GREMLIN Database
YDAS - UPF0410 protein YdaS
UniProt: P96594 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 85 (79)
Sequences: 417 (205)
Seq/√Len: 23.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
72_F76_L3.2381.00
38_L58_F3.1761.00
12_I30_I3.1171.00
48_L65_I3.0001.00
3_S7_S2.6810.99
27_P32_G2.4560.98
54_S59_A2.3210.97
43_I70_F2.1790.96
7_S38_L2.0880.95
17_I20_A2.0590.95
12_I34_M1.9360.92
53_P60_I1.8770.91
41_A63_A1.8700.91
28_G32_G1.7130.87
53_P61_F1.6430.84
70_F74_L1.5900.82
73_L77_I1.5290.80
64_I68_A1.4990.78
47_L69_I1.4280.75
14_I71_V1.4220.75
41_A71_V1.4150.74
6_V58_F1.3950.73
25_R32_G1.3840.73
11_A33_S1.3430.70
14_I63_A1.2900.67
72_F77_I1.2880.67
8_L33_S1.2480.64
12_I33_S1.2150.62
17_I25_R1.1750.60
16_L20_A1.1530.58
25_R28_G1.1040.55
32_G42_W1.0730.53
51_W61_F1.0710.53
3_S45_H1.0690.52
12_I16_L1.0650.52
57_G61_F1.0430.51
4_F7_S1.0340.50
45_H48_L1.0170.49
23_G68_A0.9760.46
18_G75_G0.9390.43
7_S58_F0.9390.43
25_R77_I0.9080.41
76_L79_R0.9060.41
36_A74_L0.8960.40
56_A59_A0.8900.40
26_L32_G0.8870.40
50_T67_A0.8860.40
35_I61_F0.8710.39
44_G49_G0.8700.39
11_A19_S0.8650.38
19_S22_V0.8600.38
42_W46_G0.8490.37
4_F42_W0.8360.36
38_L64_I0.8280.36
23_G26_L0.8260.36
13_V17_I0.8220.36
58_F63_A0.8130.35
38_L45_H0.7890.34
27_P42_W0.7690.32
7_S56_A0.7580.32
16_L78_F0.7410.31
34_M77_I0.7410.31
19_S75_G0.7320.30
68_A72_F0.7230.30
4_F65_I0.6990.28
8_L75_G0.6970.28
43_I46_G0.6950.28
6_V10_V0.6870.28
2_L16_L0.6850.27
13_V78_F0.6840.27
13_V54_S0.6790.27
33_S68_A0.6600.26
48_L51_W0.6500.25
3_S54_S0.6480.25
59_A69_I0.6430.25
14_I56_A0.6400.25
24_N27_P0.6390.25
21_I68_A0.6350.25
6_V24_N0.6240.24
21_I75_G0.6220.24
2_L67_A0.6200.24
39_I48_L0.6170.24
20_A31_F0.6160.24
59_A62_P0.6140.24
72_F80_G0.6080.23
31_F50_T0.6070.23
76_L80_G0.6070.23
54_S60_I0.6030.23
11_A68_A0.6020.23
44_G62_P0.5990.23
46_G50_T0.5960.23
13_V16_L0.5890.22
34_M75_G0.5870.22
47_L59_A0.5860.22
2_L14_I0.5790.22
48_L69_I0.5740.22
4_F54_S0.5690.21
10_V57_G0.5600.21
48_L54_S0.5590.21
6_V11_A0.5560.21
30_I34_M0.5550.21
65_I71_V0.5470.20
56_A64_I0.5440.20
39_I47_L0.5430.20
12_I24_N0.5430.20
14_I48_L0.5390.20
25_R33_S0.5310.20
13_V46_G0.5240.19
7_S45_H0.5210.19
16_L30_I0.5210.19
47_L57_G0.5210.19
17_I60_I0.5150.19
20_A25_R0.5150.19
48_L61_F0.5090.19
74_L78_F0.5070.19
35_I64_I0.5020.18
35_I73_L0.5000.18
18_G69_I0.5000.18
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  
4z7fA 2 0.9882 30.8 0.907 Contact Map
4tkrA 2 0.9294 21.8 0.914 Contact Map
4rp9A 2 0.9765 20.2 0.915 Contact Map
2j69A 1 0.7765 19.6 0.915 Contact Map
4rfsS 1 0.9294 18.3 0.917 Contact Map
3dh4A 3 0.9529 14.5 0.92 Contact Map
3rlbA 1 0.9294 12.2 0.923 Contact Map
2xq2A 2 0.9529 11.7 0.924 Contact Map
4huqS 1 0.9765 11.3 0.924 Contact Map
3qnqA 2 0.9059 10.9 0.925 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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