DUF3796 - PFAM28P - GREMLIN Contacts

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DUF3796 - Protein of unknown function (DUF3796)

PFAM:	PF12676	Sequences: NKLGYLGFLGFLGFLGFFTFVTGNPGFFGFFGFFGFFGYFFEGKLSGTIPDERFRENVRKAALNAFFVGLVLLFLALLILLLLGNLEALELAFALLFAVLILTFALSLFLYEYLLYRYDH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (111)
Sequences:	570 (450)
Seq/√Len:	42.7
META:	0.821

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_G	31_F	3.197	1.00
29_G	32_G	3.173	1.00
10_G	34_F	2.929	1.00
9_L	12_L	2.646	1.00
57_N	61_A	2.640	1.00
7_G	10_G	2.453	1.00
13_G	16_G	2.434	1.00
13_G	34_F	2.383	1.00
7_G	37_F	2.130	0.99
4_G	40_F	2.025	0.99
35_G	38_G	2.014	0.99
6_L	9_L	1.950	0.99
4_G	13_G	1.933	0.99
26_G	29_G	1.917	0.99
10_G	37_F	1.729	0.98
97_F	101_I	1.647	0.97
28_F	31_F	1.455	0.94
107_S	111_Y	1.447	0.93
53_R	63_L	1.426	0.93
66_F	70_L	1.415	0.93
66_F	107_S	1.412	0.93
65_A	68_V	1.410	0.93
31_F	101_I	1.365	0.91
20_F	28_F	1.360	0.91
59_R	63_L	1.341	0.90
104_F	109_F	1.338	0.90
97_F	104_F	1.331	0.90
25_P	28_F	1.301	0.89
50_P	58_V	1.286	0.89
98_A	102_L	1.277	0.88
10_G	13_G	1.267	0.88
3_L	6_L	1.251	0.87
90_E	98_A	1.250	0.87
33_F	55_R	1.247	0.87
50_P	54_F	1.231	0.86
12_L	30_F	1.229	0.86
75_L	80_L	1.211	0.85
10_G	15_L	1.198	0.85
13_G	31_F	1.193	0.84
105_A	108_L	1.176	0.84
62_A	67_F	1.163	0.83
14_F	17_F	1.163	0.83
57_N	60_K	1.145	0.82
108_L	111_Y	1.144	0.82
33_F	36_F	1.142	0.82
54_F	58_V	1.134	0.81
100_L	103_T	1.092	0.79
50_P	55_R	1.089	0.79
59_R	62_A	1.068	0.77
76_A	95_L	1.068	0.77
108_L	112_E	1.063	0.77
71_V	75_L	1.061	0.77
52_E	57_N	1.057	0.76
73_L	103_T	1.051	0.76
79_I	83_L	1.045	0.76
73_L	77_L	1.026	0.74
6_L	15_L	1.021	0.74
97_F	108_L	1.014	0.73
99_V	104_F	1.004	0.73
80_L	85_N	1.003	0.73
103_T	107_S	1.002	0.72
34_F	37_F	1.002	0.72
30_F	36_F	0.994	0.72
54_F	69_G	0.992	0.72
39_Y	49_I	0.989	0.71
60_K	65_A	0.984	0.71
5_Y	59_R	0.974	0.70
64_N	68_V	0.964	0.69
49_I	91_L	0.963	0.69
26_G	32_G	0.960	0.69
13_G	37_F	0.955	0.69
56_E	60_K	0.946	0.68
101_I	105_A	0.931	0.67
22_T	32_G	0.929	0.67
59_R	64_N	0.929	0.67
65_A	75_L	0.928	0.67
109_F	113_Y	0.927	0.66
30_F	33_F	0.922	0.66
58_V	71_V	0.921	0.66
89_L	92_A	0.912	0.65
93_F	98_A	0.901	0.64
61_A	86_L	0.894	0.64
53_R	110_L	0.865	0.61
10_G	69_G	0.862	0.61
35_G	39_Y	0.855	0.60
14_F	32_G	0.853	0.60
79_I	112_E	0.852	0.60
87_E	90_E	0.849	0.60
52_E	65_A	0.844	0.59
87_E	91_L	0.835	0.58
21_V	78_L	0.833	0.58
51_D	65_A	0.827	0.58
27_F	31_F	0.823	0.57
48_T	54_F	0.808	0.56
97_F	100_L	0.804	0.55
56_E	83_L	0.792	0.54
50_P	67_F	0.777	0.53
96_L	99_V	0.774	0.53
98_A	113_Y	0.771	0.52
89_L	93_F	0.763	0.52
49_I	54_F	0.762	0.51
54_F	66_F	0.751	0.50
100_L	109_F	0.742	0.50
69_G	107_S	0.734	0.49
61_A	65_A	0.723	0.48
93_F	96_L	0.716	0.47
105_A	109_F	0.714	0.47
94_A	100_L	0.710	0.47
77_L	80_L	0.703	0.46
91_L	103_T	0.695	0.45
36_F	79_I	0.691	0.45
32_G	104_F	0.690	0.45
14_F	21_V	0.685	0.44
97_F	112_E	0.682	0.44
5_Y	13_G	0.676	0.43
9_L	75_L	0.674	0.43
14_F	22_T	0.670	0.43
64_N	107_S	0.669	0.43
29_G	66_F	0.664	0.42
79_I	84_G	0.661	0.42
53_R	57_N	0.659	0.42
31_F	34_F	0.654	0.41
55_R	59_R	0.653	0.41
102_L	105_A	0.649	0.41
39_Y	56_E	0.629	0.39
4_G	72_L	0.626	0.39
17_F	56_E	0.616	0.38
98_A	101_I	0.616	0.38
8_F	16_G	0.602	0.37
12_L	27_F	0.602	0.37
42_E	46_S	0.600	0.36
77_L	81_L	0.597	0.36
4_G	7_G	0.596	0.36
39_Y	42_E	0.595	0.36
79_I	110_L	0.587	0.35
11_F	77_L	0.586	0.35
19_T	22_T	0.582	0.35
2_K	55_R	0.581	0.35
107_S	113_Y	0.575	0.34
83_L	87_E	0.574	0.34
53_R	83_L	0.573	0.34
36_F	39_Y	0.572	0.34
12_L	32_G	0.569	0.34
96_L	103_T	0.566	0.34
80_L	112_E	0.553	0.32
96_L	113_Y	0.553	0.32
8_F	14_F	0.550	0.32
88_A	106_L	0.548	0.32
103_T	112_E	0.546	0.32
6_L	25_P	0.542	0.32
51_D	57_N	0.540	0.31
52_E	61_A	0.540	0.31
2_K	75_L	0.539	0.31
82_L	85_N	0.535	0.31
67_F	72_L	0.530	0.31
54_F	62_A	0.524	0.30
10_G	25_P	0.524	0.30
51_D	61_A	0.522	0.30
64_N	103_T	0.522	0.30
102_L	110_L	0.520	0.30
88_A	92_A	0.519	0.30
94_A	98_A	0.516	0.29
11_F	31_F	0.515	0.29
80_L	84_G	0.510	0.29
61_A	64_N	0.505	0.29
60_K	70_L	0.500	0.28

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
3aqpA	1	0.9583	3.7	0.93	Contact Map
3wdoA	1	0.5833	3.5	0.931	Contact Map
2cfqA	1	0.5917	2.2	0.938	Contact Map
3j1zP	8	0.6083	2.1	0.939	Contact Map
4pypA	1	0.525	1.8	0.94	Contact Map
4dx5A	3	0.9333	1.8	0.94	Contact Map
4k5yA	1	0.5583	1.8	0.94	Contact Map
3dl8G	1	0.8833	1.8	0.94	Contact Map
4oo9A	1	0.7667	1.8	0.941	Contact Map
3w9iA	3	0.9333	1.6	0.942	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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