Vma12 - PFAM28P - GREMLIN Contacts

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Vma12 - Endoplasmic reticulum-based factor for assembly of V-ATPase

PFAM:	PF11712	Sequences: ELLRGSEVYLPPPPPKPEPSPELKARLERLRAEQEEREYQRMTKNVDPSEKSTFEDRPSADDVTGEEVKSVKRQLSLILNVLVSVVAVFAAGYYAARYWFGPSTPARVLLGLIGALVVAVAEVYLYAGYLRKVEEAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (130)
Sequences:	514 (379)
Seq/√Len:	33.2
META:	0.265

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_G	114_G	3.783	1.00
23_L	26_R	3.648	1.00
27_L	31_R	3.516	1.00
36_E	40_Q	3.083	1.00
23_L	27_L	2.826	1.00
21_P	25_A	2.528	1.00
89_F	111_G	2.471	1.00
89_F	93_Y	2.294	0.99
118_V	121_A	2.275	0.99
33_E	37_R	2.136	0.99
86_V	90_A	2.001	0.98
88_V	92_G	1.977	0.98
19_P	23_L	1.934	0.97
9_Y	12_P	1.922	0.97
122_E	125_L	1.904	0.97
84_S	118_V	1.855	0.97
71_V	86_V	1.772	0.96
31_R	35_E	1.763	0.95
122_E	126_Y	1.740	0.95
90_A	94_Y	1.733	0.95
121_A	124_Y	1.650	0.94
88_V	118_V	1.634	0.93
21_P	24_K	1.608	0.93
28_E	33_E	1.566	0.92
94_Y	107_R	1.553	0.91
121_A	125_L	1.546	0.91
17_P	32_A	1.545	0.91
124_Y	128_G	1.508	0.90
85_V	125_L	1.485	0.89
77_L	80_N	1.440	0.88
81_V	126_Y	1.429	0.87
87_A	95_A	1.426	0.87
112_L	122_E	1.386	0.86
34_Q	38_E	1.359	0.84
85_V	119_A	1.353	0.84
118_V	125_L	1.344	0.84
91_A	124_Y	1.309	0.82
125_L	128_G	1.307	0.82
78_I	85_V	1.267	0.80
26_R	30_L	1.266	0.80
20_S	26_R	1.239	0.78
20_S	23_L	1.229	0.78
57_R	115_A	1.215	0.77
3_L	25_A	1.211	0.77
84_S	88_V	1.189	0.76
120_V	123_V	1.169	0.74
14_P	29_R	1.155	0.73
24_K	28_E	1.142	0.72
84_S	122_E	1.140	0.72
63_V	133_V	1.129	0.72
13_P	18_E	1.117	0.71
117_V	121_A	1.112	0.70
83_V	86_V	1.101	0.70
34_Q	37_R	1.063	0.67
87_A	118_V	1.062	0.67
18_E	24_K	1.057	0.66
84_S	105_P	1.049	0.66
81_V	123_V	1.047	0.66
5_G	8_V	1.031	0.65
54_F	57_R	1.028	0.64
25_A	29_R	1.027	0.64
111_G	133_V	1.022	0.64
29_R	33_E	1.022	0.64
67_E	71_V	1.022	0.64
96_A	110_L	1.018	0.64
27_L	30_L	1.010	0.63
20_S	24_K	1.009	0.63
95_A	119_A	1.005	0.62
36_E	48_P	1.000	0.62
27_L	108_V	0.982	0.61
107_R	115_A	0.966	0.59
77_L	95_A	0.958	0.59
28_E	32_A	0.940	0.57
116_L	126_Y	0.940	0.57
50_E	57_R	0.935	0.57
69_K	109_L	0.934	0.57
47_D	50_E	0.933	0.57
30_L	111_G	0.928	0.56
77_L	125_L	0.924	0.56
75_L	79_L	0.922	0.56
76_S	88_V	0.913	0.55
78_I	118_V	0.911	0.55
76_S	87_A	0.911	0.55
85_V	120_V	0.893	0.53
68_V	111_G	0.892	0.53
43_T	132_K	0.889	0.53
85_V	121_A	0.888	0.53
28_E	112_L	0.886	0.53
40_Q	86_V	0.881	0.52
101_G	110_L	0.875	0.52
76_S	79_L	0.873	0.52
121_A	129_Y	0.853	0.50
7_E	11_P	0.840	0.49
5_G	15_P	0.828	0.48
107_R	121_A	0.827	0.48
81_V	98_Y	0.825	0.48
33_E	46_V	0.814	0.47
70_S	129_Y	0.813	0.47
76_S	125_L	0.801	0.46
8_V	32_A	0.801	0.46
98_Y	125_L	0.792	0.45
30_L	74_Q	0.784	0.44
34_Q	47_D	0.784	0.44
11_P	123_V	0.784	0.44
119_A	122_E	0.783	0.44
38_E	127_A	0.778	0.44
34_Q	42_M	0.770	0.43
43_T	46_V	0.765	0.43
30_L	107_R	0.764	0.43
28_E	102_P	0.763	0.43
28_E	36_E	0.761	0.42
88_V	114_G	0.755	0.42
7_E	10_L	0.754	0.42
76_S	91_A	0.753	0.42
69_K	72_K	0.751	0.42
127_A	130_L	0.741	0.41
77_L	110_L	0.741	0.41
105_P	119_A	0.733	0.40
87_A	128_G	0.732	0.40
107_R	118_V	0.730	0.40
93_Y	124_Y	0.730	0.40
74_Q	110_L	0.730	0.40
122_E	128_G	0.728	0.40
38_E	43_T	0.727	0.40
96_A	107_R	0.723	0.39
18_E	28_E	0.695	0.37
7_E	86_V	0.685	0.36
5_G	12_P	0.680	0.36
72_K	76_S	0.677	0.36
104_T	119_A	0.671	0.35
16_K	19_P	0.665	0.35
10_L	55_E	0.657	0.34
47_D	56_D	0.650	0.34
81_V	131_R	0.649	0.34
78_I	87_A	0.642	0.33
89_F	99_W	0.638	0.33
91_A	98_Y	0.631	0.32
115_A	122_E	0.631	0.32
30_L	34_Q	0.626	0.32
9_Y	78_I	0.623	0.32
21_P	134_E	0.623	0.32
94_Y	97_R	0.622	0.32
49_S	103_S	0.620	0.31
97_R	107_R	0.616	0.31
67_E	80_N	0.612	0.31
79_L	119_A	0.612	0.31
37_R	132_K	0.610	0.31
32_A	113_I	0.607	0.31
78_I	127_A	0.602	0.30
3_L	17_P	0.602	0.30
23_L	29_R	0.602	0.30
78_I	125_L	0.599	0.30
108_V	112_L	0.597	0.30
79_L	83_V	0.596	0.30
42_M	63_V	0.593	0.30
35_E	108_V	0.589	0.29
39_Y	42_M	0.587	0.29
110_L	113_I	0.585	0.29
87_A	98_Y	0.580	0.29
69_K	108_V	0.580	0.29
90_A	98_Y	0.580	0.29
42_M	104_T	0.574	0.28
42_M	96_A	0.574	0.28
14_P	18_E	0.573	0.28
19_P	127_A	0.571	0.28
112_L	120_V	0.568	0.28
40_Q	57_R	0.565	0.28
43_T	134_E	0.562	0.27
25_A	32_A	0.562	0.27
93_Y	111_G	0.556	0.27
21_P	86_V	0.556	0.27
27_L	96_A	0.556	0.27
77_L	85_V	0.552	0.27
84_S	119_A	0.548	0.27
54_F	127_A	0.547	0.26
78_I	121_A	0.546	0.26
78_I	126_Y	0.542	0.26
88_V	111_G	0.542	0.26
74_Q	93_Y	0.538	0.26
53_T	56_D	0.537	0.26
4_R	7_E	0.536	0.26
51_K	57_R	0.535	0.26
111_G	131_R	0.531	0.25
93_Y	107_R	0.528	0.25
26_R	111_G	0.528	0.25
15_P	18_E	0.522	0.25
43_T	53_T	0.522	0.25
43_T	71_V	0.518	0.25
8_V	102_P	0.517	0.25
3_L	83_V	0.516	0.25
80_N	84_S	0.514	0.24
44_K	63_V	0.509	0.24
19_P	27_L	0.509	0.24
30_L	128_G	0.509	0.24
4_R	13_P	0.500	0.24

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
3zymA	1	0.2409	9.2	0.932	Contact Map
4i0uA	4	0.781	8.9	0.933	Contact Map
3ne5A	3	0.9197	7.6	0.935	Contact Map
2m20A	2	0.2409	7.3	0.935	Contact Map
2kncB	1	0.3066	7.1	0.936	Contact Map
4tllB	2	0.6496	7	0.936	Contact Map
2dprA	3	0.1533	6.8	0.936	Contact Map
1zrtD	1	0.6715	6.3	0.937	Contact Map
4hhuA	1	0.3869	5.7	0.938	Contact Map
4ev6A	3	0.7956	5.3	0.939	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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