Phage_holin_3_6 - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

Phage_holin_3_6 - Putative Actinobacterial Holin-X, holin superfamily III

PFAM:	PF07332	Sequences: GELVRDLAEDLSTLVRQELELAKAELKEKAKRAGRGAGLLAAAAVLALLALLFLLAALVLALAARWLAALIVAGVLLLVAAVLALVGRRRLKRASPVPERTIEELKEDVEWLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (110)
Sequences:	35733 (25450)
Seq/√Len:	2426.6
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_L	76_L	3.763	1.00
81_A	85_L	2.612	1.00
60_L	65_R	2.523	1.00
50_A	77_L	2.499	1.00
88_R	92_K	2.427	1.00
82_V	86_V	2.399	1.00
86_V	90_R	2.140	1.00
13_T	17_Q	2.079	1.00
85_L	88_R	1.804	1.00
59_V	69_A	1.799	1.00
57_A	70_L	1.717	1.00
107_E	111_W	1.702	1.00
84_A	88_R	1.672	1.00
98_P	102_I	1.630	1.00
85_L	89_R	1.629	1.00
34_G	38_G	1.619	1.00
60_L	69_A	1.566	1.00
104_E	107_E	1.554	1.00
54_L	73_A	1.523	1.00
57_A	73_A	1.514	1.00
50_A	80_A	1.494	1.00
31_K	34_G	1.491	1.00
43_A	84_A	1.452	1.00
105_L	108_D	1.400	1.00
49_L	52_L	1.384	1.00
53_F	59_V	1.383	1.00
47_A	80_A	1.381	1.00
56_A	60_L	1.375	1.00
27_K	31_K	1.371	1.00
45_V	48_L	1.355	1.00
86_V	89_R	1.343	1.00
40_L	87_G	1.307	1.00
20_E	23_K	1.301	1.00
65_R	69_A	1.283	1.00
23_K	27_K	1.258	1.00
78_L	82_V	1.244	1.00
58_L	72_V	1.236	1.00
65_R	68_A	1.223	1.00
52_L	56_A	1.216	1.00
48_L	52_L	1.216	1.00
60_L	63_A	1.209	1.00
105_L	109_V	1.206	1.00
56_A	69_A	1.185	1.00
17_Q	20_E	1.183	1.00
50_A	73_A	1.135	1.00
29_K	32_R	1.133	1.00
108_D	111_W	1.133	1.00
46_L	76_L	1.121	1.00
27_K	30_A	1.109	1.00
35_R	38_G	1.076	1.00
102_I	106_K	1.062	1.00
12_S	16_R	1.055	1.00
38_G	42_A	1.052	1.00
89_R	93_R	1.049	1.00
31_K	35_R	1.044	1.00
35_R	90_R	1.037	1.00
49_L	53_F	1.010	1.00
101_T	104_E	1.007	1.00
61_A	64_A	1.006	1.00
39_L	86_V	1.003	1.00
66_W	69_A	1.002	1.00
36_G	91_L	0.992	1.00
51_L	76_L	0.984	1.00
57_A	61_A	0.982	1.00
82_V	85_L	0.974	1.00
6_D	10_D	0.964	1.00
95_S	99_E	0.963	1.00
53_F	56_A	0.955	1.00
107_E	110_E	0.955	1.00
73_A	77_L	0.934	1.00
18_E	108_D	0.924	1.00
90_R	93_R	0.914	1.00
49_L	55_L	0.913	1.00
26_L	30_A	0.911	1.00
89_R	92_K	0.907	1.00
66_W	70_L	0.903	1.00
67_L	70_L	0.886	1.00
98_P	101_T	0.881	1.00
24_A	28_E	0.879	1.00
30_A	34_G	0.878	1.00
43_A	87_G	0.873	1.00
103_E	107_E	0.863	1.00
37_A	41_A	0.858	1.00
58_L	61_A	0.849	1.00
103_E	106_K	0.840	1.00
39_L	83_L	0.834	1.00
14_L	18_E	0.829	1.00
54_L	57_A	0.827	1.00
101_T	105_L	0.826	1.00
9_E	12_S	0.822	1.00
68_A	72_V	0.818	1.00
3_L	10_D	0.817	1.00
14_L	17_Q	0.809	1.00
74_G	78_L	0.809	1.00
8_A	12_S	0.796	1.00
16_R	20_E	0.796	1.00
30_A	33_A	0.791	1.00
36_G	87_G	0.789	1.00
75_V	79_V	0.785	1.00
59_V	72_V	0.785	1.00
81_A	84_A	0.780	1.00
67_L	71_I	0.762	1.00
56_A	59_V	0.756	1.00
100_R	104_E	0.753	1.00
100_R	103_E	0.750	1.00
22_A	25_E	0.744	1.00
21_L	24_A	0.743	1.00
51_L	55_L	0.743	1.00
11_L	15_V	0.735	1.00
5_R	9_E	0.730	1.00
39_L	42_A	0.727	1.00
42_A	83_L	0.725	1.00
61_A	66_W	0.720	1.00
77_L	81_A	0.719	1.00
63_A	68_A	0.718	1.00
19_L	23_K	0.712	1.00
59_V	68_A	0.705	1.00
26_L	29_K	0.704	1.00
53_F	73_A	0.703	1.00
25_E	101_T	0.698	1.00
21_L	25_E	0.695	1.00
8_A	11_L	0.692	1.00
44_A	48_L	0.684	1.00
72_V	76_L	0.682	1.00
106_K	110_E	0.676	1.00
32_R	90_R	0.667	1.00
106_K	109_V	0.665	1.00
45_V	51_L	0.661	1.00
55_L	72_V	0.656	1.00
18_E	22_A	0.654	1.00
9_E	13_T	0.645	1.00
46_L	79_V	0.636	1.00
20_E	24_A	0.627	1.00
106_K	111_W	0.626	1.00
74_G	81_A	0.623	1.00
99_E	102_I	0.622	1.00
26_L	98_P	0.620	1.00
70_L	74_G	0.619	1.00
99_E	103_E	0.609	1.00
96_P	99_E	0.607	1.00
29_K	97_V	0.606	1.00
43_A	83_L	0.596	1.00
35_R	39_L	0.589	1.00
3_L	7_L	0.583	1.00
3_L	6_D	0.572	1.00
6_D	9_E	0.561	1.00
49_L	76_L	0.560	1.00
97_V	102_I	0.560	1.00
65_R	70_L	0.554	1.00
42_A	45_V	0.550	1.00
36_G	90_R	0.548	1.00
102_I	105_L	0.547	1.00
32_R	35_R	0.547	1.00
15_V	19_L	0.538	1.00
57_A	66_W	0.531	1.00
83_L	87_G	0.528	1.00
28_E	32_R	0.527	1.00
40_L	84_A	0.527	1.00
81_A	88_R	0.525	1.00
13_T	16_R	0.516	1.00
10_D	13_T	0.514	1.00
34_G	37_A	0.513	1.00
39_L	90_R	0.506	1.00
7_L	10_D	0.501	1.00
68_A	71_I	0.500	1.00

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
4ev6A	3	0.8053	30.2	0.834	Contact Map
4i0uA	4	0.7522	23.4	0.842	Contact Map
4ry2A	2	0.7876	17.5	0.851	Contact Map
4q4hA	1	0.7965	17.3	0.851	Contact Map
3wmgA	1	0.7965	16.3	0.853	Contact Map
4a82A	2	0.7965	14.2	0.857	Contact Map
3zdqA	2	0.7965	13.9	0.858	Contact Map
2m20A	2	0.4425	13.6	0.858	Contact Map
3b60A	2	0.7965	13.5	0.858	Contact Map
3b5xA	2	0.7965	12	0.862	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.

Page generated in 0.0057 seconds.