VPS13_C - PFAM28P - GREMLIN Contacts

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VPS13_C - Vacuolar-sorting-associated 13 protein C-terminal

PFAM:	PF16909	Sequences: KIYFELLHLSPIKLNLSFSRTPRSNAEDKLSSSSNPLSLLLLLNSLGMTLGNIDDAPIKLNALELENVFESLSELLSRIIKHYKQQLLRQLYKILGSLDFLGNPVGLFNNLGSGVKDFFYEPYQGLVQGPEEFGEGLAKGTKSLVKNTVGGVSGSVSKITGSLGKGLAALTMDKEYQQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	178 (171)
Sequences:	1055 (800)
Seq/√Len:	61.1
META:	0.421

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
117_D	143_S	8.368	1.00
118_F	144_L	7.337	1.00
118_F	141_T	4.749	1.00
125_G	136_G	3.497	1.00
143_S	147_N	3.191	1.00
107_L	155_S	3.032	1.00
99_D	158_K	2.838	1.00
121_E	139_K	2.652	1.00
11_P	120_Y	2.601	1.00
125_G	133_F	2.397	1.00
134_G	138_A	2.315	1.00
63_L	82_H	2.199	1.00
80_I	84_K	2.166	1.00
129_G	132_E	2.156	1.00
62_A	120_Y	2.015	1.00
90_Q	93_K	1.960	1.00
113_S	143_S	1.938	1.00
3_Y	67_N	1.894	1.00
60_L	87_L	1.892	1.00
129_G	133_F	1.854	1.00
171_T	177_Q	1.839	1.00
110_N	150_G	1.836	1.00
96_G	105_V	1.792	1.00
164_G	168_A	1.759	0.99
154_G	158_K	1.705	0.99
76_L	80_I	1.659	0.99
15_N	57_P	1.646	0.99
152_V	156_V	1.617	0.99
141_T	144_L	1.573	0.99
108_F	112_G	1.561	0.99
122_P	136_G	1.522	0.98
126_L	133_F	1.517	0.98
159_I	162_S	1.479	0.98
73_S	76_L	1.458	0.98
65_L	68_V	1.408	0.97
107_L	151_G	1.401	0.97
103_N	106_G	1.383	0.97
100_F	152_V	1.379	0.97
53_I	56_A	1.367	0.97
82_H	86_Q	1.324	0.96
88_L	92_Y	1.320	0.96
128_Q	132_E	1.312	0.96
121_E	125_G	1.280	0.95
125_G	129_G	1.277	0.95
71_S	74_E	1.236	0.94
47_G	51_G	1.197	0.93
44_N	47_G	1.184	0.93
3_Y	43_L	1.172	0.93
115_V	120_Y	1.170	0.92
144_L	147_N	1.167	0.92
95_L	98_L	1.152	0.92
114_G	140_G	1.151	0.92
94_I	150_G	1.130	0.91
60_L	83_Y	1.125	0.91
102_G	162_S	1.123	0.91
162_S	171_T	1.112	0.90
114_G	136_G	1.107	0.90
110_N	147_N	1.106	0.90
52_N	98_L	1.091	0.90
150_G	154_G	1.079	0.89
120_Y	127_V	1.075	0.89
86_Q	103_N	1.063	0.88
102_G	107_L	1.062	0.88
22_P	25_N	1.057	0.88
72_L	76_L	1.054	0.88
168_A	171_T	1.039	0.87
92_Y	103_N	1.034	0.87
125_G	130_P	1.029	0.87
17_S	52_N	1.025	0.86
5_E	13_K	1.014	0.86
10_S	120_Y	1.007	0.85
16_L	53_I	0.996	0.85
155_S	162_S	0.992	0.85
51_G	113_S	0.985	0.84
2_I	79_I	0.985	0.84
7_L	75_L	0.985	0.84
12_I	16_L	0.983	0.84
113_S	147_N	0.975	0.84
85_Q	117_D	0.975	0.84
115_V	119_F	0.971	0.83
164_G	172_M	0.971	0.83
28_D	174_K	0.969	0.83
133_F	148_T	0.967	0.83
75_L	101_L	0.966	0.83
74_E	78_R	0.963	0.83
120_Y	123_Y	0.954	0.82
174_K	177_Q	0.951	0.82
173_D	176_Y	0.939	0.81
129_G	136_G	0.932	0.81
70_E	75_L	0.912	0.79
59_K	120_Y	0.910	0.79
114_G	144_L	0.901	0.78
82_H	111_L	0.900	0.78
17_S	20_R	0.890	0.78
4_F	7_L	0.882	0.77
154_G	165_K	0.881	0.77
162_S	175_E	0.880	0.77
121_E	133_F	0.879	0.77
94_I	139_K	0.876	0.76
29_K	34_S	0.860	0.75
16_L	30_L	0.855	0.75
164_G	171_T	0.851	0.74
10_S	121_E	0.849	0.74
146_K	150_G	0.845	0.74
65_L	108_F	0.835	0.73
136_G	140_G	0.828	0.72
100_F	149_V	0.823	0.72
127_V	165_K	0.819	0.71
118_F	147_N	0.817	0.71
155_S	159_I	0.816	0.71
129_G	141_T	0.815	0.71
81_K	84_K	0.815	0.71
56_A	82_H	0.811	0.71
112_G	169_A	0.810	0.71
168_A	176_Y	0.809	0.70
119_F	122_P	0.808	0.70
126_L	137_L	0.808	0.70
63_L	70_E	0.807	0.70
93_K	105_V	0.802	0.70
106_G	161_G	0.798	0.69
117_D	136_G	0.782	0.68
36_P	39_L	0.778	0.67
133_F	138_A	0.776	0.67
96_G	114_G	0.771	0.67
10_S	62_A	0.770	0.67
56_A	97_S	0.768	0.66
65_L	149_V	0.765	0.66
6_L	13_K	0.763	0.66
148_T	168_A	0.757	0.65
130_P	133_F	0.750	0.65
106_G	109_N	0.741	0.64
80_I	111_L	0.740	0.64
83_Y	146_K	0.735	0.63
65_L	70_E	0.734	0.63
47_G	92_Y	0.734	0.63
65_L	112_G	0.729	0.62
23_R	39_L	0.729	0.62
36_P	58_I	0.727	0.62
136_G	141_T	0.725	0.62
126_L	130_P	0.723	0.62
122_P	125_G	0.721	0.62
98_L	150_G	0.717	0.61
97_S	107_L	0.716	0.61
47_G	50_L	0.713	0.61
167_L	170_L	0.713	0.61
86_Q	124_Q	0.709	0.60
47_G	110_N	0.708	0.60
73_S	135_E	0.707	0.60
51_G	111_L	0.702	0.60
86_Q	89_R	0.698	0.59
52_N	166_G	0.697	0.59
14_L	19_S	0.696	0.59
159_I	166_G	0.696	0.59
127_V	130_P	0.690	0.58
21_T	24_S	0.689	0.58
40_L	174_K	0.685	0.58
81_K	85_Q	0.682	0.57
82_H	148_T	0.681	0.57
22_P	56_A	0.681	0.57
4_F	177_Q	0.678	0.57
118_F	136_G	0.678	0.57
169_A	174_K	0.677	0.57
52_N	56_A	0.674	0.56
109_N	159_I	0.669	0.56
166_G	170_L	0.668	0.56
4_F	68_V	0.665	0.55
30_L	35_N	0.665	0.55
63_L	108_F	0.664	0.55
50_L	151_G	0.661	0.55
11_P	62_A	0.660	0.55
28_D	137_L	0.652	0.54
34_S	79_I	0.652	0.54
17_S	83_Y	0.651	0.54
119_F	123_Y	0.649	0.54
83_Y	103_N	0.648	0.53
12_I	75_L	0.644	0.53
63_L	122_P	0.642	0.53
71_S	163_L	0.641	0.53
64_E	129_G	0.637	0.52
18_F	119_F	0.636	0.52
116_K	141_T	0.635	0.52
19_S	146_K	0.632	0.52
53_I	79_I	0.631	0.52
163_L	169_A	0.628	0.51
140_G	143_S	0.628	0.51
20_R	46_L	0.627	0.51
134_G	137_L	0.625	0.51
57_P	97_S	0.625	0.51
70_E	78_R	0.623	0.51
172_M	177_Q	0.621	0.50
30_L	36_P	0.613	0.50
111_L	169_A	0.612	0.49
56_A	167_L	0.607	0.49
90_Q	98_L	0.602	0.48
154_G	160_T	0.601	0.48
116_K	120_Y	0.598	0.48
56_A	104_P	0.598	0.48
15_N	53_I	0.597	0.48
23_R	28_D	0.594	0.47
122_P	130_P	0.593	0.47
39_L	81_K	0.591	0.47
8_H	14_L	0.591	0.47
44_N	48_M	0.589	0.47
96_G	106_G	0.589	0.47
75_L	154_G	0.588	0.47
168_A	172_M	0.588	0.47
117_D	122_P	0.587	0.47
14_L	77_S	0.586	0.46
12_I	19_S	0.582	0.46
45_S	94_I	0.581	0.46
119_F	127_V	0.577	0.45
53_I	58_I	0.574	0.45
160_T	164_G	0.573	0.45
163_L	172_M	0.572	0.45
76_L	84_K	0.569	0.45
4_F	170_L	0.566	0.44
15_N	59_K	0.564	0.44
70_E	74_E	0.562	0.44
21_T	30_L	0.562	0.44
99_D	103_N	0.560	0.44
107_L	159_I	0.559	0.43
105_V	119_F	0.559	0.43
99_D	165_K	0.557	0.43
3_Y	19_S	0.556	0.43
105_V	134_G	0.555	0.43
100_F	119_F	0.554	0.43
82_H	96_G	0.554	0.43
62_A	79_I	0.553	0.43
124_Q	130_P	0.552	0.43
75_L	133_F	0.547	0.42
24_S	29_K	0.546	0.42
46_L	74_E	0.546	0.42
57_P	134_G	0.546	0.42
73_S	126_L	0.545	0.42
46_L	109_N	0.543	0.42
53_I	167_L	0.542	0.42
35_N	38_S	0.538	0.41
151_G	164_G	0.537	0.41
133_F	136_G	0.537	0.41
99_D	161_G	0.533	0.41
165_K	169_A	0.526	0.40
97_S	102_G	0.523	0.39
88_L	108_F	0.522	0.39
90_Q	121_E	0.520	0.39
9_L	79_I	0.519	0.39
114_G	118_F	0.516	0.39
122_P	133_F	0.516	0.39
4_F	12_I	0.514	0.39
115_V	118_F	0.513	0.38
48_M	154_G	0.511	0.38
150_G	153_S	0.510	0.38
34_S	58_I	0.508	0.38
37_L	139_K	0.506	0.38
87_L	141_T	0.505	0.38
60_L	77_S	0.503	0.37
67_N	89_R	0.500	0.37

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
2k4nA	1	0.2079	4.2	0.944	Contact Map
3zldB	1	0.1404	2.4	0.951	Contact Map
4ftbD	1	0.118	2.3	0.951	Contact Map
1f8vD	3	0.1629	2.2	0.952	Contact Map
1novD	1	0.1124	2	0.953	Contact Map
4irzA	1	0.3483	1.7	0.954	Contact Map
4chdA	1	0.3202	1.6	0.955	Contact Map
1v18B	1	0.1629	1.6	0.955	Contact Map
3fcsB	1	0.9438	1.5	0.956	Contact Map
3b4sA	6	0.4719	1.5	0.956	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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