DUF2312 - PFAM28P - GREMLIN Contacts

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DUF2312 - Uncharacterized protein conserved in bacteria (DUF2312)

PFAM:	PF10073	Sequences: AADQLRSFIERIERLEEEKKAIADDIKEVYAEAKGNGFDVKILRKIIRLRKMDPDERQEEEALLDLYLAALG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (71)
Sequences:	7540 (3919)
Seq/√Len:	465.1
META:	0.934

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_Q	36_N	2.714	1.00
45_K	48_R	2.310	1.00
19_K	23_A	2.239	1.00
30_Y	44_R	2.210	1.00
49_L	68_L	2.204	1.00
52_M	60_E	2.070	1.00
33_A	43_L	2.029	1.00
19_K	26_I	2.008	1.00
13_E	50_R	1.913	1.00
54_P	58_Q	1.908	1.00
45_K	60_E	1.677	1.00
12_I	26_I	1.499	1.00
12_I	30_Y	1.484	1.00
34_K	40_V	1.466	1.00
16_E	26_I	1.453	1.00
16_E	20_K	1.396	1.00
16_E	51_K	1.329	1.00
15_L	22_I	1.292	1.00
58_Q	62_A	1.269	1.00
27_K	31_A	1.258	1.00
30_Y	47_I	1.219	1.00
65_D	69_A	1.213	1.00
61_E	68_L	1.208	1.00
52_M	57_R	1.196	1.00
52_M	56_E	1.173	1.00
17_E	21_A	1.168	1.00
20_K	24_D	1.166	1.00
11_R	29_V	1.161	1.00
21_A	25_D	1.141	1.00
55_D	58_Q	1.123	1.00
42_I	63_L	1.120	1.00
39_D	42_I	1.105	1.00
53_D	56_E	1.093	1.00
42_I	64_L	1.077	1.00
49_L	64_L	1.074	1.00
8_F	36_N	1.042	1.00
8_F	43_L	1.030	1.00
45_K	64_L	1.023	1.00
16_E	19_K	1.018	1.00
15_L	29_V	1.009	1.00
18_E	22_I	1.006	1.00
9_I	43_L	1.002	1.00
49_L	61_E	0.987	1.00
46_I	68_L	0.969	1.00
48_R	52_M	0.969	1.00
62_A	66_L	0.942	1.00
8_F	33_A	0.934	1.00
48_R	51_K	0.918	1.00
12_I	47_I	0.915	1.00
24_D	27_K	0.905	1.00
6_R	10_E	0.904	1.00
23_A	26_I	0.904	1.00
20_K	23_A	0.895	1.00
11_R	32_E	0.894	1.00
15_L	26_I	0.888	1.00
20_K	51_K	0.887	1.00
42_I	60_E	0.852	1.00
41_K	60_E	0.846	1.00
49_L	57_R	0.840	1.00
4_Q	7_S	0.834	1.00
30_Y	43_L	0.806	1.00
46_I	64_L	0.803	1.00
22_I	25_D	0.796	1.00
14_R	17_E	0.795	1.00
19_K	22_I	0.785	1.00
42_I	45_K	0.780	1.00
57_R	61_E	0.779	1.00
24_D	28_E	0.754	1.00
60_E	64_L	0.745	1.00
14_R	18_E	0.740	1.00
45_K	49_L	0.727	1.00
7_S	11_R	0.716	1.00
5_L	38_F	0.715	1.00
18_E	25_D	0.709	1.00
18_E	21_A	0.693	1.00
31_A	35_G	0.691	1.00
2_A	38_F	0.688	1.00
64_L	68_L	0.679	1.00
29_V	32_E	0.661	1.00
65_D	68_L	0.654	1.00
15_L	18_E	0.654	1.00
4_Q	8_F	0.642	1.00
9_I	47_I	0.634	1.00
66_L	69_A	0.596	0.99
57_R	68_L	0.596	0.99
11_R	25_D	0.594	0.99
49_L	52_M	0.592	0.99
8_F	32_E	0.589	0.99
28_E	31_A	0.588	0.99
8_F	11_R	0.586	0.99
10_E	14_R	0.584	0.99
26_I	30_Y	0.579	0.99
62_A	65_D	0.579	0.99
13_E	51_K	0.575	0.99
60_E	63_L	0.573	0.99
3_D	6_R	0.566	0.99
14_R	25_D	0.565	0.99
63_L	66_L	0.559	0.99
12_I	29_V	0.558	0.99
4_Q	38_F	0.554	0.99
54_P	57_R	0.548	0.99
15_L	25_D	0.547	0.99
3_D	7_S	0.530	0.98
5_L	43_L	0.518	0.98
68_L	72_G	0.504	0.98
16_E	47_I	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
4ut1A	1	0.7083	17.7	0.831	Contact Map
1gaxA	1	1	17.2	0.832	Contact Map
3kxeC	2	0.6944	12.5	0.841	Contact Map
1i84S	2	0	12.1	0.842	Contact Map
4rsiA	1	0.7361	10.5	0.847	Contact Map
2zdiC	2	0.5833	9.5	0.85	Contact Map
2d4yA	1	0.6806	9.4	0.851	Contact Map
2ma3A	1	0.9167	8.7	0.852	Contact Map
2q7tA	1	0.5139	8.4	0.854	Contact Map
4abxA	2	0.9167	7.2	0.857	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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