Vps54 - PFAM28P - GREMLIN Contacts

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Vps54 - Vps54-like protein

PFAM:	PF07928	Sequences: EEKFIVVGSALLLLKMLSEYLQLAANLPSLATDIASRLLELLKLFNSRTCQLVLGAGATRSAGLKNITAKHLALASQSLSFIIALIPYIREFLRRHLPPKQASLLAEFDKVKRDYQEHQNEIHAKLVSIMSDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	133 (132)
Sequences:	511 (364)
Seq/√Len:	31.7
META:	0.352

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_L	38_L	3.574	1.00
47_S	51_Q	3.573	1.00
16_M	41_L	3.116	1.00
42_L	115_Y	3.106	1.00
49_T	75_A	2.953	1.00
72_L	122_I	2.614	1.00
97_L	101_Q	2.513	1.00
50_C	121_E	2.469	0.99
90_R	109_D	2.423	0.99
51_Q	57_G	2.242	0.99
13_L	41_L	2.110	0.98
91_E	95_R	2.074	0.98
48_R	51_Q	2.064	0.98
24_A	93_L	2.047	0.98
6_V	10_A	2.023	0.98
46_N	50_C	1.962	0.97
127_V	130_M	1.859	0.96
13_L	16_M	1.787	0.95
63_G	130_M	1.771	0.95
37_R	40_E	1.750	0.95
51_Q	55_G	1.719	0.94
50_C	114_D	1.689	0.93
82_I	115_Y	1.671	0.93
10_A	78_S	1.645	0.93
123_H	126_L	1.634	0.92
126_L	130_M	1.632	0.92
19_E	22_Q	1.619	0.92
114_D	121_E	1.548	0.90
39_L	108_F	1.467	0.87
11_L	15_K	1.439	0.86
30_L	44_L	1.398	0.85
66_N	91_E	1.397	0.85
46_N	118_H	1.387	0.84
68_T	129_I	1.385	0.84
77_Q	80_S	1.375	0.84
37_R	100_K	1.345	0.82
40_E	56_A	1.315	0.81
53_V	93_L	1.308	0.80
58_A	64_L	1.300	0.80
70_K	127_V	1.298	0.80
41_L	49_T	1.260	0.78
31_A	89_I	1.259	0.78
52_L	122_I	1.243	0.77
3_K	13_L	1.233	0.76
97_L	100_K	1.221	0.76
69_A	78_S	1.210	0.75
70_K	107_E	1.191	0.74
17_L	89_I	1.187	0.74
47_S	55_G	1.183	0.73
121_E	128_S	1.144	0.71
89_I	112_K	1.124	0.69
38_L	69_A	1.123	0.69
59_T	62_A	1.117	0.69
39_L	111_V	1.091	0.67
6_V	9_S	1.057	0.64
130_M	133_R	1.051	0.64
47_S	56_A	1.047	0.64
15_K	19_E	1.046	0.64
76_S	119_Q	1.039	0.63
53_V	91_E	1.038	0.63
25_A	116_Q	1.023	0.62
13_L	22_Q	1.020	0.62
8_G	15_K	1.018	0.62
58_A	67_I	1.003	0.60
12_L	15_K	0.986	0.59
52_L	66_N	0.970	0.58
12_L	20_Y	0.962	0.57
83_I	112_K	0.956	0.57
69_A	132_D	0.954	0.56
52_L	87_P	0.952	0.56
54_L	67_I	0.951	0.56
56_A	66_N	0.949	0.56
43_K	84_A	0.949	0.56
17_L	124_A	0.914	0.53
12_L	16_M	0.913	0.53
34_I	74_L	0.913	0.53
119_Q	123_H	0.913	0.53
4_F	12_L	0.908	0.53
50_C	55_G	0.904	0.52
45_F	82_I	0.895	0.52
54_L	125_K	0.880	0.50
75_A	79_L	0.875	0.50
56_A	59_T	0.870	0.50
88_Y	95_R	0.864	0.49
69_A	73_A	0.863	0.49
114_D	117_E	0.855	0.48
59_T	69_A	0.854	0.48
7_V	13_L	0.854	0.48
45_F	87_P	0.851	0.48
33_D	92_F	0.848	0.48
46_N	54_L	0.834	0.47
120_N	124_A	0.832	0.47
53_V	78_S	0.828	0.46
43_K	50_C	0.820	0.46
73_A	126_L	0.814	0.45
42_L	87_P	0.798	0.44
83_I	86_I	0.796	0.44
9_S	25_A	0.789	0.43
5_I	10_A	0.786	0.43
15_K	27_L	0.786	0.43
16_M	30_L	0.780	0.42
125_K	129_I	0.774	0.42
91_E	94_R	0.774	0.42
51_Q	60_R	0.773	0.42
121_E	126_L	0.767	0.41
24_A	41_L	0.764	0.41
53_V	130_M	0.764	0.41
128_S	132_D	0.758	0.41
56_A	60_R	0.755	0.40
11_L	89_I	0.752	0.40
80_S	119_Q	0.746	0.40
45_F	65_K	0.745	0.40
101_Q	105_L	0.744	0.40
56_A	64_L	0.736	0.39
48_R	56_A	0.736	0.39
16_M	78_S	0.732	0.39
44_L	110_K	0.727	0.38
8_G	11_L	0.725	0.38
56_A	129_I	0.721	0.38
97_L	105_L	0.718	0.38
56_A	62_A	0.709	0.37
10_A	68_T	0.703	0.36
33_D	37_R	0.700	0.36
52_L	82_I	0.699	0.36
6_V	108_F	0.697	0.36
49_T	111_V	0.691	0.35
6_V	23_L	0.689	0.35
69_A	81_F	0.684	0.35
7_V	81_F	0.680	0.35
58_A	68_T	0.671	0.34
104_L	107_E	0.668	0.34
31_A	128_S	0.667	0.34
48_R	114_D	0.666	0.34
6_V	81_F	0.662	0.33
4_F	10_A	0.660	0.33
44_L	88_Y	0.653	0.33
20_Y	97_L	0.652	0.33
63_G	73_A	0.651	0.33
123_H	130_M	0.651	0.33
90_R	94_R	0.650	0.32
112_K	116_Q	0.645	0.32
19_E	98_P	0.645	0.32
34_I	93_L	0.644	0.32
52_L	61_S	0.643	0.32
101_Q	112_K	0.642	0.32
5_I	69_A	0.639	0.32
128_S	131_S	0.636	0.31
13_L	127_V	0.633	0.31
13_L	40_E	0.633	0.31
43_K	126_L	0.629	0.31
4_F	20_Y	0.626	0.31
12_L	111_V	0.623	0.31
68_T	78_S	0.613	0.30
123_H	129_I	0.609	0.30
27_L	50_C	0.603	0.29
53_V	102_A	0.603	0.29
9_S	13_L	0.600	0.29
45_F	128_S	0.599	0.29
29_S	38_L	0.597	0.29
60_R	78_S	0.596	0.29
2_E	8_G	0.596	0.29
76_S	123_H	0.590	0.28
80_S	114_D	0.585	0.28
45_F	77_Q	0.585	0.28
49_T	53_V	0.580	0.28
113_R	116_Q	0.577	0.27
14_L	31_A	0.575	0.27
33_D	53_V	0.574	0.27
121_E	124_A	0.574	0.27
77_Q	126_L	0.572	0.27
2_E	26_N	0.571	0.27
32_T	68_T	0.567	0.27
48_R	62_A	0.567	0.27
10_A	81_F	0.563	0.27
57_G	79_L	0.561	0.26
71_H	84_A	0.557	0.26
105_L	109_D	0.557	0.26
16_M	19_E	0.553	0.26
27_L	123_H	0.547	0.26
48_R	64_L	0.543	0.25
22_Q	101_Q	0.542	0.25
5_I	8_G	0.541	0.25
14_L	19_E	0.539	0.25
77_Q	119_Q	0.537	0.25
50_C	61_S	0.536	0.25
118_H	122_I	0.535	0.25
110_K	130_M	0.534	0.25
111_V	127_V	0.534	0.25
71_H	77_Q	0.527	0.24
43_K	123_H	0.523	0.24
71_H	127_V	0.522	0.24
25_A	74_L	0.521	0.24
90_R	122_I	0.519	0.24
71_H	80_S	0.513	0.24
77_Q	84_A	0.509	0.23
4_F	86_I	0.503	0.23
6_V	78_S	0.503	0.23
39_L	104_L	0.500	0.23

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
2fji1	1	1	12.4	0.933	Contact Map
4jjnC	2	0.6992	9.9	0.936	Contact Map
4g92C	1	0.5714	9.6	0.936	Contact Map
3q7rA	2	0.609	9.5	0.936	Contact Map
2f8nK	1	0.6767	8.9	0.937	Contact Map
4csrB	1	0.5865	8.7	0.937	Contact Map
2f8nG	1	0.6541	8.3	0.938	Contact Map
2nqbC	2	0.6541	7	0.94	Contact Map
2qk2A	1	0.8647	6.8	0.941	Contact Map
1tzyA	2	0.6466	6.6	0.941	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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