GREMLIN Database
PHA_gran_rgn - Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
PFAM: PF09650 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 87 (83)
Sequences: 10903 (6947)
Seq/√Len: 762.5
META: 0.956

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_E41_R2.5761.00
54_T57_E2.4961.00
4_S57_E2.4071.00
76_E80_R2.2991.00
15_R19_E2.2271.00
10_G13_E2.0961.00
2_D61_E1.9471.00
11_K55_D1.9471.00
39_T52_D1.9281.00
39_T50_T1.9091.00
2_D59_R1.8241.00
13_E17_R1.7551.00
13_E16_R1.7241.00
72_K76_E1.6871.00
11_K38_D1.6551.00
67_L70_A1.6441.00
4_S59_R1.6121.00
26_A33_E1.5931.00
42_F49_G1.4961.00
5_I84_D1.4811.00
19_E23_E1.4111.00
78_E81_K1.4081.00
74_K77_S1.3971.00
41_R50_T1.3481.00
50_T61_E1.3281.00
80_R84_D1.3251.00
54_T59_R1.3081.00
24_K28_K1.2851.00
34_T41_R1.2821.00
19_E33_E1.2541.00
24_K27_E1.2491.00
77_S81_K1.2341.00
9_L17_R1.2131.00
16_R20_K1.1651.00
15_R38_D1.1511.00
48_S63_D1.1201.00
36_E39_T1.1131.00
73_G76_E1.1131.00
78_E82_E1.1031.00
21_G25_L1.0721.00
43_S48_S1.0641.00
44_R65_P1.0361.00
74_K78_E1.0041.00
69_A72_K0.9891.00
52_D59_R0.9721.00
10_G14_A0.9611.00
11_K15_R0.9401.00
23_E33_E0.9391.00
10_G56_D0.9071.00
12_E16_R0.8891.00
66_F70_A0.8731.00
63_D66_F0.8711.00
30_G44_R0.8661.00
5_I80_R0.8571.00
23_E26_A0.8531.00
10_G55_D0.8491.00
70_A74_K0.8491.00
52_D61_E0.8461.00
73_G77_S0.8451.00
71_F74_K0.8401.00
12_E55_D0.8271.00
15_R53_V0.8271.00
32_E43_S0.8271.00
6_P57_E0.8191.00
19_E35_W0.8121.00
20_K24_K0.8091.00
21_G24_K0.8071.00
15_R35_W0.7981.00
44_R47_V0.7931.00
28_K82_E0.7861.00
9_L13_E0.7811.00
64_L75_I0.7811.00
16_R19_E0.7801.00
77_S80_R0.7801.00
43_S46_G0.7761.00
23_E27_E0.7701.00
33_E40_L0.7571.00
50_T63_D0.7561.00
14_A53_V0.7501.00
66_F69_A0.7471.00
20_K23_E0.7461.00
70_A73_G0.7231.00
47_V62_V0.7221.00
22_A33_E0.7211.00
75_I78_E0.6981.00
3_I60_L0.6901.00
34_T43_S0.6881.00
30_G45_S0.6801.00
22_A25_L0.6731.00
35_W40_L0.6611.00
6_P56_D0.6571.00
18_A21_G0.6511.00
41_R48_S0.6431.00
18_A40_L0.6421.00
74_K82_E0.6401.00
80_R83_L0.6331.00
8_S56_D0.6321.00
11_K54_T0.6221.00
40_L44_R0.6201.00
18_A51_I0.6151.00
75_I79_I0.6131.00
18_A22_A0.6091.00
10_G16_R0.6081.00
5_I83_L0.5991.00
67_L71_F0.5991.00
65_P68_L0.5981.00
33_E44_R0.5911.00
25_L29_F0.5881.00
17_R65_P0.5831.00
9_L14_A0.5821.00
46_G65_P0.5751.00
68_L71_F0.5711.00
67_L72_K0.5591.00
64_L68_L0.5561.00
49_G62_V0.5491.00
47_V65_P0.5331.00
25_L58_V0.5331.00
26_A31_L0.5291.00
31_L45_S0.5231.00
37_G52_D0.5211.00
45_S70_A0.5071.00
46_G66_F0.5021.00
17_R20_K0.5001.00
49_G60_L0.5001.00
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

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  
3lnoA 1 0.8506 27.8 0.851 Contact Map
2gjhA 2 0.6092 23.2 0.857 Contact Map
3cq1A 2 0.8046 21.3 0.859 Contact Map
3udcA 3 0.8736 18.1 0.864 Contact Map
2jpiA 1 0.954 15.5 0.867 Contact Map
3ux2A 2 0.8621 15.2 0.868 Contact Map
2mblA 1 0.6552 14.8 0.869 Contact Map
2mobA 1 0.7126 14.3 0.87 Contact Map
1usuB 1 0.8966 14.2 0.87 Contact Map
1uwdA 1 0.8161 13.8 0.87 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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