DUF1456 - PFAM28P - GREMLIN Contacts

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DUF1456 - Protein of unknown function (DUF1456)

PFAM:	PF07308	Sequences: NNDILRKLRYALDLKDEDMIEIFALAGFEVSKHELSAFLRKEDHPNYRECGDQVLRNFLNGLIIKKRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (68)
Sequences:	8634 (4793)
Seq/√Len:	581.2
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_G	54_V	2.255	1.00
31_S	34_E	2.058	1.00
28_F	57_N	2.010	1.00
21_E	65_K	1.995	1.00
16_D	32_K	1.841	1.00
25_L	64_I	1.787	1.00
24_A	29_E	1.738	1.00
30_V	38_F	1.723	1.00
38_F	54_V	1.721	1.00
26_A	57_N	1.696	1.00
18_D	65_K	1.696	1.00
25_L	65_K	1.653	1.00
15_K	18_D	1.592	1.00
28_F	54_V	1.553	1.00
22_I	65_K	1.544	1.00
20_I	35_L	1.500	1.00
26_A	64_I	1.478	1.00
9_R	16_D	1.466	1.00
37_A	48_R	1.407	1.00
12_L	62_L	1.406	1.00
14_L	22_I	1.317	1.00
4_I	55_L	1.313	1.00
16_D	36_S	1.290	1.00
22_I	61_G	1.275	1.00
60_N	64_I	1.272	1.00
32_K	36_S	1.260	1.00
53_Q	57_N	1.249	1.00
60_N	63_I	1.242	1.00
20_I	32_K	1.242	1.00
18_D	21_E	1.235	1.00
37_A	46_N	1.174	1.00
7_K	11_A	1.161	1.00
50_C	54_V	1.156	1.00
23_F	54_V	1.147	1.00
5_L	19_M	1.140	1.00
17_E	32_K	1.130	1.00
19_M	35_L	1.099	1.00
8_L	11_A	1.086	1.00
6_R	10_Y	1.066	1.00
37_A	40_R	1.051	1.00
6_R	16_D	1.043	1.00
26_A	61_G	1.025	1.00
40_R	46_N	1.022	1.00
33_H	36_S	1.003	1.00
21_E	24_A	0.991	1.00
30_V	35_L	0.985	1.00
19_M	58_F	0.972	1.00
8_L	59_L	0.967	1.00
38_F	50_C	0.966	1.00
14_L	62_L	0.913	1.00
21_E	25_L	0.891	1.00
62_L	66_K	0.885	1.00
23_F	28_F	0.884	1.00
22_I	58_F	0.865	1.00
30_V	54_V	0.835	1.00
22_I	62_L	0.823	1.00
33_H	37_A	0.819	1.00
36_S	40_R	0.812	1.00
17_E	21_E	0.806	1.00
54_V	57_N	0.780	1.00
1_N	52_D	0.774	1.00
34_E	48_R	0.750	1.00
28_F	53_Q	0.743	1.00
3_D	7_K	0.733	1.00
63_I	68_G	0.729	1.00
42_E	47_Y	0.716	1.00
56_R	60_N	0.703	1.00
35_L	39_L	0.703	1.00
19_M	23_F	0.695	1.00
39_L	50_C	0.690	1.00
59_L	63_I	0.690	1.00
14_L	19_M	0.686	1.00
31_S	36_S	0.686	1.00
7_K	10_Y	0.686	1.00
41_K	44_H	0.660	1.00
9_R	13_D	0.641	1.00
63_I	66_K	0.623	1.00
5_L	38_F	0.622	1.00
23_F	35_L	0.610	1.00
5_L	50_C	0.609	1.00
23_F	30_V	0.608	1.00
14_L	18_D	0.603	1.00
26_A	60_N	0.601	1.00
3_D	6_R	0.601	1.00
40_R	44_H	0.576	1.00
3_D	9_R	0.570	1.00
11_A	14_L	0.554	0.99
6_R	9_R	0.552	0.99
20_I	29_E	0.544	0.99
19_M	39_L	0.539	0.99
20_I	24_A	0.538	0.99
2_N	47_Y	0.536	0.99
23_F	58_F	0.533	0.99
3_D	63_I	0.527	0.99
20_I	30_V	0.522	0.99
47_Y	50_C	0.512	0.99
20_I	36_S	0.509	0.99
34_E	37_A	0.507	0.99
52_D	56_R	0.506	0.99
10_Y	41_K	0.506	0.99
27_G	64_I	0.501	0.99
34_E	38_F	0.500	0.99

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
2bl0C	1	0.8824	28.5	0.857	Contact Map
2dsjA	2	0.9559	28.1	0.857	Contact Map
4hkmA	2	0.9559	27.8	0.857	Contact Map
1tizA	1	0.8529	26.4	0.859	Contact Map
2m1uA	1	0.9412	25.6	0.859	Contact Map
2pmyA	4	0.8971	25.6	0.859	Contact Map
2kn2A	1	1	25.1	0.86	Contact Map
1yx7A	1	0.9853	24.8	0.861	Contact Map
2becA	1	1	24.5	0.861	Contact Map
1brwA	2	0.9559	23.9	0.862	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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