GVPA2 - HALSA - GREMLIN Contacts

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

GVPA2 - Gas vesicle structural protein 2

UniProt:	P08959	Sequences: MAQPDSSSLAEVLDRVLDKGVVVDVWARISLVGIEILTVEARVVAASVDTFLHYAEEIAKIEQAELTAGAEAPEPAPEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	79 (64)
Sequences:	134 (40)
Seq/√Len:	5.0

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_I	37_L	4.032	0.90
26_W	40_E	2.226	0.47
39_V	45_A	2.185	0.45
10_A	19_K	1.988	0.39
52_L	55_A	1.952	0.38
53_H	57_E	1.949	0.38
16_V	55_A	1.750	0.32
54_Y	59_A	1.720	0.31
16_V	52_L	1.692	0.31
26_W	58_I	1.641	0.29
11_E	48_V	1.628	0.29
19_K	38_T	1.603	0.28
40_E	54_Y	1.530	0.26
25_V	57_E	1.485	0.25
27_A	31_L	1.436	0.24
32_V	52_L	1.433	0.24
30_S	47_S	1.413	0.23
5_D	11_E	1.391	0.23
4_P	13_L	1.383	0.23
51_F	60_K	1.342	0.22
57_E	60_K	1.317	0.21
59_A	62_E	1.312	0.21
36_I	43_V	1.275	0.20
32_V	55_A	1.227	0.19
18_D	41_A	1.165	0.18
13_L	39_V	1.163	0.18
23_V	36_I	1.139	0.18
28_R	38_T	1.073	0.16
13_L	16_V	1.071	0.16
4_P	60_K	1.041	0.16
38_T	49_D	1.028	0.16
53_H	60_K	1.014	0.15
51_F	57_E	1.006	0.15
42_R	52_L	1.002	0.15
8_S	37_L	0.993	0.15
7_S	28_R	0.982	0.15
54_Y	60_K	0.966	0.15
15_R	54_Y	0.965	0.15
32_V	59_A	0.964	0.15
15_R	21_V	0.954	0.14
15_R	25_V	0.941	0.14
25_V	39_V	0.916	0.14
26_W	37_L	0.912	0.14
31_L	38_T	0.899	0.14
6_S	45_A	0.895	0.14
53_H	61_I	0.884	0.13
16_V	32_V	0.873	0.13
40_E	60_K	0.866	0.13
42_R	55_A	0.857	0.13
40_E	62_E	0.857	0.13
15_R	60_K	0.839	0.13
45_A	63_Q	0.833	0.13
4_P	28_R	0.832	0.13
13_L	67_T	0.791	0.12
11_E	54_Y	0.787	0.12
5_D	51_F	0.760	0.12
21_V	56_E	0.759	0.12
49_D	53_H	0.754	0.12
15_R	40_E	0.748	0.11
10_A	58_I	0.736	0.11
56_E	62_E	0.735	0.11
7_S	29_I	0.718	0.11
4_P	62_E	0.712	0.11
54_Y	62_E	0.710	0.11
31_L	67_T	0.710	0.11
49_D	65_E	0.703	0.11
6_S	43_V	0.684	0.11
47_S	50_T	0.683	0.11
40_E	53_H	0.680	0.11
16_V	42_R	0.672	0.10
40_E	58_I	0.663	0.10
23_V	65_E	0.642	0.10
12_V	52_L	0.638	0.10
38_T	47_S	0.627	0.10
25_V	63_Q	0.618	0.10
11_E	15_R	0.618	0.10
25_V	43_V	0.617	0.10
12_V	50_T	0.614	0.10
49_D	56_E	0.604	0.10
18_D	66_L	0.591	0.10
10_A	67_T	0.588	0.09
8_S	21_V	0.577	0.09
32_V	42_R	0.577	0.09
4_P	43_V	0.570	0.09
13_L	49_D	0.560	0.09
25_V	51_F	0.559	0.09
21_V	47_S	0.552	0.09
11_E	21_V	0.536	0.09
4_P	49_D	0.521	0.09
11_E	26_W	0.514	0.09
11_E	49_D	0.510	0.09
58_I	67_T	0.510	0.09
40_E	63_Q	0.505	0.09
29_I	62_E	0.504	0.09
26_W	64_A	0.501	0.09
11_E	40_E	0.500	0.09

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
1vjoA	2	0.6709	14.6	0.92	Contact Map
2qmxA	3	0.8354	9	0.927	Contact Map
3e9kA	2	0.6835	7.9	0.929	Contact Map
3mwbA	3	0.8354	7.2	0.93	Contact Map
4lhdA	2	0.9494	7.1	0.93	Contact Map
4lubA	2	0.8228	7.1	0.93	Contact Map
3luyA	2	0.9873	6.4	0.932	Contact Map
2dw0A	1	0.962	6.2	0.932	Contact Map
2yrrA	2	0.6835	6.2	0.932	Contact Map
1eluA	2	0.6582	5.8	0.933	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 0.0045 seconds.