DUF1294 - PFAM28P - GREMLIN Contacts

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DUF1294 - Protein of unknown function (DUF1294)

PFAM:	PF06961	Sequences: NLVTFLLYGIDKRAARRGRWRIPEKTLHLLALLGGWPGALLAMRLFRHKTRKQSF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (55)
Sequences:	13815 (10110)
Seq/√Len:	1363.2
META:	0.873

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_G	46_F	2.836	1.00
10_I	14_A	2.821	1.00
7_L	30_L	2.548	1.00
8_Y	39_A	2.491	1.00
4_T	39_A	2.214	1.00
4_T	30_L	2.162	1.00
5_F	45_L	2.139	1.00
13_R	17_R	1.914	1.00
31_A	55_F	1.886	1.00
31_A	39_A	1.867	1.00
28_H	31_A	1.660	1.00
14_A	19_R	1.637	1.00
5_F	42_A	1.494	1.00
9_G	13_R	1.449	1.00
28_H	54_S	1.404	1.00
23_P	26_T	1.378	1.00
6_L	10_I	1.367	1.00
47_R	50_T	1.367	1.00
13_R	19_R	1.310	1.00
42_A	46_F	1.234	1.00
38_G	42_A	1.167	1.00
8_Y	28_H	1.100	1.00
4_T	8_Y	1.099	1.00
40_L	44_R	1.080	1.00
41_L	45_L	1.072	1.00
10_I	22_I	1.059	1.00
4_T	31_A	1.034	1.00
3_V	26_T	1.024	1.00
5_F	46_F	1.015	1.00
13_R	16_R	1.002	1.00
27_L	39_A	0.966	1.00
40_L	43_M	0.903	1.00
14_A	20_W	0.883	1.00
36_W	40_L	0.878	1.00
28_H	43_M	0.844	1.00
31_A	36_W	0.842	1.00
7_L	22_I	0.834	1.00
47_R	51_R	0.813	1.00
29_L	33_L	0.787	1.00
14_A	22_I	0.773	1.00
22_I	26_T	0.769	1.00
44_R	50_T	0.728	1.00
25_K	29_L	0.716	1.00
7_L	27_L	0.715	1.00
1_N	36_W	0.714	1.00
43_M	52_K	0.708	1.00
4_T	34_G	0.701	1.00
1_N	38_G	0.701	1.00
46_F	50_T	0.695	1.00
4_T	35_G	0.694	1.00
26_T	30_L	0.683	1.00
6_L	9_G	0.659	1.00
30_L	34_G	0.654	1.00
20_W	23_P	0.648	1.00
14_A	17_R	0.645	1.00
21_R	24_E	0.642	1.00
10_I	19_R	0.639	1.00
8_Y	42_A	0.639	1.00
1_N	4_T	0.630	1.00
9_G	42_A	0.610	1.00
5_F	41_L	0.607	1.00
3_V	7_L	0.603	1.00
8_Y	40_L	0.600	1.00
28_H	40_L	0.591	1.00
26_T	29_L	0.589	1.00
28_H	32_L	0.580	1.00
10_I	13_R	0.578	1.00
36_W	43_M	0.570	1.00
12_K	15_A	0.553	1.00
51_R	54_S	0.551	1.00
4_T	7_L	0.545	1.00
29_L	32_L	0.545	1.00
15_A	21_R	0.538	1.00
20_W	25_K	0.529	1.00
35_G	38_G	0.523	1.00
8_Y	31_A	0.517	1.00
3_V	30_L	0.511	1.00
20_W	26_T	0.511	1.00
44_R	47_R	0.509	1.00
28_H	36_W	0.504	1.00
5_F	9_G	0.503	1.00
43_M	50_T	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
2qtsA	4	0.8364	12.2	0.847	Contact Map
3cx5D	2	0.9455	7	0.863	Contact Map
1pp9D	2	0.9455	6.8	0.864	Contact Map
4d6uD	1	0.9455	6.2	0.866	Contact Map
1afoA	2	0.7273	5.6	0.869	Contact Map
2w3zA	1	0	5.5	0.869	Contact Map
1k7kA	1	1	5	0.872	Contact Map
2qjyB	1	0.8364	4.2	0.876	Contact Map
3tquA	2	1	3.5	0.881	Contact Map
4bnqA	2	1	3.3	0.882	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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