PGG - PFAM28P - GREMLIN Contacts

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PGG - Domain of unknown function

PFAM:	PF13962	Sequences: EEWLKKTRNSLLVVATLIATVTFAAGFTPPGGYWQDDDHDAGTPILAKKPRRFKVFFISNTIAFFASLVAILLLLISTLEDDFLRSLPRKLIVLLVLLFLSLLSMMVAFAAGSYRV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (112)
Sequences:	3181 (1924)
Seq/√Len:	181.8
META:	0.075

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_S	107_V	3.751	1.00
6_K	9_N	3.339	1.00
32_G	42_G	2.643	1.00
11_L	74_L	2.493	1.00
60_N	113_S	2.342	1.00
55_V	111_A	2.325	1.00
25_A	56_F	2.243	1.00
36_D	39_H	2.215	1.00
15_A	71_I	2.184	1.00
37_D	40_D	2.056	1.00
12_L	16_T	1.996	1.00
57_F	113_S	1.858	1.00
34_W	39_H	1.841	1.00
83_F	87_L	1.809	1.00
32_G	46_L	1.795	1.00
36_D	40_D	1.703	1.00
31_G	42_G	1.655	1.00
62_I	100_L	1.654	1.00
27_F	60_N	1.628	1.00
13_V	16_T	1.615	1.00
18_I	105_M	1.559	1.00
26_G	60_N	1.540	1.00
22_T	63_A	1.521	1.00
36_D	41_A	1.515	1.00
32_G	45_I	1.515	1.00
44_P	47_A	1.507	1.00
56_F	60_N	1.501	1.00
34_W	41_A	1.481	1.00
35_Q	42_G	1.402	1.00
61_T	65_F	1.384	1.00
83_F	86_S	1.371	1.00
59_S	111_A	1.362	1.00
26_G	112_G	1.328	1.00
15_A	67_S	1.321	1.00
96_V	99_F	1.312	1.00
63_A	104_S	1.301	1.00
85_R	88_P	1.286	1.00
34_W	37_D	1.239	1.00
55_V	59_S	1.236	1.00
16_T	71_I	1.196	1.00
108_A	111_A	1.185	1.00
18_I	63_A	1.175	1.00
94_L	100_L	1.164	1.00
12_L	71_I	1.160	1.00
91_L	94_L	1.159	1.00
64_F	76_I	1.157	1.00
52_R	114_Y	1.148	1.00
24_A	28_T	1.137	1.00
85_R	89_R	1.137	1.00
34_W	45_I	1.135	1.00
60_N	109_F	1.105	1.00
10_S	17_L	1.102	1.00
84_L	88_P	1.097	1.00
31_G	53_F	1.047	1.00
86_S	89_R	1.036	1.00
95_L	99_F	1.029	1.00
65_F	71_I	1.027	1.00
78_T	87_L	1.007	0.99
74_L	94_L	1.006	0.99
20_T	28_T	1.004	0.99
16_T	19_A	0.978	0.99
10_S	13_V	0.969	0.99
63_A	66_A	0.966	0.99
43_T	49_K	0.960	0.99
42_G	53_F	0.943	0.99
21_V	64_F	0.933	0.99
89_R	92_I	0.926	0.99
42_G	46_L	0.925	0.99
47_A	50_P	0.923	0.99
58_I	62_I	0.904	0.99
25_A	63_A	0.902	0.99
23_F	27_F	0.887	0.99
19_A	68_L	0.882	0.99
42_G	45_I	0.881	0.98
37_D	45_I	0.876	0.98
44_P	53_F	0.846	0.98
73_L	78_T	0.845	0.98
27_F	108_A	0.843	0.98
17_L	21_V	0.839	0.98
35_Q	45_I	0.837	0.98
41_A	45_I	0.836	0.98
47_A	52_R	0.832	0.98
80_E	97_L	0.828	0.98
57_F	60_N	0.826	0.98
74_L	102_L	0.814	0.97
20_T	30_P	0.809	0.97
62_I	66_A	0.804	0.97
34_W	40_D	0.766	0.96
10_S	16_T	0.757	0.96
91_L	95_L	0.754	0.96
29_P	57_F	0.751	0.96
92_I	100_L	0.741	0.96
19_A	22_T	0.740	0.96
47_A	53_F	0.739	0.96
20_T	24_A	0.737	0.95
81_D	85_R	0.734	0.95
27_F	33_Y	0.733	0.95
27_F	57_F	0.730	0.95
23_F	57_F	0.720	0.95
95_L	105_M	0.718	0.95
97_L	100_L	0.718	0.95
29_P	33_Y	0.718	0.95
22_T	60_N	0.700	0.94
66_A	98_L	0.696	0.94
23_F	101_S	0.689	0.94
14_V	18_I	0.689	0.94
3_W	12_L	0.688	0.94
66_A	100_L	0.688	0.94
82_D	87_L	0.685	0.93
86_S	92_I	0.685	0.93
50_P	55_V	0.680	0.93
35_Q	50_P	0.676	0.93
80_E	83_F	0.676	0.93
5_K	9_N	0.675	0.93
52_R	57_F	0.671	0.93
27_F	114_Y	0.668	0.93
9_N	81_D	0.667	0.92
77_S	90_K	0.665	0.92
24_A	68_L	0.662	0.92
50_P	54_K	0.661	0.92
35_Q	41_A	0.661	0.92
16_T	47_A	0.661	0.92
62_I	104_S	0.655	0.92
101_S	104_S	0.651	0.92
65_F	69_V	0.637	0.91
17_L	20_T	0.634	0.90
45_I	48_K	0.628	0.90
62_I	115_R	0.625	0.90
26_G	64_F	0.625	0.90
11_L	75_L	0.618	0.89
22_T	67_S	0.612	0.89
72_L	90_K	0.612	0.89
86_S	96_V	0.605	0.88
60_N	108_A	0.605	0.88
52_R	58_I	0.604	0.88
68_L	106_M	0.604	0.88
25_A	30_P	0.604	0.88
93_V	107_V	0.601	0.88
22_T	84_L	0.597	0.88
25_A	108_A	0.597	0.88
12_L	88_P	0.595	0.87
25_A	60_N	0.594	0.87
37_D	41_A	0.592	0.87
29_P	71_I	0.592	0.87
20_T	63_A	0.591	0.87
64_F	67_S	0.590	0.87
102_L	113_S	0.590	0.87
20_T	101_S	0.578	0.86
70_A	75_L	0.573	0.85
82_D	86_S	0.570	0.85
11_L	29_P	0.569	0.85
26_G	113_S	0.565	0.85
32_G	35_Q	0.554	0.84
29_P	106_M	0.550	0.83
101_S	105_M	0.549	0.83
87_L	90_K	0.544	0.82
26_G	46_L	0.540	0.82
28_T	94_L	0.540	0.82
31_G	44_P	0.539	0.82
76_I	99_F	0.533	0.81
77_S	93_V	0.524	0.80
21_V	30_P	0.523	0.80
49_K	52_R	0.515	0.79
12_L	69_V	0.513	0.79
52_R	55_V	0.509	0.78
52_R	56_F	0.508	0.78
9_N	13_V	0.502	0.77
21_V	44_P	0.500	0.77

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
4o9uB	2	0.7672	2.8	0.929	Contact Map
3cw1L	1	0.1638	2.5	0.931	Contact Map
4or2A	2	0.9483	2	0.934	Contact Map
4a34A	5	0.2845	1.8	0.936	Contact Map
1ci4A	2	0.2586	1.8	0.936	Contact Map
4oo9A	1	0.8793	1.6	0.938	Contact Map
2kbvA	1	0.2241	1.5	0.938	Contact Map
3j39U	1	0.3276	1.5	0.939	Contact Map
4ev6A	3	0.5862	1.4	0.94	Contact Map
4pypA	1	0.8793	1.4	0.94	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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