DUF951 - PFAM28P - GREMLIN Contacts

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DUF951 - Bacterial protein of unknown function (DUF951)

PFAM:	PF06107	Sequences: YRLGDIVRLKKPHPCGSNEWEVVRLGADIGLKCLGCGRRVMLPRRKFEKRIKKII	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (54)
Sequences:	6340 (3116)
Seq/√Len:	424.0
META:	0.885

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_S	35_G	2.784	1.00
21_E	34_L	2.360	1.00
8_R	18_N	2.312	1.00
30_G	39_R	2.273	1.00
8_R	53_K	2.128	1.00
12_P	18_N	2.022	1.00
19_E	34_L	1.887	1.00
21_E	32_K	1.867	1.00
6_I	34_L	1.838	1.00
43_P	46_K	1.743	1.00
4_G	21_E	1.740	1.00
6_I	19_E	1.718	1.00
46_K	50_R	1.656	1.00
7_V	47_F	1.560	1.00
32_K	37_G	1.507	1.00
8_R	19_E	1.473	1.00
23_V	39_R	1.420	1.00
42_L	47_F	1.416	1.00
23_V	30_G	1.329	1.00
31_L	47_F	1.307	1.00
3_L	25_L	1.202	1.00
32_K	39_R	1.186	1.00
25_L	29_I	1.144	1.00
6_I	21_E	1.061	1.00
2_R	5_D	1.046	1.00
45_R	48_E	1.044	1.00
20_W	38_R	1.030	1.00
7_V	22_V	1.023	1.00
47_F	51_I	1.015	1.00
23_V	32_K	0.949	1.00
30_G	41_M	0.936	1.00
1_Y	51_I	0.931	1.00
27_A	45_R	0.911	1.00
20_W	40_V	0.907	1.00
51_I	54_I	0.895	1.00
27_A	41_M	0.889	1.00
16_G	38_R	0.874	1.00
9_L	50_R	0.871	1.00
1_Y	48_E	0.851	1.00
31_L	40_V	0.832	1.00
46_K	49_K	0.823	1.00
24_R	41_M	0.771	1.00
9_L	31_L	0.759	1.00
22_V	31_L	0.753	1.00
12_P	16_G	0.742	1.00
8_R	52_K	0.737	1.00
12_P	17_S	0.728	1.00
3_L	23_V	0.706	1.00
33_C	36_C	0.692	1.00
44_R	48_E	0.673	1.00
18_N	52_K	0.650	0.99
48_E	51_I	0.645	0.99
40_V	50_R	0.640	0.99
9_L	44_R	0.630	0.99
28_D	43_P	0.619	0.99
22_V	25_L	0.608	0.99
28_D	44_R	0.604	0.99
17_S	34_L	0.602	0.99
5_D	54_I	0.596	0.99
31_L	42_L	0.595	0.99
9_L	47_F	0.593	0.99
1_Y	22_V	0.589	0.99
28_D	41_M	0.573	0.99
7_V	54_I	0.568	0.98
29_I	48_E	0.566	0.98
34_L	37_G	0.565	0.98
42_L	46_K	0.564	0.98
24_R	27_A	0.561	0.98
14_P	17_S	0.556	0.98
3_L	41_M	0.547	0.98
25_L	45_R	0.544	0.98
33_C	37_G	0.544	0.98
43_P	48_E	0.543	0.98
16_G	20_W	0.536	0.98
24_R	28_D	0.534	0.98
29_I	44_R	0.531	0.98
29_I	41_M	0.531	0.98
2_R	25_L	0.520	0.97
11_K	49_K	0.513	0.97
27_A	43_P	0.512	0.97
15_C	33_C	0.500	0.97

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
3zey9	1	0.7091	22.7	0.866	Contact Map
4hw9A	3	0.8909	20.3	0.869	Contact Map
2k4xA	1	0.8364	18.8	0.871	Contact Map
4ujpg	1	0.7455	17.2	0.873	Contact Map
3udcA	3	0.8727	16.9	0.874	Contact Map
5ajiA	3	0.8909	15.8	0.875	Contact Map
1neeA	1	0.8	13.6	0.879	Contact Map
4cuyf	1	0.7455	13.1	0.879	Contact Map
4uer9	1	0.7455	13.1	0.879	Contact Map
2e9hA	1	1	12.5	0.881	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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