DUF805 - PFAM28P - GREMLIN Contacts

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DUF805 - Protein of unknown function (DUF805)

PFAM:	PF05656	Sequences: YFSFSGRASRSEYWWFVLFNLIVSIVLGILDGALGGGGGGGILSLLFSLALLIPSLAVTVRRLHDTGRSGWWLLLGLIPLIGLIVLLVLLFLPGTPGPNRYGPDP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (104)
Sequences:	34214 (28757)
Seq/√Len:	2819.9
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_S	15_W	3.349	1.00
60_V	73_L	3.029	1.00
8_A	12_E	2.693	1.00
85_V	89_L	2.534	1.00
4_F	57_A	2.346	1.00
72_W	75_L	2.297	1.00
64_H	70_G	2.236	1.00
98_P	103_P	2.067	1.00
93_P	96_P	2.041	1.00
84_I	88_V	1.987	1.00
88_V	92_L	1.984	1.00
9_S	12_E	1.928	1.00
14_W	90_L	1.879	1.00
66_T	92_L	1.868	1.00
59_T	73_L	1.837	1.00
60_V	70_G	1.809	1.00
47_F	51_L	1.777	1.00
67_G	100_R	1.731	1.00
53_I	57_A	1.683	1.00
8_A	58_V	1.672	1.00
20_N	47_F	1.667	1.00
57_A	61_R	1.634	1.00
8_A	61_R	1.615	1.00
97_G	104_D	1.560	1.00
67_G	95_T	1.535	1.00
9_S	104_D	1.504	1.00
20_N	24_S	1.483	1.00
3_S	6_G	1.442	1.00
59_T	90_L	1.438	1.00
66_T	88_V	1.384	1.00
71_W	74_L	1.341	1.00
68_R	88_V	1.304	1.00
27_L	31_D	1.250	1.00
60_V	64_H	1.206	1.00
50_A	54_P	1.195	1.00
16_F	58_V	1.188	1.00
20_N	51_L	1.169	1.00
7_R	65_D	1.166	1.00
13_Y	59_T	1.159	1.00
31_D	39_G	1.128	1.00
13_Y	90_L	1.099	1.00
20_N	55_S	1.097	1.00
15_W	19_F	1.075	1.00
3_S	8_A	1.068	1.00
2_F	53_I	1.056	1.00
9_S	93_P	1.055	1.00
31_D	44_S	1.054	1.00
73_L	76_G	1.038	1.00
96_P	104_D	1.030	1.00
16_F	20_N	1.021	1.00
93_P	104_D	1.010	1.00
94_G	104_D	1.009	1.00
59_T	63_L	0.994	1.00
87_L	91_F	0.977	1.00
63_L	73_L	0.969	1.00
75_L	78_I	0.969	1.00
29_I	33_A	0.967	1.00
24_S	28_G	0.962	1.00
16_F	19_F	0.951	1.00
66_T	89_L	0.950	1.00
89_L	92_L	0.932	1.00
41_G	45_L	0.926	1.00
25_I	29_I	0.921	1.00
17_V	20_N	0.916	1.00
44_S	48_S	0.890	1.00
76_G	83_L	0.882	1.00
86_L	90_L	0.863	1.00
57_A	60_V	0.849	1.00
17_V	21_L	0.846	1.00
17_V	55_S	0.833	1.00
42_I	46_L	0.826	1.00
59_T	76_G	0.825	1.00
69_S	72_W	0.814	1.00
68_R	72_W	0.814	1.00
87_L	90_L	0.806	1.00
45_L	49_L	0.795	1.00
63_L	68_R	0.789	1.00
99_N	102_G	0.786	1.00
31_D	41_G	0.784	1.00
23_V	47_F	0.783	1.00
68_R	92_L	0.782	1.00
63_L	85_V	0.773	1.00
66_T	94_G	0.769	1.00
54_P	57_A	0.768	1.00
46_L	50_A	0.765	1.00
24_S	44_S	0.761	1.00
76_G	86_L	0.755	1.00
31_D	34_L	0.747	1.00
4_F	56_L	0.743	1.00
4_F	60_V	0.741	1.00
82_G	85_V	0.739	1.00
10_R	93_P	0.739	1.00
98_P	104_D	0.726	1.00
27_L	47_F	0.716	1.00
95_T	104_D	0.709	1.00
24_S	48_S	0.703	1.00
54_P	58_V	0.700	1.00
17_V	24_S	0.699	1.00
27_L	44_S	0.695	1.00
19_F	23_V	0.693	1.00
78_I	82_G	0.693	1.00
28_G	32_G	0.691	1.00
42_I	45_L	0.691	1.00
75_L	82_G	0.689	1.00
21_L	25_I	0.686	1.00
11_S	14_W	0.683	1.00
31_D	35_G	0.683	1.00
22_I	26_V	0.678	1.00
56_L	60_V	0.676	1.00
79_P	82_G	0.668	1.00
63_L	72_W	0.666	1.00
6_G	61_R	0.665	1.00
39_G	42_I	0.664	1.00
63_L	66_T	0.664	1.00
53_I	61_R	0.661	1.00
56_L	73_L	0.658	1.00
60_V	69_S	0.653	1.00
66_T	90_L	0.647	1.00
63_L	89_L	0.643	1.00
28_G	44_S	0.642	1.00
70_G	73_L	0.641	1.00
94_G	101_Y	0.639	1.00
95_T	101_Y	0.628	1.00
8_A	16_F	0.627	1.00
31_D	36_G	0.625	1.00
15_W	18_L	0.623	1.00
33_A	36_G	0.619	1.00
14_W	66_T	0.612	1.00
98_P	102_G	0.611	1.00
2_F	54_P	0.611	1.00
94_G	99_N	0.606	1.00
19_F	22_I	0.601	1.00
48_S	51_L	0.598	1.00
81_I	84_I	0.596	1.00
60_V	71_W	0.595	1.00
88_V	91_F	0.594	1.00
32_G	36_G	0.581	1.00
26_V	29_I	0.578	1.00
92_L	95_T	0.564	1.00
41_G	44_S	0.560	1.00
52_L	55_S	0.558	1.00
74_L	77_L	0.556	1.00
7_R	64_H	0.549	1.00
38_G	42_I	0.544	1.00
18_L	22_I	0.537	1.00
31_D	42_I	0.535	1.00
82_G	86_L	0.534	1.00
20_N	23_V	0.518	1.00
23_V	26_V	0.515	1.00
76_G	82_G	0.514	1.00
38_G	41_G	0.513	1.00
96_P	100_R	0.512	1.00
10_R	14_W	0.512	1.00
86_L	89_L	0.511	1.00
26_V	30_L	0.509	1.00
4_F	53_I	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
2mkcC	1	0.1524	5.6	0.9	Contact Map
4wd8A	3	0.9048	4.6	0.904	Contact Map
3ux4A	3	0.981	3.1	0.912	Contact Map
2kogA	1	0.381	3.1	0.912	Contact Map
4rdqA	5	0.7714	3.1	0.912	Contact Map
2a65A	2	0.9619	2.6	0.914	Contact Map
1fftA	1	0.7714	2.4	0.916	Contact Map
4pgrA	1	0.9143	2.2	0.918	Contact Map
1rypF	1	0.8571	2.2	0.918	Contact Map
3mk7A	1	0.781	2.1	0.919	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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