DUF3606 - PFAM28P - GREMLIN Contacts

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DUF3606 - Protein of unknown function (DUF3606)

PFAM:	PF12244	Sequences: DKTKRGPQDRSRINLNEDYEVRYWAKKLGVSEEELRAAVKKVGNSAAAVRKYLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (51)
Sequences:	13400 (8124)
Seq/√Len:	1137.6
META:	0.957

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_K	52_Y	2.504	1.00
45_S	48_A	2.138	1.00
32_E	36_R	1.939	1.00
38_A	52_Y	1.929	1.00
25_A	32_E	1.781	1.00
31_S	34_E	1.716	1.00
48_A	51_K	1.710	1.00
27_K	50_R	1.687	1.00
24_W	28_L	1.670	1.00
7_P	11_S	1.605	1.00
38_A	42_V	1.602	1.00
30_V	35_L	1.543	1.00
18_D	22_R	1.434	1.00
12_R	44_N	1.342	1.00
21_V	32_E	1.318	1.00
28_L	50_R	1.309	1.00
15_L	36_R	1.309	1.00
33_E	37_A	1.284	1.00
23_Y	27_K	1.264	1.00
34_E	37_A	1.256	1.00
39_V	49_V	1.179	1.00
15_L	39_V	1.144	1.00
36_R	40_K	1.125	1.00
22_R	32_E	1.106	1.00
46_A	50_R	1.033	1.00
47_A	51_K	1.000	1.00
24_W	49_V	0.985	1.00
30_V	34_E	0.981	1.00
21_V	25_A	0.974	1.00
11_S	45_S	0.964	1.00
30_V	38_A	0.956	1.00
6_G	10_R	0.951	1.00
14_N	17_E	0.950	1.00
38_A	49_V	0.949	1.00
22_R	26_K	0.945	1.00
15_L	21_V	0.941	1.00
49_V	53_L	0.914	1.00
18_D	32_E	0.904	1.00
24_W	46_A	0.868	1.00
13_I	24_W	0.833	1.00
4_K	8_Q	0.832	1.00
12_R	45_S	0.819	1.00
37_A	40_K	0.813	1.00
14_N	20_E	0.808	1.00
17_E	20_E	0.802	1.00
42_V	48_A	0.792	1.00
21_V	36_R	0.789	1.00
24_W	35_L	0.771	1.00
7_P	10_R	0.767	1.00
15_L	44_N	0.760	1.00
23_Y	26_K	0.747	1.00
42_V	52_Y	0.745	1.00
34_E	38_A	0.740	1.00
20_E	23_Y	0.735	1.00
37_A	41_K	0.730	1.00
19_Y	23_Y	0.718	1.00
35_L	38_A	0.680	1.00
25_A	35_L	0.676	1.00
14_N	44_N	0.672	1.00
7_P	23_Y	0.634	1.00
38_A	53_L	0.617	1.00
8_Q	11_S	0.614	1.00
35_L	46_A	0.605	1.00
5_R	10_R	0.602	1.00
28_L	38_A	0.600	1.00
13_I	49_V	0.583	1.00
42_V	49_V	0.573	1.00
5_R	8_Q	0.567	1.00
4_K	7_P	0.558	1.00
28_L	35_L	0.540	1.00
18_D	26_K	0.522	1.00
3_T	8_Q	0.515	1.00
9_D	12_R	0.515	1.00
3_T	6_G	0.513	1.00
33_E	36_R	0.503	1.00
15_L	40_K	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
2hu9A	1	0.963	27.8	0.79	Contact Map
4fe7A	2	1	16.7	0.81	Contact Map
3mklA	1	1	16.2	0.811	Contact Map
3gbgA	1	1	15.8	0.812	Contact Map
4e6kG	1	0.5926	14.9	0.815	Contact Map
3zf7w	1	1	13.9	0.817	Contact Map
3j61F	1	1	13.5	0.818	Contact Map
2k27A	1	0.9815	13.2	0.819	Contact Map
3oioA	1	1	12.9	0.82	Contact Map
3oouA	1	1	12.7	0.821	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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