GREMLIN Database
YBDZ - Uncharacterized protein YbdZ
UniProt: P18393 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14353
Length: 72 (64)
Sequences: 1318 (864)
Seq/√Len: 108.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
63_T67_Q3.6861.00
47_A51_Q3.3511.00
22_G66_T2.7551.00
8_D14_F2.6421.00
45_S48_S2.4861.00
44_Q48_S2.4051.00
22_G63_T1.8021.00
21_Q64_N1.8011.00
13_A43_P1.7781.00
51_Q55_A1.7681.00
41_C44_Q1.7351.00
29_Q43_P1.7241.00
15_Y39_I1.6291.00
63_T66_T1.5751.00
17_L26_L1.5141.00
52_W56_H1.4961.00
20_A38_D1.4721.00
24_F60_L1.4341.00
44_Q49_C1.4111.00
40_V52_W1.3671.00
10_P47_A1.3340.99
15_Y43_P1.3140.99
33_L39_I1.3120.99
18_R38_D1.3110.99
17_L25_S1.2650.99
16_I53_L1.2300.99
41_C49_C1.2080.99
18_R24_F1.1910.99
18_R40_V1.0160.97
16_I24_F0.9920.96
42_Q52_W0.9630.95
61_T65_F0.9560.95
15_Y33_L0.9310.95
12_G30_Q0.9290.95
51_Q54_E0.9000.94
16_I52_W0.8830.93
32_V35_A0.8640.92
16_I49_C0.8530.92
19_N23_Q0.8490.91
46_Q50_Q0.8170.90
15_Y42_Q0.8110.89
61_T64_N0.8100.89
10_P46_Q0.8010.89
15_Y29_Q0.8010.89
13_A29_Q0.7880.88
28_P68_L0.7800.88
15_Y49_C0.7780.87
17_L50_Q0.7720.87
20_A63_T0.7370.84
7_F17_L0.7360.84
26_L46_Q0.7330.84
42_Q48_S0.7300.84
22_G38_D0.7220.83
24_F56_H0.7210.83
14_F65_F0.6940.81
60_L65_F0.6890.80
48_S51_Q0.6780.79
6_P30_Q0.6590.77
23_Q32_V0.6580.77
21_Q58_R0.6560.77
50_Q54_E0.6550.77
15_Y46_Q0.6500.76
17_L31_C0.6440.76
38_D67_Q0.6430.75
9_D68_L0.6350.75
12_G43_P0.6240.73
7_F14_F0.6130.72
10_P32_V0.6130.72
24_F40_V0.6120.72
9_D12_G0.6070.71
35_A54_E0.5800.68
12_G28_P0.5780.68
12_G26_L0.5760.67
56_H67_Q0.5750.67
41_C66_T0.5710.67
24_F59_T0.5690.66
34_P37_W0.5550.64
21_Q34_P0.5520.64
17_L41_C0.5490.64
59_T64_N0.5490.64
26_L50_Q0.5460.63
16_I65_F0.5450.63
21_Q53_L0.5390.62
16_I59_T0.5380.62
28_P33_L0.5370.62
18_R39_I0.5320.61
6_P9_D0.5240.60
51_Q58_R0.5210.60
7_F26_L0.5170.59
14_F25_S0.5160.59
35_A68_L0.5090.58
11_Q14_F0.5090.58
42_Q56_H0.5070.58
41_C48_S0.5050.57
20_A35_A0.5020.57
49_C54_E0.5000.57
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  
2khrA 1 1 100 0.085 Contact Map
2pstX 1 0.8472 100 0.085 Contact Map
2lpdA 1 1 100 0.097 Contact Map
2myyA 1 1 100 0.098 Contact Map
4gr5A 1 0.9861 99.7 0.529 Contact Map
1eg3A 1 0.6944 29 0.914 Contact Map
1jmqA 1 0.6111 20.3 0.92 Contact Map
1yrtA 1 0.9028 15.5 0.924 Contact Map
1wr4A 1 0.5 13.7 0.925 Contact Map
2jv4A 1 0.6389 10.7 0.929 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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