Dickkopf_N - PFAM28P - GREMLIN Contacts

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Dickkopf_N - Dickkopf N-terminal cysteine-rich region

PFAM:	PF04706	Sequences: ECTSDSDCGAGLYCDAGTGGGGTCVPLKAAGAACTRDAECASGLVCVNGVCT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (49)
Sequences:	1801 (1556)
Seq/√Len:	222.3
META:	0.82

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_L	41_A	3.403	1.00
9_G	12_L	3.387	1.00
28_K	32_A	2.994	1.00
15_D	25_V	2.113	1.00
12_L	26_P	1.994	1.00
13_Y	28_K	1.751	1.00
35_T	39_E	1.702	1.00
24_C	27_L	1.653	1.00
28_K	39_E	1.621	1.00
27_L	42_S	1.597	1.00
34_C	46_C	1.520	1.00
41_A	44_L	1.392	1.00
29_A	32_A	1.345	1.00
13_Y	31_G	1.317	1.00
48_N	51_C	1.306	1.00
2_C	7_D	1.267	1.00
5_D	38_A	1.153	1.00
3_T	16_A	1.141	1.00
47_V	51_C	1.121	1.00
26_P	30_A	1.094	1.00
12_L	44_L	1.039	1.00
30_A	44_L	1.023	1.00
5_D	36_R	1.012	1.00
11_G	27_L	0.991	1.00
13_Y	27_L	0.946	1.00
2_C	8_C	0.941	1.00
36_R	39_E	0.937	1.00
3_T	7_D	0.921	0.99
26_P	29_A	0.919	0.99
13_Y	25_V	0.888	0.99
31_G	44_L	0.882	0.99
37_D	40_C	0.864	0.99
13_Y	39_E	0.855	0.99
20_G	37_D	0.850	0.99
23_T	50_V	0.847	0.99
17_G	20_G	0.847	0.99
35_T	50_V	0.845	0.99
3_T	9_G	0.821	0.99
27_L	38_A	0.784	0.98
7_D	47_V	0.754	0.98
28_K	41_A	0.753	0.98
18_T	23_T	0.749	0.98
3_T	45_V	0.743	0.98
4_S	32_A	0.742	0.98
35_T	42_S	0.737	0.98
23_T	37_D	0.729	0.97
31_G	48_N	0.712	0.97
11_G	14_C	0.706	0.97
3_T	6_S	0.706	0.97
45_V	51_C	0.702	0.97
5_D	13_Y	0.684	0.96
18_T	32_A	0.676	0.96
19_G	24_C	0.658	0.95
37_D	47_V	0.647	0.95
16_A	21_G	0.626	0.94
5_D	9_G	0.625	0.94
17_G	35_T	0.616	0.93
30_A	47_V	0.615	0.93
16_A	38_A	0.602	0.93
4_S	12_L	0.591	0.92
18_T	48_N	0.575	0.91
31_G	41_A	0.563	0.90
15_D	19_G	0.562	0.90
26_P	33_A	0.557	0.89
42_S	45_V	0.557	0.89
14_C	51_C	0.556	0.89
2_C	5_D	0.540	0.88
10_A	42_S	0.537	0.88
32_A	44_L	0.533	0.87
8_C	11_G	0.526	0.86
6_S	10_A	0.523	0.86
45_V	50_V	0.514	0.85
23_T	30_A	0.501	0.84
35_T	49_G	0.500	0.84

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
2jtkA	1	0.9808	83.6	0.574	Contact Map
3s2kC	1	0.9808	78.1	0.597	Contact Map
2kraA	1	1	74.9	0.608	Contact Map
1imtA	1	1	67.6	0.629	Contact Map
1lpbA	1	0.9808	55.1	0.656	Contact Map
4tpvA	2	0.9231	32	0.701	Contact Map
1oigA	1	0.4231	31.3	0.704	Contact Map
4pmkA	1	0.0577	27	0.713	Contact Map
2l1qA	1	0.6538	25.6	0.715	Contact Map
4cpaI	1	0.5385	21.6	0.726	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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