GREMLIN Database
YDCH - Uncharacterized protein YdcH
UniProt: P0ACW6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12865
Length: 74 (70)
Sequences: 239 (163)
Seq/√Len: 19.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
11_R15_E3.9591.00
25_K54_Q2.4580.97
8_L66_L2.4150.96
36_K48_V2.3700.96
10_S13_K2.0980.92
31_H35_R2.0140.91
35_R40_D2.0000.90
57_Q61_E1.9520.89
39_S42_R1.8410.86
58_L62_M1.7210.82
28_K32_E1.6900.81
18_R21_S1.6850.81
3_P66_L1.5760.76
15_E20_M1.5240.73
14_N20_M1.5240.73
65_I69_E1.4470.69
10_S27_N1.3440.63
24_D31_H1.3290.62
3_P67_Q1.3090.61
36_K43_G1.2990.61
23_F27_N1.2730.59
9_I23_F1.2600.58
15_E46_A1.2450.57
3_P11_R1.2040.55
17_P21_S1.1730.53
31_H40_D1.1370.50
22_L66_L1.1360.50
25_K53_K1.1360.50
50_R57_Q1.1330.50
22_L48_V1.0890.47
54_Q60_D1.0740.46
25_K61_E1.0580.45
3_P69_E1.0560.45
49_V63_L1.0430.44
10_S14_N1.0250.43
17_P47_E1.0070.42
24_D47_E1.0040.42
31_H38_G1.0040.42
16_N68_Q0.9990.42
18_R41_G0.9950.41
21_S25_K0.9900.41
7_D53_K0.9660.40
14_N39_S0.9590.39
5_Y34_A0.9410.38
32_E41_G0.9330.38
49_V60_D0.9170.37
27_N37_E0.9170.37
24_D61_E0.9090.36
34_A40_D0.9060.36
6_R27_N0.9050.36
24_D38_G0.9000.36
34_A38_G0.8640.34
14_N62_M0.8560.33
17_P50_R0.8550.33
22_L62_M0.8450.33
11_R32_E0.8440.32
22_L65_I0.8220.31
17_P46_A0.8000.30
56_L59_K0.7930.30
9_I27_N0.7760.29
57_Q65_I0.7710.28
38_G42_R0.7450.27
20_M24_D0.7440.27
13_K62_M0.7370.27
36_K51_M0.7320.26
41_G45_N0.7240.26
56_L60_D0.7120.26
47_E68_Q0.7060.25
24_D45_N0.7040.25
61_E69_E0.6950.25
45_N61_E0.6790.24
37_E47_E0.6670.23
2_F12_L0.6660.23
11_R61_E0.6600.23
49_V53_K0.6430.22
2_F62_M0.6420.22
8_L22_L0.6410.22
16_N65_I0.6250.22
62_M66_L0.6230.21
60_D63_L0.6220.21
15_E70_S0.6210.21
11_R14_N0.6140.21
3_P70_S0.6120.21
6_R30_D0.6010.20
13_K27_N0.5990.20
10_S51_M0.5960.20
21_S48_V0.5910.20
24_D58_L0.5820.20
7_D29_L0.5820.20
21_S39_S0.5800.20
3_P8_L0.5740.19
7_D21_S0.5670.19
36_K39_S0.5550.19
17_P44_Y0.5520.19
38_G44_Y0.5480.18
33_I41_G0.5470.18
48_V62_M0.5450.18
7_D16_N0.5310.18
28_K68_Q0.5230.17
13_K35_R0.5220.17
65_I68_Q0.5070.17
44_Y47_E0.5070.17
17_P33_I0.5040.17
28_K50_R0.5020.17
10_S47_E0.5000.17
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  
1zhcA 1 0.973 99.9 0.319 Contact Map
3ghgA 2 0.9054 17.6 0.91 Contact Map
3ojaB 1 0.9324 15.8 0.912 Contact Map
2v6eA 2 0.8649 15 0.912 Contact Map
2dq3A 2 0.8378 13.5 0.914 Contact Map
4atmA 2 0.9459 12.6 0.915 Contact Map
2x6uA 1 0.2297 11.9 0.916 Contact Map
4r3zB 1 0.8784 10.6 0.918 Contact Map
2dfsA 2 1 10.2 0.918 Contact Map
1deqA 1 0.9595 8.7 0.921 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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