YRZS - BACSU - GREMLIN Contacts

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YRZS - Uncharacterized membrane protein YrzS

UniProt:	C0H463	Sequences: MTEFPKIIMILGAVLLIIGAVLHFVGKMPGDIFVKKGNVTFFFPVVTCIIISVVLSILLNLFGRMK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	66 (61)
Sequences:	337 (276)
Seq/√Len:	35.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_K	40_T	4.168	1.00
58_L	62_F	3.531	1.00
9_M	16_L	2.992	1.00
13_A	16_L	2.590	1.00
46_V	50_I	2.429	1.00
33_F	40_T	2.305	0.99
6_K	35_K	1.826	0.97
48_C	53_V	1.754	0.96
56_S	60_N	1.689	0.95
5_P	23_H	1.561	0.93
4_F	22_L	1.541	0.92
13_A	17_I	1.518	0.92
8_I	15_L	1.472	0.90
34_V	37_G	1.469	0.90
36_K	39_V	1.434	0.89
60_N	63_G	1.420	0.89
55_L	59_L	1.397	0.88
9_M	20_A	1.371	0.87
9_M	36_K	1.344	0.86
14_V	58_L	1.308	0.84
33_F	42_F	1.308	0.84
50_I	61_L	1.236	0.80
14_V	54_V	1.222	0.80
9_M	19_G	1.200	0.78
25_V	37_G	1.127	0.74
7_I	11_L	1.124	0.74
9_M	13_A	1.089	0.71
56_S	63_G	1.054	0.69
57_I	64_R	0.950	0.61
24_F	51_I	0.945	0.60
8_I	18_I	0.935	0.59
57_I	60_N	0.914	0.58
41_F	51_I	0.913	0.58
10_I	50_I	0.899	0.56
42_F	47_T	0.893	0.56
9_M	15_L	0.877	0.54
5_P	63_G	0.817	0.49
39_V	42_F	0.804	0.48
5_P	16_L	0.802	0.48
21_V	54_V	0.774	0.46
27_K	35_K	0.770	0.45
46_V	60_N	0.769	0.45
16_L	62_F	0.769	0.45
4_F	64_R	0.767	0.45
24_F	34_V	0.759	0.44
23_H	39_V	0.756	0.44
14_V	18_I	0.746	0.43
17_I	63_G	0.742	0.43
35_K	64_R	0.735	0.42
51_I	59_L	0.733	0.42
20_A	35_K	0.733	0.42
20_A	23_H	0.728	0.42
27_K	53_V	0.722	0.41
59_L	63_G	0.717	0.41
11_L	54_V	0.711	0.40
18_I	25_V	0.695	0.39
27_K	47_T	0.686	0.38
48_C	59_L	0.669	0.37
9_M	22_L	0.668	0.37
8_I	11_L	0.664	0.36
6_K	64_R	0.655	0.36
39_V	46_V	0.636	0.34
38_N	59_L	0.635	0.34
21_V	57_I	0.631	0.34
13_A	20_A	0.625	0.33
49_I	53_V	0.622	0.33
25_V	28_M	0.621	0.33
36_K	60_N	0.617	0.33
13_A	25_V	0.610	0.32
22_L	51_I	0.598	0.31
5_P	22_L	0.598	0.31
17_I	21_V	0.596	0.31
4_F	7_I	0.584	0.30
8_I	16_L	0.584	0.30
36_K	64_R	0.583	0.30
60_N	64_R	0.582	0.30
21_V	63_G	0.575	0.30
35_K	48_C	0.573	0.30
34_V	41_F	0.573	0.30
50_I	57_I	0.570	0.29
10_I	17_I	0.566	0.29
14_V	21_V	0.559	0.29
20_A	58_L	0.544	0.27
48_C	63_G	0.543	0.27
18_I	60_N	0.539	0.27
9_M	46_V	0.538	0.27
17_I	61_L	0.538	0.27
43_F	51_I	0.528	0.26
7_I	10_I	0.518	0.26
17_I	32_I	0.514	0.25
41_F	49_I	0.507	0.25
27_K	60_N	0.500	0.25

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
4ev6A	3	0.8788	38.8	0.882	Contact Map
4i0uA	4	0.8788	26.1	0.892	Contact Map
4djkA	2	0.9242	11.5	0.908	Contact Map
1fftA	1	0.8636	10.7	0.909	Contact Map
3ayfA	2	0.8788	10.6	0.909	Contact Map
1pfiA	7	0.4242	7.8	0.915	Contact Map
3w9iA	3	0.9242	5.9	0.919	Contact Map
1fftB	1	0.6667	5.5	0.921	Contact Map
2m59A	2	0.4848	5	0.922	Contact Map
2yevB	1	0.697	4.9	0.922	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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