
26_T	29_R	0.668	0.61
27_P	31_R	0.668	0.61
52_Q	57_Y	0.663	0.61
114_I	117_L	0.655	0.60
113_T	116_D	0.655	0.60
26_T	30_L	0.652	0.59
16_R	27_P	0.650	0.59
99_A	109_E	0.643	0.58
11_D	34_L	0.635	0.57
119_R	123_W	0.633	0.57
7_W	60_L	0.627	0.56
10_I	79_R	0.627	0.56
95_R	107_A	0.626	0.56
77_L	80_R	0.626	0.56
13_A	112_E	0.621	0.56
24_T	97_Y	0.618	0.55
92_E	98_D	0.617	0.55
61_A	75_V	0.616	0.55
112_E	115_D	0.616	0.55
38_M	68_I	0.614	0.55
1_I	6_F	0.614	0.55
126_R	130_G	0.611	0.54
43_R	77_L	0.609	0.54
51_A	55_A	0.603	0.54
67_Q	72_S	0.597	0.53
67_Q	70_G	0.597	0.53
32_D	71_E	0.593	0.52
13_A	27_P	0.592	0.52
95_R	111_E	0.591	0.52
87_K	112_E	0.587	0.52
95_R	99_A	0.586	0.51
23_G	41_V	0.585	0.51
37_A	80_R	0.576	0.50
36_A	76_H	0.575	0.50
29_R	119_R	0.575	0.50
132_P	136_V	0.569	0.49
74_L	126_R	0.569	0.49
60_L	70_G	0.567	0.49
14_D	17_E	0.566	0.49
57_Y	74_L	0.564	0.49
68_I	72_S	0.564	0.49
11_D	27_P	0.564	0.49
47_A	62_D	0.562	0.49
47_A	58_A	0.562	0.49
6_F	21_L	0.561	0.48
39_A	76_H	0.559	0.48
36_A	89_D	0.559	0.48
126_R	135_T	0.552	0.47
98_D	103_G	0.550	0.47
51_A	62_D	0.540	0.46
99_A	106_R	0.537	0.46
100_T	108_E	0.537	0.46
25_V	94_Y	0.537	0.46
40_E	44_E	0.532	0.45
50_A	54_A	0.532	0.45
89_D	123_W	0.529	0.45
29_R	92_E	0.529	0.45
84_A	117_L	0.527	0.44
10_I	83_Y	0.527	0.44
17_E	102_S	0.526	0.44
97_Y	101_A	0.525	0.44
12_L	16_R	0.524	0.44
38_M	41_V	0.524	0.44
23_G	30_L	0.523	0.44
3_N	6_F	0.520	0.43
19_M	83_Y	0.520	0.43
74_L	77_L	0.520	0.43
37_A	138_L	0.519	0.43
29_R	100_T	0.511	0.42
96_D	105_K	0.509	0.42
1_I	38_M	0.508	0.42
90_L	102_S	0.507	0.42
20_R	25_V	0.506	0.42
96_D	100_T	0.503	0.41
50_A	53_Q	0.503	0.41
95_R	98_D	0.502	0.41
54_A	61_A	0.501	0.41
46_A	66_E	0.500	0.41

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
2i5uA	1	0.3885	18.5	0.931	Contact Map
3c8gA	2	0.3165	13.2	0.935	Contact Map
2bolA	2	0.259	11.5	0.937	Contact Map
4m7uA	1	0.295	8.9	0.94	Contact Map
4kt0J	1	0.1007	8.6	0.94	Contact Map
4xk8J	1	0.0935	8.6	0.94	Contact Map
1cb8A	1	0.8489	8.1	0.941	Contact Map
1repC	1	0.4892	7.9	0.941	Contact Map
2cazB	1	0.6475	6	0.945	Contact Map
3u52C	2	0.6475	5.5	0.946	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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