GREMLIN Database
YWKD - Uncharacterized protein YwkD
UniProt: P45871 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 128 (119)
Sequences: 3598 (1957)
Seq/√Len: 179.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
21_A25_H5.8921.00
90_Q94_E3.9411.00
84_S87_K3.1161.00
91_E95_K2.6311.00
98_E116_F2.4251.00
31_V34_E2.2991.00
16_Y45_L2.2951.00
92_L97_I2.0641.00
15_D18_K2.0291.00
111_R127_E1.9801.00
31_V45_L1.9111.00
21_A26_K1.8541.00
89_V93_H1.7911.00
29_F49_L1.7711.00
35_T107_L1.7661.00
69_R72_A1.7571.00
41_G62_D1.6981.00
5_S81_T1.6491.00
86_D111_R1.6401.00
32_I48_S1.6261.00
36_Y43_Y1.5681.00
93_H99_T1.5511.00
88_A91_E1.5281.00
24_V30_Q1.5091.00
19_S57_L1.4841.00
89_V113_T1.4811.00
14_S63_P1.4671.00
26_K95_K1.4281.00
116_F120_Q1.4241.00
18_K21_A1.3651.00
114_F124_E1.3171.00
63_P73_A1.3081.00
116_F122_P1.2851.00
86_D90_Q1.2731.00
38_E41_G1.2621.00
18_K119_D1.2551.00
7_H81_T1.2291.00
41_G61_P1.2031.00
25_H95_K1.1981.00
20_K47_L1.1741.00
112_F126_Y1.1611.00
93_H101_P1.1591.00
113_T125_L1.1511.00
43_Y61_P1.1501.00
19_S119_D1.1501.00
87_K91_E1.1471.00
30_Q50_N1.1411.00
14_S65_E1.1141.00
80_F123_L1.1121.00
78_L123_L1.1101.00
100_E116_F1.0851.00
77_H124_E1.0811.00
17_E21_A1.0801.00
13_C16_Y1.0801.00
14_S64_P1.0791.00
36_Y41_G1.0781.00
87_K90_Q1.0481.00
30_Q48_S1.0471.00
36_Y61_P1.0361.00
37_R42_S1.0300.99
115_F123_L1.0280.99
92_L125_L1.0250.99
19_S23_Y1.0140.99
90_Q93_H1.0130.99
85_L89_V0.9960.99
49_L80_F0.9930.99
26_K92_L0.9780.99
8_H79_A0.9690.99
9_I53_Y0.9620.99
29_F80_F0.9450.99
27_L115_F0.9390.99
8_H56_E0.9350.99
34_E43_Y0.9240.99
100_E122_P0.9220.99
8_H77_H0.9190.99
82_V88_A0.9010.99
23_Y117_D0.8940.99
42_S60_F0.8810.98
104_T107_L0.8800.98
85_L111_R0.8730.98
7_H126_Y0.8730.98
49_L52_S0.8630.98
75_L78_L0.8600.98
37_R40_R0.8530.98
14_S18_K0.8530.98
55_I78_L0.8510.98
34_E45_L0.8460.98
27_L125_L0.8390.98
10_A58_F0.8320.98
77_H114_F0.8270.98
13_C45_L0.8170.97
45_L59_S0.8010.97
91_E94_E0.7960.97
105_D108_T0.7840.97
30_Q51_G0.7770.97
10_A76_R0.7760.97
14_S119_D0.7630.96
16_Y59_S0.7560.96
63_P69_R0.7550.96
101_P113_T0.7470.96
43_Y59_S0.7350.95
35_T44_K0.7340.95
51_G54_V0.7330.95
12_I121_L0.7320.95
62_D65_E0.7250.95
115_F125_L0.7120.94
71_E74_G0.7100.94
97_I115_F0.6970.94
89_V99_T0.6950.94
69_R116_F0.6940.94
26_K97_I0.6920.93
44_K58_F0.6850.93
11_I23_Y0.6830.93
12_I60_F0.6740.93
9_I78_L0.6740.93
13_C21_A0.6740.93
21_A95_K0.6720.92
31_V43_Y0.6650.92
7_H79_A0.6630.92
5_S52_S0.6620.92
38_E61_P0.6590.92
65_E70_P0.6580.92
6_I9_I0.6500.91
37_R41_G0.6490.91
17_E34_E0.6480.91
30_Q98_E0.6450.91
92_L113_T0.6430.91
106_P109_G0.6410.91
103_R106_P0.6310.90
104_T109_G0.6290.90
24_V47_L0.6280.90
59_S63_P0.6220.89
117_D121_L0.6190.89
50_N53_Y0.6160.89
19_S118_P0.6160.89
99_T115_F0.6150.89
89_V98_E0.6140.89
42_S105_D0.6070.88
36_Y59_S0.6060.88
25_H91_E0.5990.87
48_S52_S0.5980.87
106_P110_K0.5870.86
5_S51_G0.5860.86
65_E73_A0.5850.86
24_V31_V0.5830.86
42_S58_F0.5800.86
69_R79_A0.5800.86
79_A114_F0.5760.85
10_A60_F0.5730.85
81_T126_Y0.5730.85
70_P73_A0.5710.85
56_E60_F0.5600.84
50_N54_V0.5600.84
71_E75_L0.5570.83
11_I78_L0.5570.83
107_L110_K0.5530.83
79_A124_E0.5530.83
93_H96_G0.5520.83
22_F115_F0.5510.83
20_K24_V0.5490.83
42_S112_F0.5400.82
9_I123_L0.5400.82
88_A125_L0.5370.81
29_F73_A0.5360.81
30_Q33_Q0.5330.81
13_C59_S0.5310.80
85_L112_F0.5290.80
6_I11_I0.5230.79
72_A79_A0.5220.79
101_P108_T0.5210.79
86_D104_T0.5140.78
19_S117_D0.5120.78
37_R44_K0.5100.78
33_Q52_S0.5050.77
104_T111_R0.5050.77
35_T53_Y0.5040.77
40_R43_Y0.5000.76
13_C29_F0.5000.76
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  
2p25A 2 0.9844 99.9 0.355 Contact Map
2c21A 2 0.9297 99.9 0.362 Contact Map
1ss4A 4 0.9922 99.9 0.363 Contact Map
3l7tA 2 0.9766 99.9 0.364 Contact Map
3w0tA 2 0.9922 99.9 0.372 Contact Map
3hdpA 2 0.9844 99.9 0.372 Contact Map
3gm5A 2 0.9766 99.9 0.381 Contact Map
1jc4A 2 1 99.9 0.382 Contact Map
4mtsA 2 0.9531 99.9 0.386 Contact Map
1f9zA 2 0.9531 99.9 0.39 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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