DUF3995 - PFAM28P - GREMLIN Contacts

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DUF3995 - Protein of unknown function (DUF3995)

PFAM:	PF13160	Sequences: LLALAALHVYWALGGTWGLDTLADAVVPTARGGPMPSPAATLAVALLLLAAALLVLALAGLLGRPLPRRLLRLGGWALAAVFLLRGIGDFRYVGFFKRVRGTPPFARLDTRLYSPLCLLLGLGF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (121)
Sequences:	3205 (2537)
Seq/√Len:	230.6
META:	0.818

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_Y	15_G	5.865	1.00
83_L	121_G	4.608	1.00
9_V	45_A	3.908	1.00
5_A	49_L	3.264	1.00
12_A	42_L	2.824	1.00
108_L	112_L	2.610	1.00
58_L	75_G	2.428	1.00
95_F	114_S	2.340	1.00
37_S	40_A	2.278	1.00
97_K	110_T	2.221	1.00
57_A	71_L	2.166	1.00
2_L	52_A	2.084	1.00
86_G	95_F	1.955	1.00
3_A	7_L	1.844	1.00
4_L	48_L	1.844	1.00
86_G	118_L	1.771	1.00
51_A	78_L	1.709	1.00
82_F	120_L	1.619	1.00
73_L	77_A	1.613	1.00
12_A	41_T	1.584	1.00
107_R	111_R	1.564	1.00
79_A	121_G	1.547	1.00
38_P	41_T	1.458	1.00
54_L	74_G	1.456	1.00
47_L	51_A	1.428	1.00
105_F	109_D	1.419	1.00
119_L	123_G	1.397	1.00
80_A	84_L	1.370	1.00
12_A	45_A	1.366	1.00
109_D	114_S	1.361	1.00
41_T	44_V	1.303	1.00
43_A	47_L	1.295	1.00
14_G	17_W	1.292	1.00
54_L	78_L	1.290	1.00
4_L	120_L	1.251	1.00
106_A	109_D	1.250	1.00
23_A	26_V	1.242	1.00
89_D	92_Y	1.221	1.00
76_W	79_A	1.202	1.00
55_V	75_G	1.175	1.00
97_K	100_R	1.158	1.00
99_V	102_T	1.145	1.00
9_V	42_L	1.107	1.00
86_G	114_S	1.102	1.00
38_P	42_L	1.093	1.00
90_F	94_G	1.080	1.00
94_G	97_K	1.077	1.00
89_D	93_V	1.071	1.00
8_H	85_R	1.054	1.00
37_S	41_T	1.046	1.00
8_H	44_V	1.036	1.00
55_V	58_L	1.026	1.00
15_G	18_G	1.026	1.00
93_V	96_F	1.020	1.00
31_R	34_P	1.005	1.00
108_L	113_Y	0.991	1.00
5_A	9_V	0.979	1.00
117_C	120_L	0.977	1.00
78_L	82_F	0.967	1.00
99_V	103_P	0.956	1.00
2_L	49_L	0.950	1.00
8_H	48_L	0.947	1.00
51_A	81_V	0.944	1.00
9_V	49_L	0.932	1.00
55_V	79_A	0.930	1.00
70_L	74_G	0.927	1.00
116_L	120_L	0.923	1.00
58_L	71_L	0.918	1.00
18_G	26_V	0.912	1.00
44_V	48_L	0.894	0.99
97_K	109_D	0.891	0.99
85_R	109_D	0.887	0.99
56_L	61_L	0.885	0.99
83_L	118_L	0.857	0.99
120_L	123_G	0.850	0.99
46_L	50_A	0.841	0.99
30_A	33_G	0.836	0.99
85_R	114_S	0.836	0.99
108_L	111_R	0.835	0.99
19_L	22_L	0.832	0.99
10_Y	13_L	0.819	0.99
85_R	88_G	0.817	0.99
94_G	100_R	0.812	0.99
42_L	45_A	0.806	0.99
24_D	28_P	0.801	0.99
88_G	105_F	0.787	0.99
96_F	99_V	0.777	0.98
4_L	117_C	0.769	0.98
92_Y	99_V	0.769	0.98
110_T	114_S	0.767	0.98
52_A	56_L	0.763	0.98
69_R	73_L	0.760	0.98
96_F	100_R	0.758	0.98
21_T	25_A	0.757	0.98
58_L	72_R	0.752	0.98
29_T	33_G	0.752	0.98
13_L	42_L	0.747	0.98
5_A	45_A	0.745	0.98
10_Y	17_W	0.740	0.98
22_L	28_P	0.737	0.98
22_L	26_V	0.727	0.98
58_L	74_G	0.727	0.98
4_L	8_H	0.723	0.98
91_R	97_K	0.719	0.97
56_L	62_L	0.716	0.97
85_R	105_F	0.713	0.97
96_F	103_P	0.711	0.97
54_L	75_G	0.710	0.97
10_Y	16_T	0.708	0.97
87_I	90_F	0.703	0.97
72_R	75_G	0.700	0.97
14_G	18_G	0.699	0.97
94_G	106_A	0.696	0.97
25_A	108_L	0.695	0.97
39_A	43_A	0.694	0.97
8_H	11_W	0.687	0.97
74_G	78_L	0.685	0.97
12_A	38_P	0.680	0.96
113_Y	120_L	0.673	0.96
11_W	14_G	0.672	0.96
118_L	122_L	0.670	0.96
30_A	92_Y	0.669	0.96
68_R	72_R	0.669	0.96
103_P	108_L	0.667	0.96
7_L	17_W	0.665	0.96
60_G	63_G	0.663	0.96
64_R	67_P	0.658	0.96
94_G	99_V	0.653	0.96
54_L	71_L	0.651	0.95
71_L	75_G	0.649	0.95
9_V	12_A	0.646	0.95
97_K	106_A	0.643	0.95
19_L	25_A	0.639	0.95
16_T	19_L	0.636	0.95
7_L	11_W	0.631	0.95
52_A	55_V	0.628	0.94
48_L	55_V	0.623	0.94
15_G	19_L	0.622	0.94
95_F	118_L	0.622	0.94
53_L	57_A	0.620	0.94
10_Y	19_L	0.620	0.94
62_L	65_P	0.618	0.94
3_A	6_A	0.615	0.94
24_D	32_G	0.614	0.94
113_Y	117_C	0.614	0.94
86_G	89_D	0.608	0.93
112_L	115_P	0.605	0.93
62_L	67_P	0.596	0.93
65_P	71_L	0.589	0.92
59_A	63_G	0.585	0.92
63_G	66_L	0.584	0.92
25_A	28_P	0.582	0.92
95_F	100_R	0.580	0.92
24_D	103_P	0.580	0.92
18_G	113_Y	0.578	0.92
41_T	45_A	0.573	0.91
8_H	105_F	0.567	0.91
6_A	10_Y	0.566	0.91
89_D	114_S	0.560	0.90
18_G	112_L	0.557	0.90
55_V	78_L	0.552	0.90
82_F	116_L	0.552	0.90
27_V	32_G	0.551	0.90
54_L	57_A	0.547	0.89
65_P	70_L	0.547	0.89
4_L	41_T	0.544	0.89
88_G	91_R	0.544	0.89
7_L	36_P	0.543	0.89
57_A	65_P	0.539	0.89
9_V	46_L	0.538	0.89
94_G	98_R	0.538	0.89
63_G	71_L	0.529	0.88
109_D	113_Y	0.529	0.88
90_F	96_F	0.527	0.88
51_A	82_F	0.526	0.87
77_A	80_A	0.514	0.86
88_G	114_S	0.508	0.86
73_L	76_W	0.507	0.86
48_L	85_R	0.504	0.85
76_W	122_L	0.504	0.85
59_A	72_R	0.503	0.85
106_A	110_T	0.500	0.85

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
2k1aA	1	0.3387	1.4	0.935	Contact Map
4p02A	1	0.5484	1.4	0.936	Contact Map
1xaxA	1	0.2903	1.3	0.937	Contact Map
2l2tA	2	0.3387	0.8	0.945	Contact Map
1iijA	1	0.2823	0.7	0.946	Contact Map
4djkA	2	0.9274	0.7	0.947	Contact Map
3aofA	1	0.2823	0.7	0.947	Contact Map
1jb0A	1	0.621	0.6	0.95	Contact Map
3rqwA	4	0.6613	0.6	0.95	Contact Map
2kncA	1	0.4355	0.5	0.951	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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