Phage_tail_S - PFAM28P - GREMLIN Contacts

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Phage_tail_S - Phage virion morphogenesis family

PFAM:	PF05069	Sequences: DDLEELEAALARLLARPADRRPLMREIGEELRRSTQERFEAQGAPDGTPWAPLKPSTLRAKKGRGKRGGKILQKTGRLRRSITYQADADSVVVGTNVPYAAIHQFGGKAGRDRVSRGGPKVTIPARPFLGLSDEDEEEILDIILDHLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	148 (143)
Sequences:	5289 (4326)
Seq/√Len:	361.7
META:	0.732

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
102_I	107_G	4.812	1.00
44_A	48_T	3.695	1.00
34_S	135_D	3.073	1.00
77_R	97_V	3.065	1.00
87_D	90_S	2.833	1.00
102_I	123_I	2.771	1.00
23_L	143_I	2.638	1.00
101_A	105_F	2.494	1.00
73_Q	79_R	2.425	1.00
27_I	139_I	2.377	1.00
28_G	84_Y	2.375	1.00
30_E	142_I	2.370	1.00
53_L	71_I	2.365	1.00
42_Q	71_I	2.151	1.00
28_G	91_V	2.150	1.00
39_F	50_W	2.111	1.00
30_E	138_E	2.015	1.00
104_Q	127_P	1.855	1.00
42_Q	73_Q	1.844	1.00
37_E	41_A	1.835	1.00
82_I	128_F	1.823	1.00
20_R	23_L	1.804	1.00
32_R	36_Q	1.719	1.00
38_R	43_G	1.696	1.00
24_M	86_A	1.654	1.00
36_Q	79_R	1.603	1.00
95_T	100_A	1.600	1.00
31_L	93_V	1.512	1.00
107_G	123_I	1.493	1.00
54_K	57_T	1.435	1.00
38_R	44_A	1.406	1.00
104_Q	128_F	1.392	1.00
21_R	88_A	1.364	1.00
26_E	142_I	1.355	1.00
133_D	136_E	1.324	1.00
32_R	84_Y	1.311	1.00
55_P	59_R	1.295	1.00
12_R	16_R	1.286	1.00
44_A	127_P	1.262	1.00
115_S	118_G	1.253	1.00
57_T	60_A	1.250	1.00
34_S	132_S	1.229	1.00
27_I	143_I	1.222	1.00
38_R	130_G	1.211	1.00
100_A	128_F	1.204	1.00
132_S	135_D	1.197	1.00
35_T	38_R	1.191	1.00
140_L	144_L	1.187	1.00
136_E	140_L	1.184	1.00
85_Q	92_V	1.174	1.00
24_M	91_V	1.163	1.00
25_R	84_Y	1.153	1.00
70_K	73_Q	1.141	1.00
73_Q	76_G	1.135	1.00
116_R	119_P	1.133	1.00
30_E	34_S	1.122	1.00
19_D	22_P	1.101	1.00
23_L	142_I	1.101	1.00
38_R	135_D	1.092	1.00
53_L	61_K	1.090	1.00
21_R	25_R	1.073	1.00
38_R	132_S	1.057	1.00
118_G	121_V	1.038	1.00
78_L	99_Y	1.030	1.00
9_A	12_R	1.012	1.00
103_H	125_A	1.006	1.00
23_L	27_I	1.002	1.00
35_T	129_L	0.982	1.00
81_S	95_T	0.979	1.00
29_E	32_R	0.979	1.00
114_V	117_G	0.962	1.00
24_M	90_S	0.939	1.00
8_A	12_R	0.938	1.00
115_S	120_K	0.936	1.00
29_E	84_Y	0.927	1.00
35_T	93_V	0.920	1.00
78_L	100_A	0.917	1.00
111_R	114_V	0.912	1.00
103_H	123_I	0.911	1.00
7_E	11_A	0.911	1.00
112_D	118_G	0.904	1.00
17_P	20_R	0.903	1.00
40_E	79_R	0.901	1.00
107_G	121_V	0.893	1.00
78_L	81_S	0.892	1.00
99_Y	103_H	0.892	1.00
4_E	8_A	0.891	1.00
109_A	112_D	0.883	1.00
44_A	132_S	0.880	1.00
28_G	86_A	0.878	1.00
35_T	130_G	0.875	1.00
66_K	74_K	0.875	1.00
5_E	8_A	0.874	1.00
32_R	82_I	0.868	1.00
38_R	46_D	0.860	1.00
115_S	121_V	0.847	1.00
108_K	122_T	0.842	1.00
65_G	68_G	0.838	1.00
138_E	142_I	0.821	1.00
33_R	36_Q	0.821	1.00
20_R	24_M	0.821	1.00
16_R	146_H	0.820	1.00
82_I	95_T	0.809	1.00
11_A	15_A	0.808	1.00
87_D	92_V	0.807	1.00
28_G	32_R	0.805	1.00
35_T	128_F	0.793	1.00
109_A	121_V	0.790	1.00
21_R	86_A	0.786	1.00
77_R	80_R	0.786	1.00
44_A	50_W	0.784	1.00
104_Q	125_A	0.782	1.00
19_D	88_A	0.778	1.00
42_Q	70_K	0.771	1.00
138_E	141_D	0.768	1.00
112_D	119_P	0.766	1.00
116_R	120_K	0.764	1.00
11_A	14_L	0.755	1.00
46_D	132_S	0.754	1.00
115_S	119_P	0.752	1.00
114_V	119_P	0.748	1.00
112_D	120_K	0.731	1.00
44_A	47_G	0.728	1.00
30_E	33_R	0.723	1.00
81_S	96_N	0.723	1.00
55_P	58_L	0.715	0.99
35_T	82_I	0.711	0.99
23_L	146_H	0.709	0.99
39_F	79_R	0.708	0.99
86_A	91_V	0.707	0.99
119_P	122_T	0.704	0.99
60_A	64_R	0.703	0.99
53_L	58_L	0.703	0.99
131_L	139_I	0.702	0.99
60_A	74_K	0.701	0.99
34_S	38_R	0.693	0.99
12_R	15_A	0.692	0.99
69_G	74_K	0.691	0.99
53_L	57_T	0.690	0.99
35_T	104_Q	0.688	0.99
76_G	79_R	0.687	0.99
45_P	135_D	0.685	0.99
107_G	122_T	0.683	0.99
83_T	96_N	0.679	0.99
51_A	71_I	0.671	0.99
31_L	135_D	0.657	0.99
29_E	33_R	0.656	0.99
71_I	74_K	0.654	0.99
31_L	139_I	0.652	0.99
131_L	136_E	0.650	0.99
101_A	107_G	0.648	0.99
42_Q	50_W	0.643	0.99
33_R	37_E	0.640	0.99
27_I	30_E	0.639	0.99
134_E	138_E	0.636	0.99
111_R	122_T	0.634	0.99
76_G	80_R	0.634	0.99
57_T	61_K	0.633	0.99
46_D	130_G	0.633	0.99
130_G	135_D	0.624	0.99
31_L	34_S	0.620	0.99
86_A	90_S	0.619	0.98
44_A	130_G	0.613	0.98
58_L	61_K	0.607	0.98
37_E	40_E	0.604	0.98
117_G	120_K	0.600	0.98
67_R	74_K	0.596	0.98
25_R	29_E	0.596	0.98
30_E	139_I	0.593	0.98
112_D	116_R	0.590	0.98
99_Y	102_I	0.590	0.98
20_R	88_A	0.589	0.98
14_L	18_A	0.589	0.98
57_T	65_G	0.588	0.98
112_D	121_V	0.587	0.98
63_G	66_K	0.582	0.98
104_Q	129_L	0.581	0.98
112_D	117_G	0.579	0.98
26_E	30_E	0.577	0.98
31_L	91_V	0.577	0.98
102_I	105_F	0.576	0.98
52_P	58_L	0.568	0.97
43_G	49_P	0.567	0.97
31_L	131_L	0.566	0.97
131_L	135_D	0.564	0.97
72_L	75_T	0.563	0.97
26_E	146_H	0.559	0.97
38_R	45_P	0.558	0.97
109_A	120_K	0.553	0.97
56_S	60_A	0.553	0.97
117_G	121_V	0.546	0.97
135_D	138_E	0.544	0.97
72_L	103_H	0.544	0.97
114_V	118_G	0.543	0.97
110_G	117_G	0.540	0.96
106_G	125_A	0.538	0.96
84_Y	91_V	0.537	0.96
51_A	124_P	0.534	0.96
82_I	93_V	0.531	0.96
66_K	69_G	0.530	0.96
94_G	129_L	0.530	0.96
4_E	7_E	0.530	0.96
137_E	140_L	0.528	0.96
139_I	143_I	0.527	0.96
111_R	120_K	0.523	0.96
110_G	116_R	0.520	0.96
24_M	88_A	0.518	0.96
56_S	59_R	0.509	0.95
98_P	101_A	0.508	0.95
66_K	75_T	0.507	0.95
34_S	130_G	0.507	0.95
38_R	41_A	0.504	0.95
114_V	120_K	0.504	0.95
111_R	118_G	0.500	0.95

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
4bolA	2	0.3919	8.6	0.921	Contact Map
3d2yA	3	0.4122	5.2	0.928	Contact Map
3ebbA	2	0.2162	4.3	0.931	Contact Map
4w7sA	2	0.8919	4.3	0.931	Contact Map
4bxjA	4	0.4054	3.8	0.933	Contact Map
3omsA	2	0.3243	3.4	0.934	Contact Map
2f95B	2	0	3.4	0.935	Contact Map
4n4pA	3	0.8108	3.2	0.935	Contact Map
1gotG	1	0.3378	3.2	0.935	Contact Map
3zifN	3	0.223	3.2	0.935	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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