SNARE_assoc - PFAM28P - GREMLIN Contacts

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SNARE_assoc - SNARE associated Golgi protein

PFAM:	PF09335	Sequences: LPGEVLLLAAGALFGLWLGLLLATLGAVLGALLAYLIGRYLGRRRLRRRLLKPERLERAERFFERHGGKAVFLARFVPIVPRTLINLVAGLTRMPFRRFLLATALGALPWTLLLVLLGYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (118)
Sequences:	88631 (57428)
Seq/√Len:	5286.6
META:	0.802

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_L	96_F	3.758	1.00
95_P	98_R	2.917	1.00
68_G	102_A	2.828	1.00
15_G	18_L	2.670	1.00
68_G	98_R	2.667	1.00
32_L	100_L	2.621	1.00
24_T	108_L	2.256	1.00
36_L	96_F	2.236	1.00
66_H	69_K	1.969	1.00
28_V	104_A	1.958	1.00
20_L	112_L	1.937	1.00
24_T	104_A	1.881	1.00
60_E	64_E	1.728	1.00
36_L	40_Y	1.715	1.00
97_R	101_L	1.616	1.00
20_L	115_V	1.606	1.00
38_G	90_G	1.578	1.00
109_P	112_L	1.573	1.00
28_V	100_L	1.551	1.00
96_F	100_L	1.543	1.00
45_R	48_R	1.532	1.00
62_F	70_A	1.471	1.00
75_R	107_A	1.466	1.00
18_L	22_L	1.460	1.00
46_L	49_R	1.392	1.00
52_K	55_R	1.384	1.00
51_L	54_E	1.383	1.00
32_L	36_L	1.344	1.00
54_E	58_R	1.311	1.00
39_R	93_R	1.310	1.00
45_R	49_R	1.293	1.00
53_P	57_E	1.288	1.00
34_A	87_L	1.285	1.00
16_L	20_L	1.277	1.00
47_R	53_P	1.266	1.00
17_W	20_L	1.265	1.00
46_L	51_L	1.261	1.00
18_L	21_L	1.227	1.00
31_A	103_T	1.202	1.00
15_G	19_G	1.181	1.00
57_E	60_E	1.175	1.00
44_R	48_R	1.171	1.00
97_R	100_L	1.160	1.00
57_E	61_R	1.159	1.00
74_A	85_I	1.157	1.00
35_Y	99_F	1.150	1.00
43_R	60_E	1.130	1.00
98_R	101_L	1.114	1.00
23_A	115_V	1.092	1.00
61_R	64_E	1.087	1.00
31_A	75_R	1.069	1.00
22_L	26_G	1.058	1.00
116_L	119_Y	1.054	1.00
55_R	58_R	1.054	1.00
45_R	50_L	1.053	1.00
10_A	19_G	1.047	1.00
44_R	47_R	1.038	1.00
21_L	24_T	1.035	1.00
24_T	28_V	1.032	1.00
17_W	21_L	1.029	1.00
36_L	39_R	1.008	1.00
72_F	105_L	1.007	1.00
82_R	107_A	0.993	1.00
24_T	111_T	0.984	1.00
82_R	110_W	0.984	1.00
20_L	24_T	0.980	1.00
100_L	104_A	0.980	1.00
101_L	105_L	0.979	1.00
23_A	111_T	0.966	1.00
9_A	12_A	0.938	1.00
76_F	109_P	0.934	1.00
111_T	115_V	0.926	1.00
47_R	50_L	0.925	1.00
10_A	14_F	0.920	1.00
53_P	56_L	0.919	1.00
83_T	86_N	0.918	1.00
14_F	119_Y	0.907	1.00
69_K	73_L	0.903	1.00
74_A	89_A	0.900	1.00
72_F	102_A	0.898	1.00
9_A	13_L	0.886	1.00
75_R	103_T	0.885	1.00
105_L	109_P	0.880	1.00
17_W	116_L	0.879	1.00
37_I	41_L	0.871	1.00
44_R	49_R	0.862	1.00
71_V	102_A	0.860	1.00
46_L	50_L	0.857	1.00
98_R	102_A	0.847	1.00
7_L	23_A	0.841	1.00
113_L	116_L	0.833	1.00
107_A	110_W	0.832	1.00
47_R	51_L	0.822	1.00
72_F	106_G	0.818	1.00
102_A	106_G	0.813	1.00
71_V	89_A	0.808	1.00
112_L	115_V	0.807	1.00
59_A	62_F	0.803	1.00
35_Y	96_F	0.803	1.00
105_L	108_L	0.802	1.00
25_L	28_V	0.800	1.00
38_G	91_L	0.799	1.00
101_L	104_A	0.790	1.00
104_A	108_L	0.785	1.00
20_L	108_L	0.783	1.00
5_V	8_L	0.776	1.00
60_E	93_R	0.774	1.00
50_L	53_P	0.769	1.00
4_E	7_L	0.761	1.00
85_I	88_V	0.757	1.00
33_L	36_L	0.752	1.00
112_L	116_L	0.749	1.00
21_L	25_L	0.738	1.00
3_G	7_L	0.734	1.00
61_R	65_R	0.731	1.00
85_I	89_A	0.731	1.00
63_F	89_A	0.729	1.00
54_E	57_E	0.718	1.00
75_R	82_R	0.716	1.00
50_L	55_R	0.715	1.00
89_A	94_M	0.715	1.00
10_A	23_A	0.712	1.00
48_R	51_L	0.711	1.00
70_A	74_A	0.710	1.00
4_E	8_L	0.695	1.00
38_G	87_L	0.694	1.00
34_A	86_N	0.690	1.00
67_G	98_R	0.685	1.00
16_L	116_L	0.684	1.00
68_G	94_M	0.680	1.00
8_L	12_A	0.679	1.00
108_L	112_L	0.673	1.00
60_E	92_T	0.673	1.00
107_A	111_T	0.665	1.00
51_L	55_R	0.665	1.00
68_G	72_F	0.660	1.00
49_R	52_K	0.658	1.00
20_L	116_L	0.656	1.00
47_R	52_K	0.652	1.00
52_K	56_L	0.647	1.00
63_F	67_G	0.645	1.00
99_F	103_T	0.639	1.00
26_G	30_G	0.639	1.00
103_T	107_A	0.637	1.00
5_V	9_A	0.634	1.00
75_R	86_N	0.629	1.00
94_M	98_R	0.629	1.00
19_G	115_V	0.624	1.00
73_L	77_V	0.624	1.00
58_R	62_F	0.618	1.00
4_E	82_R	0.612	1.00
14_F	19_G	0.610	1.00
51_L	56_L	0.605	1.00
30_G	34_A	0.604	1.00
27_A	107_A	0.604	1.00
62_F	66_H	0.603	1.00
48_R	53_P	0.600	1.00
37_I	40_Y	0.588	1.00
11_G	118_G	0.582	1.00
50_L	54_E	0.577	1.00
31_A	86_N	0.574	1.00
75_R	106_G	0.571	1.00
76_F	82_R	0.568	1.00
50_L	56_L	0.564	1.00
27_A	31_A	0.558	1.00
10_A	13_L	0.551	1.00
47_R	56_L	0.547	1.00
113_L	117_L	0.544	1.00
72_F	109_P	0.534	1.00
34_A	83_T	0.532	1.00
27_A	111_T	0.525	1.00
11_G	19_G	0.523	1.00
88_V	92_T	0.519	1.00
46_L	53_P	0.518	1.00
58_R	61_R	0.507	1.00
53_P	58_R	0.507	1.00
4_E	114_L	0.500	1.00

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
4q2eA	2	0.8667	28.7	0.849	Contact Map
3qnqA	2	0.475	26.5	0.852	Contact Map
2jlnA	1	0.6	18.9	0.862	Contact Map
3tdsE	3	0.4583	7.9	0.883	Contact Map
4ev6A	3	0.3667	5.6	0.891	Contact Map
4humA	1	0.4583	5.2	0.892	Contact Map
4i0uA	4	0.35	5.2	0.893	Contact Map
4x5mA	2	0.425	5.1	0.893	Contact Map
4fc4A	3	0.3667	5	0.893	Contact Map
4dveA	3	0.9083	4.9	0.893	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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