PSD4 - PFAM28P - GREMLIN Contacts

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PSD4 - Protein of unknown function (DUF1592)

PFAM:	PF07631	Sequences: LSDYELASRLSYFLWSSMPDDELLALAAAGKLRDPAVLEAQVRRMLADPRARALVTNFAGQWLGLRNLDSVTPDPKLFPDFDDNLRQAMRRETELFFESVLREDRSVLDLLTADYTFVNERLARHYGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	128 (127)
Sequences:	54660 (32664)
Seq/√Len:	2898.4
META:	0.988

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_R	95_L	2.734	1.00
99_S	103_E	2.663	1.00
52_R	98_E	2.599	1.00
3_D	33_R	2.536	1.00
25_A	29_A	2.485	1.00
41_Q	44_R	2.282	1.00
26_L	41_Q	2.183	1.00
34_D	37_V	2.143	1.00
22_E	41_Q	1.996	1.00
88_A	119_N	1.993	1.00
31_K	37_V	1.991	1.00
31_K	34_D	1.967	1.00
4_Y	28_A	1.925	1.00
99_S	115_Y	1.901	1.00
39_E	43_R	1.884	1.00
105_R	109_D	1.867	1.00
98_E	102_R	1.852	1.00
12_Y	18_M	1.847	1.00
26_L	37_V	1.837	1.00
59_A	97_F	1.829	1.00
26_L	31_K	1.824	1.00
37_V	40_A	1.808	1.00
91_R	94_E	1.751	1.00
64_G	67_N	1.714	1.00
21_D	25_A	1.684	1.00
60_G	94_E	1.646	1.00
99_S	117_F	1.620	1.00
56_T	94_E	1.572	1.00
25_A	28_A	1.552	1.00
46_L	51_A	1.529	1.00
18_M	24_L	1.527	1.00
2_S	5_E	1.514	1.00
20_D	44_R	1.468	1.00
69_D	90_R	1.462	1.00
39_E	42_V	1.448	1.00
90_R	94_E	1.443	1.00
96_F	113_A	1.440	1.00
22_E	26_L	1.425	1.00
88_A	121_R	1.416	1.00
120_E	124_R	1.411	1.00
52_R	56_T	1.342	1.00
4_Y	24_L	1.341	1.00
33_R	37_V	1.319	1.00
15_W	50_R	1.310	1.00
15_W	48_D	1.286	1.00
95_L	98_E	1.268	1.00
84_N	88_A	1.261	1.00
82_D	121_R	1.224	1.00
74_D	77_L	1.222	1.00
3_D	30_G	1.214	1.00
24_L	28_A	1.191	1.00
35_P	39_E	1.171	1.00
92_E	116_T	1.166	1.00
16_S	57_N	1.162	1.00
81_F	86_R	1.162	1.00
16_S	54_L	1.155	1.00
15_W	45_M	1.151	1.00
22_E	25_A	1.135	1.00
99_S	102_R	1.127	1.00
95_L	99_S	1.106	1.00
67_N	70_S	1.096	1.00
60_G	65_L	1.090	1.00
43_R	47_A	1.077	1.00
65_L	93_T	1.071	1.00
95_L	117_F	1.064	1.00
84_N	121_R	1.052	1.00
37_V	41_Q	1.045	1.00
118_V	128_I	1.034	1.00
60_G	66_R	1.033	1.00
83_D	86_R	1.012	1.00
56_T	98_E	1.011	1.00
109_D	115_Y	0.990	1.00
85_L	125_H	0.980	1.00
55_V	98_E	0.978	1.00
52_R	102_R	0.965	1.00
30_G	33_R	0.964	1.00
92_E	126_Y	0.960	1.00
109_D	112_T	0.951	1.00
4_Y	8_S	0.948	1.00
36_A	39_E	0.933	1.00
89_M	122_L	0.915	1.00
57_N	61_Q	0.900	1.00
97_F	110_L	0.898	1.00
87_Q	91_R	0.895	1.00
3_D	6_L	0.876	1.00
83_D	87_Q	0.866	1.00
36_A	40_A	0.848	1.00
3_D	29_A	0.836	1.00
6_L	38_L	0.825	1.00
74_D	78_F	0.824	1.00
49_P	52_R	0.823	1.00
106_S	109_D	0.812	1.00
8_S	12_Y	0.811	1.00
53_A	56_T	0.809	1.00
4_Y	27_A	0.806	1.00
105_R	115_Y	0.803	1.00
86_R	90_R	0.799	1.00
20_D	41_Q	0.784	1.00
9_R	13_F	0.772	1.00
69_D	86_R	0.770	1.00
100_V	110_L	0.763	1.00
14_L	42_V	0.762	1.00
89_M	125_H	0.757	1.00
29_A	33_R	0.754	1.00
60_G	90_R	0.752	1.00
121_R	124_R	0.740	1.00
121_R	125_H	0.740	1.00
69_D	72_T	0.737	1.00
38_L	42_V	0.737	1.00
55_V	59_A	0.730	1.00
8_S	18_M	0.716	1.00
88_A	122_L	0.716	1.00
84_N	87_Q	0.710	1.00
52_R	55_V	0.709	1.00
99_S	105_R	0.707	1.00
108_L	112_T	0.705	1.00
82_D	85_L	0.703	1.00
55_V	97_F	0.692	1.00
22_E	40_A	0.686	1.00
11_S	15_W	0.685	1.00
93_T	96_F	0.682	1.00
69_D	87_Q	0.681	1.00
72_T	75_P	0.671	1.00
99_S	109_D	0.668	1.00
73_P	77_L	0.664	1.00
73_P	81_F	0.662	1.00
8_S	11_S	0.654	1.00
27_A	32_L	0.652	1.00
51_A	101_L	0.649	1.00
59_A	100_V	0.648	1.00
82_D	88_A	0.646	1.00
97_F	101_L	0.646	1.00
56_T	60_G	0.644	1.00
68_L	71_V	0.643	1.00
98_E	101_L	0.639	1.00
10_L	38_L	0.638	1.00
26_L	29_A	0.630	1.00
14_L	45_M	0.628	1.00
85_L	89_M	0.627	1.00
109_D	113_A	0.627	1.00
21_D	24_L	0.616	1.00
10_L	42_V	0.610	1.00
97_F	100_V	0.602	1.00
3_D	27_A	0.598	1.00
33_R	36_A	0.597	1.00
104_D	109_D	0.589	1.00
118_V	125_H	0.587	1.00
17_S	50_R	0.585	1.00
26_L	40_A	0.585	1.00
48_D	51_A	0.584	1.00
68_L	90_R	0.582	1.00
72_T	83_D	0.577	1.00
89_M	92_E	0.575	1.00
72_T	86_R	0.574	1.00
41_Q	45_M	0.572	1.00
87_Q	90_R	0.572	1.00
35_P	38_L	0.571	1.00
74_D	79_P	0.571	1.00
107_V	111_L	0.570	1.00
3_D	37_V	0.565	1.00
54_L	59_A	0.564	1.00
42_V	45_M	0.559	1.00
77_L	80_D	0.555	1.00
6_L	9_R	0.546	1.00
59_A	101_L	0.546	1.00
7_A	32_L	0.545	1.00
64_G	70_S	0.544	1.00
89_M	93_T	0.541	1.00
20_D	23_L	0.539	1.00
65_L	68_L	0.539	1.00
16_S	53_A	0.539	1.00
61_Q	66_R	0.533	1.00
81_F	89_M	0.525	1.00
40_A	43_R	0.524	1.00
22_E	44_R	0.524	1.00
101_L	104_D	0.523	1.00
75_P	84_N	0.523	1.00
55_V	101_L	0.523	1.00
45_M	48_D	0.518	1.00
100_V	109_D	0.517	1.00
92_E	96_F	0.517	1.00
80_D	84_N	0.516	1.00
67_N	71_V	0.515	1.00
72_T	76_K	0.514	1.00
6_L	33_R	0.507	1.00
80_D	125_H	0.507	1.00
55_V	94_E	0.507	1.00
7_A	11_S	0.503	1.00
76_K	79_P	0.501	1.00
57_N	66_R	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
4lloB	1	0.2656	13.3	0.918	Contact Map
2ce7A	3	0.8594	6.6	0.928	Contact Map
1whrA	1	0.5781	6.4	0.929	Contact Map
2hjeA	1	0.6094	6.4	0.929	Contact Map
3r8rA	5	0.4688	6.2	0.929	Contact Map
3c38A	1	0.6094	5.6	0.931	Contact Map
2krxA	1	0.5547	5	0.932	Contact Map
1l6wA	6	0.5234	4.7	0.933	Contact Map
4dduA	1	0.9141	4.5	0.934	Contact Map
3uq8A	1	0.6797	4.4	0.934	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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