DUF3499 - PFAM28P - GREMLIN Contacts

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DUF3499 - Protein of unknown function (DUF3499)

PFAM:	PF12005	Sequences: VRRCSRTACGRPAVATLTYVYADSTAVLGPLATYAEPHSYDLCEEHAERLTAPRGWEVVRLAGDFAPPGPSSDDLEALADAVREAARPERPPPAAPAPAAPPARPAGPGPEEGRRRGHLRVLPD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (121)
Sequences:	1830 (1031)
Seq/√Len:	93.7
META:	0.727

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_E	80_D	4.044	1.00
40_Y	50_L	2.926	1.00
112_E	115_R	2.710	1.00
39_S	51_T	2.426	1.00
111_E	123_P	2.408	1.00
63_G	68_P	2.286	1.00
44_E	48_E	2.230	1.00
3_R	10_G	2.227	1.00
72_S	76_E	2.139	1.00
92_P	95_A	2.008	1.00
113_G	123_P	1.912	1.00
111_E	114_R	1.893	1.00
52_A	58_V	1.888	1.00
11_R	45_E	1.867	1.00
28_L	61_L	1.752	1.00
18_T	27_V	1.736	1.00
104_R	108_P	1.667	1.00
36_E	40_Y	1.613	1.00
72_S	80_D	1.608	1.00
57_E	60_R	1.595	1.00
92_P	98_P	1.586	1.00
65_F	68_P	1.577	1.00
4_C	9_C	1.574	1.00
26_A	52_A	1.571	1.00
69_G	72_S	1.425	0.99
20_V	24_S	1.423	0.99
99_A	102_P	1.418	0.99
40_Y	58_V	1.402	0.99
28_L	63_G	1.391	0.99
50_L	71_S	1.384	0.99
92_P	97_A	1.356	0.99
97_A	100_A	1.337	0.99
16_T	41_D	1.334	0.99
20_V	23_D	1.333	0.99
45_E	49_R	1.321	0.99
5_S	19_Y	1.280	0.99
98_P	103_A	1.280	0.99
51_T	59_V	1.278	0.99
78_L	85_A	1.267	0.99
114_R	117_G	1.263	0.99
66_A	69_G	1.260	0.99
15_A	57_E	1.257	0.99
17_L	21_Y	1.249	0.99
110_P	123_P	1.236	0.98
71_S	86_A	1.230	0.98
51_T	76_E	1.229	0.98
6_R	26_A	1.204	0.98
21_Y	24_S	1.195	0.98
54_R	58_V	1.168	0.98
61_L	123_P	1.168	0.98
26_A	84_E	1.164	0.98
29_G	75_L	1.132	0.97
94_A	97_A	1.124	0.97
19_Y	38_H	1.056	0.96
95_A	100_A	1.050	0.96
33_T	38_H	1.044	0.96
101_P	105_P	1.042	0.96
8_A	61_L	1.037	0.96
101_P	104_R	1.025	0.95
102_P	108_P	1.024	0.95
60_R	78_L	1.012	0.95
6_R	9_C	0.996	0.94
117_G	122_L	0.990	0.94
97_A	101_P	0.955	0.93
93_P	97_A	0.955	0.93
28_L	50_L	0.941	0.93
98_P	106_A	0.938	0.92
70_P	86_A	0.937	0.92
52_A	61_L	0.936	0.92
106_A	109_G	0.934	0.92
22_A	72_S	0.930	0.92
17_L	38_H	0.929	0.92
95_A	103_A	0.925	0.92
7_T	58_V	0.925	0.92
63_G	66_A	0.923	0.92
26_A	50_L	0.915	0.91
39_S	123_P	0.912	0.91
18_T	29_G	0.910	0.91
32_A	73_D	0.899	0.91
98_P	102_P	0.896	0.91
120_R	123_P	0.895	0.91
15_A	47_A	0.894	0.91
2_R	16_T	0.892	0.90
45_E	72_S	0.887	0.90
98_P	105_P	0.887	0.90
9_C	13_A	0.885	0.90
83_R	86_A	0.879	0.90
39_S	69_G	0.873	0.89
105_P	108_P	0.872	0.89
108_P	111_E	0.864	0.89
64_D	87_R	0.858	0.89
98_P	108_P	0.850	0.88
76_E	122_L	0.837	0.87
94_A	98_P	0.834	0.87
39_S	65_F	0.822	0.86
62_A	70_P	0.819	0.86
95_A	110_P	0.818	0.86
96_P	100_A	0.817	0.86
15_A	78_L	0.807	0.85
84_E	116_R	0.796	0.85
50_L	58_V	0.792	0.84
24_S	51_T	0.789	0.84
28_L	47_A	0.787	0.84
10_G	15_A	0.786	0.84
93_P	99_A	0.781	0.83
2_R	41_D	0.776	0.83
47_A	65_F	0.776	0.83
105_P	109_G	0.768	0.82
40_Y	71_S	0.761	0.82
28_L	58_V	0.756	0.81
90_R	96_P	0.751	0.81
95_A	101_P	0.746	0.81
43_C	46_H	0.740	0.80
15_A	22_A	0.740	0.80
45_E	66_A	0.738	0.80
99_A	103_A	0.737	0.80
43_C	56_W	0.736	0.80
46_H	56_W	0.736	0.80
64_D	67_P	0.736	0.80
43_C	53_P	0.717	0.78
46_H	53_P	0.717	0.78
30_P	60_R	0.715	0.78
53_P	56_W	0.711	0.77
60_R	82_V	0.710	0.77
90_R	97_A	0.704	0.77
16_T	29_G	0.698	0.76
3_R	13_A	0.698	0.76
7_T	15_A	0.694	0.76
34_Y	40_Y	0.686	0.75
100_A	105_P	0.685	0.75
70_P	81_A	0.684	0.75
19_Y	70_P	0.683	0.74
95_A	98_P	0.682	0.74
39_S	76_E	0.673	0.73
101_P	112_E	0.665	0.73
22_A	69_G	0.651	0.71
88_P	94_A	0.650	0.71
20_V	61_L	0.645	0.70
91_P	95_A	0.643	0.70
96_P	110_P	0.642	0.70
62_A	65_F	0.639	0.70
99_A	106_A	0.634	0.69
102_P	106_A	0.634	0.69
103_A	106_A	0.618	0.67
27_V	74_D	0.617	0.67
104_R	109_G	0.617	0.67
91_P	102_P	0.615	0.67
23_D	74_D	0.612	0.66
76_E	86_A	0.605	0.65
99_A	105_P	0.596	0.64
11_R	48_E	0.586	0.63
96_P	99_A	0.585	0.63
23_D	33_T	0.583	0.62
112_E	123_P	0.581	0.62
106_A	110_P	0.581	0.62
15_A	35_A	0.578	0.62
21_Y	37_P	0.577	0.62
90_R	93_P	0.575	0.61
108_P	112_E	0.575	0.61
34_Y	48_E	0.574	0.61
92_P	108_P	0.572	0.61
51_T	123_P	0.571	0.61
38_H	84_E	0.568	0.60
88_P	91_P	0.559	0.59
5_S	40_Y	0.554	0.59
11_R	14_V	0.551	0.58
100_A	103_A	0.546	0.57
29_G	41_D	0.546	0.57
44_E	49_R	0.540	0.57
24_S	39_S	0.540	0.57
6_R	24_S	0.537	0.56
64_D	68_P	0.530	0.55
69_G	76_E	0.528	0.55
38_H	51_T	0.523	0.54
7_T	10_G	0.518	0.54
100_A	104_R	0.518	0.54
113_G	117_G	0.515	0.53
27_V	36_E	0.515	0.53
24_S	66_A	0.514	0.53
91_P	97_A	0.509	0.52
48_E	62_A	0.505	0.52
32_A	115_R	0.500	0.51

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
3zey1	1	0.5887	11	0.936	Contact Map
4bpeW	1	0.6694	6.8	0.942	Contact Map
1w4rA	3	0.3387	6.8	0.942	Contact Map
3j7aF	1	0.6694	5.7	0.944	Contact Map
3j60E	1	0.3952	5.6	0.945	Contact Map
4ujpF	1	0.6694	5.4	0.945	Contact Map
1onvB	1	0	4.4	0.947	Contact Map
1pxeA	1	0.371	3.2	0.95	Contact Map
4guaA	3	0.9194	3	0.951	Contact Map
3avrA	1	0.5403	2.7	0.953	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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