PFDB - HALSA - GREMLIN Contacts

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PFDB - Prefoldin subunit beta

UniProt:	Q9HSH0	Sequences: MQGNLPPEAQEKLEQLQDLQEKAQNVATQKQQAEQQLSEAETALDALGDIEESTTMYREVGELLVETEYDNAHDDLDEKVSDLEVRVETLQKQEDRVQEQFESLQEELQDMLGGAGGAMGGGPGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	125 (114)
Sequences:	178 (131)
Seq/√Len:	12.3

HALSA - PFDB
SULSO - PFDB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_E	71_N	2.997	0.96
48_G	77_D	2.689	0.93
23_A	97_V	2.403	0.88
103_S	107_E	2.330	0.86
52_E	69_Y	2.207	0.83
11_E	32_Q	2.146	0.81
85_V	99_E	2.016	0.76
26_V	73_H	1.936	0.73
57_Y	87_V	1.929	0.73
41_E	80_V	1.928	0.73
67_T	72_A	1.904	0.72
15_Q	95_D	1.806	0.68
13_L	81_S	1.797	0.67
24_Q	94_E	1.776	0.66
6_P	100_Q	1.745	0.65
17_Q	86_R	1.623	0.59
4_N	25_N	1.571	0.56
70_D	75_D	1.562	0.56
44_L	73_H	1.544	0.55
46_A	89_T	1.542	0.55
16_L	101_F	1.519	0.54
5_L	18_D	1.512	0.53
97_V	114_G	1.506	0.53
106_E	110_D	1.482	0.52
46_A	49_D	1.473	0.51
54_T	110_D	1.447	0.50
13_L	37_L	1.433	0.49
42_T	45_D	1.404	0.48
10_Q	78_E	1.387	0.47
21_E	24_Q	1.346	0.45
4_N	18_D	1.339	0.45
88_E	92_K	1.320	0.44
13_L	77_D	1.314	0.43
16_L	43_A	1.313	0.43
11_E	100_Q	1.313	0.43
75_D	89_T	1.312	0.43
70_D	74_D	1.304	0.43
5_L	70_D	1.304	0.43
44_L	76_L	1.297	0.43
8_E	107_E	1.295	0.42
17_Q	105_Q	1.293	0.42
5_L	74_D	1.284	0.42
56_M	80_V	1.280	0.42
107_E	111_M	1.256	0.41
73_H	98_Q	1.226	0.39
48_G	73_H	1.219	0.39
9_A	99_E	1.188	0.37
29_Q	86_R	1.183	0.37
28_T	85_V	1.166	0.36
24_Q	29_Q	1.159	0.36
15_Q	66_E	1.150	0.35
37_L	64_L	1.146	0.35
55_T	66_E	1.122	0.34
16_L	111_M	1.116	0.34
71_N	109_Q	1.116	0.34
58_R	103_S	1.116	0.34
26_V	90_L	1.114	0.34
26_V	75_D	1.105	0.33
10_Q	17_Q	1.087	0.33
58_R	75_D	1.086	0.33
91_Q	95_D	1.083	0.32
20_Q	23_A	1.063	0.32
92_K	104_L	1.055	0.31
43_A	96_R	1.051	0.31
12_K	39_E	1.047	0.31
81_S	99_E	1.041	0.31
20_Q	24_Q	1.032	0.30
11_E	101_F	0.997	0.29
34_E	57_Y	0.993	0.29
30_K	94_E	0.982	0.28
12_K	18_D	0.978	0.28
65_V	82_D	0.975	0.28
12_K	22_K	0.975	0.28
27_A	75_D	0.975	0.28
84_E	88_E	0.962	0.27
48_G	99_E	0.944	0.27
23_A	96_R	0.942	0.26
26_V	114_G	0.933	0.26
12_K	21_E	0.923	0.26
29_Q	100_Q	0.920	0.26
40_A	110_D	0.919	0.26
51_E	63_L	0.906	0.25
12_K	107_E	0.899	0.25
39_E	93_Q	0.892	0.25
45_D	79_K	0.884	0.24
65_V	72_A	0.880	0.24
86_R	105_Q	0.876	0.24
29_Q	32_Q	0.870	0.24
51_E	77_D	0.865	0.24
27_A	98_Q	0.857	0.23
66_E	74_D	0.843	0.23
32_Q	38_S	0.805	0.21
46_A	91_Q	0.805	0.21
16_L	60_V	0.802	0.21
40_A	43_A	0.800	0.21
7_P	34_E	0.780	0.21
22_K	89_T	0.771	0.20
15_Q	89_T	0.766	0.20
50_I	68_E	0.759	0.20
46_A	58_R	0.754	0.20
39_E	106_E	0.750	0.20
34_E	87_V	0.745	0.19
36_Q	87_V	0.741	0.19
30_K	92_K	0.740	0.19
59_E	81_S	0.740	0.19
45_D	77_D	0.736	0.19
45_D	82_D	0.734	0.19
50_I	53_S	0.733	0.19
36_Q	79_K	0.723	0.19
25_N	92_K	0.722	0.19
20_Q	94_E	0.721	0.19
28_T	77_D	0.719	0.19
16_L	55_T	0.712	0.18
17_Q	20_Q	0.707	0.18
49_D	56_M	0.697	0.18
22_K	38_S	0.696	0.18
103_S	111_M	0.695	0.18
46_A	66_E	0.693	0.18
31_Q	43_A	0.691	0.18
64_L	75_D	0.689	0.18
8_E	21_E	0.686	0.18
60_V	108_L	0.686	0.18
85_V	89_T	0.682	0.18
44_L	57_Y	0.676	0.17
4_N	29_Q	0.673	0.17
7_P	107_E	0.661	0.17
87_V	111_M	0.660	0.17
13_L	99_E	0.658	0.17
12_K	26_V	0.651	0.17
7_P	104_L	0.646	0.16
20_Q	86_R	0.644	0.16
24_Q	43_A	0.640	0.16
9_A	108_L	0.638	0.16
23_A	27_A	0.631	0.16
7_P	16_L	0.624	0.16
47_L	50_I	0.601	0.15
23_A	98_Q	0.594	0.15
33_A	83_L	0.592	0.15
34_E	117_G	0.585	0.15
9_A	110_D	0.581	0.15
9_A	14_E	0.578	0.15
95_D	100_Q	0.578	0.15
16_L	63_L	0.573	0.15
44_L	47_L	0.568	0.14
45_D	78_E	0.564	0.14
84_E	99_E	0.560	0.14
56_M	79_K	0.559	0.14
88_E	99_E	0.558	0.14
30_K	117_G	0.556	0.14
15_Q	85_V	0.552	0.14
42_T	49_D	0.550	0.14
16_L	79_K	0.547	0.14
30_K	78_E	0.546	0.14
30_K	43_A	0.546	0.14
6_P	95_D	0.543	0.14
16_L	104_L	0.542	0.14
75_D	87_V	0.538	0.14
31_Q	94_E	0.538	0.14
40_A	65_V	0.535	0.14
12_K	112_L	0.533	0.14
11_E	96_R	0.525	0.13
13_L	17_Q	0.524	0.13
94_E	98_Q	0.524	0.13
95_D	99_E	0.523	0.13
50_I	55_T	0.517	0.13
15_Q	29_Q	0.516	0.13
28_T	99_E	0.512	0.13
84_E	104_L	0.508	0.13
63_L	73_H	0.502	0.13
55_T	81_S	0.500	0.13
50_I	106_E	0.500	0.13

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
2zqmA	5	0.912	99.8	0.519	Contact Map
1fxkA	2	0.856	99.8	0.541	Contact Map
3aeiA	3	0.752	99.7	0.568	Contact Map
2zdiC	2	0.976	99.5	0.639	Contact Map
1fxkC	2	0.88	99.2	0.687	Contact Map
4q4gX	1	0.008	84.8	0.886	Contact Map
4cgkA	3	0.64	81.7	0.89	Contact Map
1l8dA	2	0.832	72.1	0.899	Contact Map
2dfsA	2	0.696	70.7	0.9	Contact Map
3ghgA	2	0.912	68.5	0.902	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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