GREMLIN Database
YLBD - Uncharacterized protein YlbD
UniProt: O34880 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 132 (126)
Sequences: 135 (120)
Seq/√Len: 10.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
35_Q39_E5.0821.00
19_K46_E3.6860.98
85_D88_Q3.0910.95
41_W104_Q2.9880.94
24_I34_W2.9440.93
28_R40_N2.7940.91
42_V95_K2.4100.83
48_D109_T2.3180.81
15_Q101_S2.1610.76
98_Q102_S2.0960.74
20_H100_I2.0790.73
58_E67_T2.0120.70
28_R109_T1.8460.63
103_L116_K1.7810.60
49_P52_D1.7550.59
14_K77_M1.7100.57
39_E43_L1.7060.57
70_K93_I1.7010.57
35_Q40_N1.6480.54
17_V33_S1.6250.53
35_Q44_F1.5740.51
37_V50_I1.5210.48
126_P129_F1.5050.48
17_V82_K1.5050.48
79_T100_I1.5030.47
34_W93_I1.4930.47
78_V96_M1.4690.46
11_N128_S1.4560.45
85_D99_S1.4250.44
23_L100_I1.4240.44
43_L50_I1.3790.42
44_F50_I1.3400.40
39_E82_K1.3230.39
18_K87_N1.3230.39
27_V34_W1.3080.38
72_D75_S1.3060.38
35_Q100_I1.2790.37
44_F101_S1.2450.36
77_M99_S1.2370.35
6_A10_I1.2230.35
97_S103_L1.2180.34
47_S85_D1.2040.34
32_R37_V1.1940.33
102_S105_S1.1860.33
47_S119_Q1.1610.32
125_H130_R1.1530.32
98_Q105_S1.1470.32
124_Q128_S1.1430.31
95_K105_S1.1400.31
9_S107_L1.1330.31
81_V94_N1.1070.30
109_T113_S1.1010.30
85_D103_L1.0920.29
67_T122_S1.0870.29
6_A38_Y1.0770.29
54_Y119_Q1.0770.29
35_Q82_K1.0620.28
86_V102_S1.0600.28
28_R48_D1.0560.28
19_K55_R1.0300.27
35_Q96_M1.0160.26
4_Q125_H1.0090.26
90_N111_S1.0080.26
96_M99_S1.0010.26
47_S65_P0.9990.26
24_I28_R0.9980.26
83_K114_G0.9890.25
41_W111_S0.9870.25
38_Y68_P0.9850.25
59_E69_Q0.9620.24
66_E71_N0.9510.24
31_Q52_D0.9430.24
32_R54_Y0.9380.24
88_Q96_M0.9330.23
18_K31_Q0.9210.23
85_D96_M0.9170.23
75_S110_F0.9140.23
12_D75_S0.9090.23
14_K52_D0.9060.23
26_E126_P0.9050.23
43_L55_R0.9020.22
23_L34_W0.8970.22
92_Q102_S0.8950.22
42_V105_S0.8910.22
9_S28_R0.8820.22
60_A121_G0.8770.22
27_V38_Y0.8740.22
20_H55_R0.8700.21
16_F45_G0.8520.21
13_F45_G0.8520.21
13_F16_F0.8520.21
38_Y43_L0.8480.21
127_F132_D0.8410.20
41_W44_F0.8370.20
82_K94_N0.8310.20
77_M100_I0.8090.20
83_K122_S0.8070.19
20_H77_M0.8060.19
44_F76_K0.8010.19
102_S111_S0.7980.19
73_F79_T0.7980.19
37_V95_K0.7920.19
22_K55_R0.7860.19
59_E94_N0.7860.19
76_K101_S0.7720.18
31_Q54_Y0.7610.18
33_S40_N0.7520.18
84_M128_S0.7480.18
33_S78_V0.7360.17
33_S94_N0.7330.17
25_K122_S0.7280.17
9_S38_Y0.7220.17
27_V30_E0.7170.17
101_S106_L0.7160.17
63_A120_P0.7150.17
57_P66_E0.7130.17
79_T96_M0.7110.17
49_P108_N0.7100.17
48_D96_M0.7020.17
63_A121_G0.7020.17
127_F131_K0.7000.16
111_S116_K0.6980.16
22_K57_P0.6890.16
70_K125_H0.6880.16
22_K43_L0.6800.16
39_E83_K0.6760.16
115_Q124_Q0.6720.16
39_E100_I0.6680.16
84_M89_M0.6650.16
44_F48_D0.6640.16
60_A117_H0.6620.16
32_R44_F0.6610.15
90_N104_Q0.6600.15
15_Q103_L0.6530.15
67_T121_G0.6460.15
88_Q95_K0.6430.15
57_P67_T0.6410.15
8_H42_V0.6360.15
31_Q37_V0.6280.15
32_R105_S0.6190.14
17_V42_V0.6190.14
76_K97_S0.6130.14
80_A101_S0.6100.14
23_L29_K0.6100.14
5_H63_A0.6070.14
4_Q103_L0.6060.14
65_P77_M0.6000.14
29_K92_Q0.5990.14
104_Q127_F0.5990.14
40_N95_K0.5950.14
106_L123_G0.5940.14
50_I54_Y0.5880.14
46_E73_F0.5840.14
12_D57_P0.5810.14
47_S99_S0.5760.13
69_Q91_E0.5700.13
68_P106_L0.5700.13
74_V103_L0.5690.13
103_L111_S0.5640.13
36_D87_N0.5610.13
119_Q124_Q0.5600.13
14_K130_R0.5490.13
30_E130_R0.5470.13
32_R50_I0.5440.13
20_H128_S0.5410.13
37_V97_S0.5410.13
16_F21_P0.5360.13
21_P45_G0.5360.13
13_F21_P0.5360.13
49_P53_P0.5360.13
112_G115_Q0.5330.13
30_E129_F0.5300.13
37_V42_V0.5290.12
17_V34_W0.5240.12
43_L112_G0.5240.12
69_Q87_N0.5230.12
67_T117_H0.5220.12
76_K105_S0.5200.12
53_P69_Q0.5180.12
10_I103_L0.5160.12
52_D60_A0.5160.12
77_M119_Q0.5090.12
114_G120_P0.5080.12
79_T106_L0.5060.12
48_D88_Q0.5050.12
19_K77_M0.5050.12
48_D73_F0.5040.12
91_E122_S0.5040.12
75_S112_G0.5000.12
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  
4pz1A 2 0.5455 39.2 0.932 Contact Map
2beqA 1 0.2727 13 0.946 Contact Map
2jrbA 1 0.2045 11.2 0.948 Contact Map
3sooA 2 0.2121 10.8 0.948 Contact Map
3hr1A 1 0.2955 8.3 0.951 Contact Map
1vlrA 2 0.4167 6.5 0.953 Contact Map
3l6gA 1 0.4242 6.5 0.953 Contact Map
4n17A 1 0.3258 6.3 0.953 Contact Map
3mpkA 1 0.3182 6.2 0.953 Contact Map
4wfcB 1 0.3485 6.2 0.953 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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