BLOC1_2 - PFAM28P - GREMLIN Contacts

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BLOC1_2 - Biogenesis of lysosome-related organelles complex-1 subunit 2

PFAM:	PF10046	Sequences: QDMFEEVRKYLESELEATKEDYELLEKMNKATAEKYAEMEDVAAELEKGVEELNEKYEALQPYLQQIDEIEEQVTELEAAVDELDEYSKRLEAKFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	96 (91)
Sequences:	671 (562)
Seq/√Len:	58.9
META:	0.498

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_L	91_L	2.852	1.00
34_E	37_A	2.810	1.00
72_E	76_E	2.643	1.00
29_N	36_Y	2.603	1.00
42_V	47_E	2.222	1.00
51_E	65_Q	2.089	1.00
27_K	48_K	2.082	1.00
61_Q	65_Q	2.072	1.00
75_T	89_K	1.985	1.00
10_Y	14_E	1.937	1.00
25_L	39_M	1.910	1.00
53_L	77_L	1.864	1.00
5_E	9_K	1.749	0.99
80_A	85_D	1.689	0.99
8_R	11_L	1.647	0.99
64_L	71_E	1.553	0.98
53_L	94_K	1.552	0.98
76_E	83_E	1.550	0.98
14_E	24_L	1.474	0.98
14_E	21_D	1.450	0.97
6_E	11_L	1.436	0.97
31_A	62_P	1.391	0.97
24_L	29_N	1.384	0.97
78_E	85_D	1.381	0.97
9_K	12_E	1.373	0.96
51_E	58_E	1.355	0.96
34_E	72_E	1.302	0.95
7_V	12_E	1.297	0.95
32_T	60_L	1.271	0.95
7_V	11_L	1.239	0.94
18_T	32_T	1.234	0.94
16_E	44_A	1.226	0.93
68_D	89_K	1.226	0.93
34_E	38_E	1.200	0.93
71_E	74_V	1.194	0.93
24_L	43_A	1.189	0.92
87_Y	91_L	1.178	0.92
50_V	74_V	1.169	0.92
23_E	30_K	1.165	0.92
82_D	91_L	1.150	0.91
6_E	9_K	1.126	0.90
85_D	92_E	1.110	0.89
27_K	55_E	1.075	0.88
51_E	55_E	1.066	0.87
30_K	37_A	1.049	0.87
53_L	56_K	1.027	0.85
25_L	36_Y	1.019	0.85
11_L	22_Y	1.016	0.85
31_A	74_V	1.016	0.85
43_A	67_I	1.002	0.84
17_A	41_D	1.001	0.84
71_E	78_E	0.986	0.83
56_K	63_Y	0.967	0.82
27_K	41_D	0.964	0.82
72_E	86_E	0.957	0.81
21_D	35_K	0.953	0.81
49_G	88_S	0.940	0.80
21_D	26_E	0.923	0.79
5_E	58_E	0.920	0.78
40_E	54_N	0.918	0.78
61_Q	69_E	0.912	0.78
17_A	45_E	0.911	0.78
60_L	81_V	0.909	0.78
35_K	49_G	0.873	0.75
37_A	41_D	0.870	0.74
64_L	81_V	0.864	0.74
21_D	29_N	0.859	0.74
5_E	12_E	0.854	0.73
6_E	10_Y	0.853	0.73
67_I	84_L	0.844	0.72
8_R	12_E	0.817	0.70
44_A	89_K	0.808	0.69
13_S	65_Q	0.800	0.68
33_A	37_A	0.785	0.67
30_K	44_A	0.784	0.67
16_E	20_E	0.780	0.66
34_E	41_D	0.777	0.66
71_E	75_T	0.775	0.66
41_D	79_A	0.769	0.65
21_D	60_L	0.762	0.64
61_Q	75_T	0.759	0.64
48_K	74_V	0.754	0.64
17_A	27_K	0.742	0.62
25_L	29_N	0.741	0.62
27_K	33_A	0.739	0.62
56_K	70_I	0.739	0.62
19_K	30_K	0.733	0.61
78_E	92_E	0.709	0.59
40_E	47_E	0.705	0.58
83_E	86_E	0.704	0.58
70_I	82_D	0.701	0.58
66_Q	80_A	0.693	0.57
49_G	73_Q	0.689	0.57
46_L	53_L	0.681	0.56
12_E	28_M	0.672	0.55
74_V	88_S	0.671	0.55
87_Y	90_R	0.665	0.54
72_E	83_E	0.637	0.51
83_E	90_R	0.631	0.50
58_E	61_Q	0.625	0.50
53_L	80_A	0.623	0.49
70_I	84_L	0.622	0.49
19_K	88_S	0.613	0.48
6_E	22_Y	0.607	0.48
23_E	62_P	0.606	0.47
77_L	84_L	0.604	0.47
45_E	48_K	0.601	0.47
51_E	79_A	0.601	0.47
28_M	32_T	0.600	0.47
63_Y	66_Q	0.600	0.47
41_D	65_Q	0.599	0.47
16_E	76_E	0.596	0.46
50_V	54_N	0.595	0.46
35_K	46_L	0.591	0.46
38_E	84_L	0.586	0.45
22_Y	67_I	0.578	0.44
6_E	12_E	0.577	0.44
26_E	30_K	0.572	0.44
23_E	40_E	0.570	0.43
80_A	86_E	0.561	0.42
32_T	68_D	0.558	0.42
79_A	93_A	0.547	0.41
32_T	40_E	0.544	0.41
37_A	51_E	0.540	0.40
25_L	77_L	0.532	0.39
36_Y	50_V	0.527	0.39
29_N	81_V	0.527	0.39
47_E	71_E	0.521	0.38
84_L	88_S	0.516	0.38
67_I	71_E	0.516	0.38
64_L	73_Q	0.513	0.37
21_D	25_L	0.510	0.37
69_E	72_E	0.509	0.37
15_L	68_D	0.508	0.37
44_A	68_D	0.503	0.36
64_L	68_D	0.500	0.36

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
3c9iA	5	0.9688	95.3	0.552	Contact Map
4linA	5	0.9688	94.9	0.562	Contact Map
2dfsA	2	0.9688	85.5	0.654	Contact Map
4ll8A	1	0.4583	85.3	0.655	Contact Map
1deqA	1	1	83.5	0.663	Contact Map
1i84S	2	0.2917	81.6	0.669	Contact Map
3ghgA	2	0.9479	81.3	0.67	Contact Map
1wyyA	3	0.9167	76	0.686	Contact Map
2ch7A	2	1	75.4	0.688	Contact Map
4iloA	3	0.9896	72.1	0.695	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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