DUF2914 - PFAM28P - GREMLIN Contacts

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DUF2914 - Protein of unknown function (DUF2914)

PFAM:	PF11141	Sequences: DTTIYHRWYYDGKEVARVPLPIVRGPGWRTYSSKTLLPGWPGDWRVEVETEDGQVLGRVRFTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	63 (62)
Sequences:	9338 (6138)
Seq/√Len:	779.6
META:	0.963

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_Y	47_E	2.784	1.00
5_Y	17_R	2.676	1.00
20_L	30_T	2.582	1.00
7_R	49_E	2.346	1.00
50_T	54_Q	2.194	1.00
9_Y	45_R	2.174	1.00
7_R	14_E	2.148	1.00
6_H	32_S	2.084	1.00
47_E	55_V	1.997	1.00
9_Y	14_E	1.996	1.00
14_E	17_R	1.833	1.00
3_T	19_P	1.826	1.00
45_R	58_R	1.652	1.00
11_D	43_D	1.601	1.00
37_L	40_W	1.598	1.00
43_D	62_T	1.558	1.00
7_R	17_R	1.550	1.00
25_G	28_W	1.527	1.00
10_Y	40_W	1.495	1.00
55_V	58_R	1.492	1.00
7_R	47_E	1.469	1.00
47_E	58_R	1.465	1.00
6_H	20_L	1.381	1.00
15_V	40_W	1.349	1.00
5_Y	19_P	1.336	1.00
49_E	55_V	1.067	1.00
49_E	53_G	1.053	1.00
5_Y	49_E	1.047	1.00
16_A	34_K	1.045	1.00
24_R	28_W	1.032	1.00
10_Y	15_V	1.026	1.00
3_T	21_P	1.012	1.00
6_H	48_V	1.009	1.00
15_V	34_K	0.985	1.00
43_D	60_R	0.975	1.00
4_I	56_L	0.899	1.00
3_T	51_E	0.888	1.00
18_V	34_K	0.846	1.00
15_V	44_W	0.837	1.00
18_V	32_S	0.816	1.00
48_V	57_G	0.812	1.00
16_A	33_S	0.807	1.00
34_K	37_L	0.766	1.00
21_P	24_R	0.750	1.00
10_Y	13_K	0.749	1.00
5_Y	51_E	0.742	1.00
10_Y	44_W	0.738	1.00
44_W	61_F	0.729	1.00
50_T	56_L	0.717	1.00
17_R	49_E	0.701	1.00
12_G	45_R	0.700	1.00
23_V	28_W	0.673	1.00
28_W	31_Y	0.671	1.00
10_Y	42_G	0.665	1.00
38_P	41_P	0.660	1.00
23_V	33_S	0.654	1.00
20_L	32_S	0.650	1.00
6_H	30_T	0.631	1.00
45_R	60_R	0.630	1.00
57_G	60_R	0.620	1.00
36_L	40_W	0.619	1.00
2_T	51_E	0.604	1.00
54_Q	57_G	0.603	1.00
24_R	27_G	0.595	1.00
4_I	28_W	0.595	1.00
22_I	30_T	0.593	1.00
23_V	26_P	0.592	1.00
8_W	32_S	0.590	1.00
34_K	40_W	0.590	1.00
42_G	61_F	0.588	1.00
48_V	59_V	0.568	1.00
33_S	36_L	0.567	1.00
13_K	27_G	0.566	1.00
2_T	52_D	0.563	1.00
22_I	28_W	0.560	1.00
9_Y	49_E	0.557	1.00
36_L	63_V	0.553	1.00
29_R	34_K	0.549	1.00
4_I	30_T	0.548	1.00
10_Y	41_P	0.547	1.00
16_A	19_P	0.538	1.00
35_T	40_W	0.538	1.00
16_A	23_V	0.537	1.00
23_V	35_T	0.531	1.00
2_T	22_I	0.526	1.00
25_G	29_R	0.523	1.00
35_T	39_G	0.518	1.00
44_W	63_V	0.513	1.00
37_L	41_P	0.511	1.00
5_Y	53_G	0.504	1.00
46_V	61_F	0.502	1.00
14_E	49_E	0.501	1.00
46_V	55_V	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
1bihA	2	0.9365	66.1	0.756	Contact Map
3b43A	1	1	64.1	0.759	Contact Map
3o81A	1	1	63.9	0.759	Contact Map
3p3yA	2	1	63.1	0.761	Contact Map
4i2xE	1	0.9841	62.6	0.762	Contact Map
2e7cA	1	1	62.6	0.762	Contact Map
3v2aR	1	0	59.3	0.766	Contact Map
3jtsB	1	1	59.3	0.766	Contact Map
2eysA	1	0.9683	59	0.766	Contact Map
1lk2B	1	1	58.2	0.768	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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