YDJO - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YDJO - Uncharacterized protein YdjO

UniProt:	O34759	Sequences: MSYYNKRNQEPLPKEDVSTWECTKEDCNGWTRKNFASSDTPLCPLCGSKMVDGIRSLVNLQNNSQTKTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	69 (61)
Sequences:	138 (102)
Seq/√Len:	13.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_G	45_L	3.795	0.99
35_F	62_N	2.444	0.90
21_E	47_G	2.312	0.87
18_S	52_D	2.239	0.85
34_N	62_N	2.072	0.81
4_Y	44_P	2.005	0.78
37_S	41_P	1.919	0.75
6_K	31_T	1.877	0.73
33_K	62_N	1.762	0.68
16_D	54_I	1.669	0.64
38_S	58_V	1.650	0.63
7_R	34_N	1.536	0.57
7_R	13_P	1.515	0.56
44_P	49_K	1.490	0.55
25_E	35_F	1.471	0.54
12_L	61_Q	1.453	0.53
59_N	64_S	1.406	0.51
17_V	56_S	1.355	0.48
21_E	25_E	1.313	0.46
5_N	11_P	1.244	0.42
52_D	63_N	1.219	0.41
19_T	55_R	1.178	0.39
8_N	15_E	1.168	0.38
10_E	13_P	1.165	0.38
5_N	15_E	1.136	0.37
12_L	40_T	1.126	0.36
26_D	49_K	1.113	0.36
13_P	58_V	1.111	0.35
14_K	17_V	1.100	0.35
31_T	37_S	1.075	0.34
21_E	29_G	1.057	0.33
37_S	58_V	1.054	0.33
4_Y	16_D	1.050	0.33
26_D	45_L	1.029	0.32
7_R	15_E	0.987	0.30
19_T	51_V	0.947	0.28
16_D	44_P	0.913	0.27
8_N	21_E	0.910	0.26
18_S	54_I	0.893	0.26
36_A	60_L	0.882	0.25
14_K	31_T	0.881	0.25
40_T	45_L	0.876	0.25
16_D	56_S	0.864	0.25
6_K	60_L	0.854	0.24
29_G	63_N	0.833	0.23
4_Y	64_S	0.822	0.23
15_E	59_N	0.816	0.23
8_N	23_T	0.815	0.23
14_K	37_S	0.809	0.23
55_R	60_L	0.757	0.21
35_F	59_N	0.756	0.21
19_T	53_G	0.750	0.20
21_E	51_V	0.748	0.20
25_E	60_L	0.740	0.20
12_L	24_K	0.717	0.19
33_K	59_N	0.716	0.19
9_Q	51_V	0.706	0.19
44_P	64_S	0.687	0.18
24_K	48_S	0.683	0.18
4_Y	63_N	0.680	0.18
5_N	63_N	0.676	0.18
38_S	42_L	0.673	0.18
15_E	33_K	0.670	0.18
4_Y	26_D	0.661	0.18
13_P	36_A	0.654	0.17
7_R	55_R	0.649	0.17
54_I	59_N	0.644	0.17
42_L	49_K	0.638	0.17
34_N	42_L	0.627	0.17
23_T	26_D	0.624	0.17
33_K	55_R	0.622	0.16
4_Y	47_G	0.617	0.16
16_D	60_L	0.616	0.16
15_E	25_E	0.609	0.16
9_Q	19_T	0.598	0.16
18_S	36_A	0.593	0.16
17_V	23_T	0.591	0.16
11_P	33_K	0.585	0.15
12_L	63_N	0.580	0.15
49_K	58_V	0.576	0.15
10_E	39_D	0.549	0.14
52_D	64_S	0.545	0.14
5_N	16_D	0.542	0.14
5_N	39_D	0.539	0.14
38_S	64_S	0.532	0.14
47_G	60_L	0.529	0.14
26_D	35_F	0.528	0.14
10_E	45_L	0.528	0.14
6_K	23_T	0.520	0.14
11_P	28_N	0.518	0.14
41_P	57_L	0.517	0.14
11_P	14_K	0.500	0.13

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
2kn9A	1	0.8406	51.6	0.89	Contact Map
1s24A	1	0.5942	37.9	0.899	Contact Map
1yk4A	1	0.5362	29.3	0.905	Contact Map
4d02A	2	0	28.8	0.905	Contact Map
2v3bB	1	0.5507	27.5	0.906	Contact Map
1x3zA	1	0.9275	17.1	0.915	Contact Map
1lkoA	3	0.7971	15.9	0.916	Contact Map
1e8jA	1	0.5362	15.2	0.917	Contact Map
2f4mA	2	0.9275	13.8	0.918	Contact Map
6rxnA	1	0.5362	13.1	0.919	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.

Page generated in 0.0046 seconds.