GREMLIN Database
YFED - Uncharacterized protein YfeD
UniProt: P27238 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11432
Length: 130 (114)
Sequences: 104 (62)
Seq/√Len: 5.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
49_I97_I4.0760.94
49_I96_A3.2240.82
76_E81_Y3.1670.81
26_R45_R2.5720.64
39_P58_F2.3740.58
21_K47_R2.3480.57
15_E89_A2.1590.50
58_F107_K2.1110.49
53_T89_A2.0240.46
102_D128_E1.9800.44
34_K98_D1.9290.42
90_Y98_D1.8120.38
20_A42_K1.7860.38
111_F115_E1.7620.37
51_V98_D1.6380.33
39_P117_I1.6340.33
52_D96_A1.5730.31
17_L64_A1.5190.29
82_A88_P1.4790.28
38_F63_P1.4650.28
7_K29_R1.4620.28
10_T19_V1.4560.28
20_A45_R1.4540.27
20_A26_R1.4500.27
26_R63_P1.4480.27
25_N35_T1.4280.27
24_V59_I1.4210.27
38_F42_K1.4160.26
38_F89_A1.3870.26
31_K50_L1.3850.26
121_L126_I1.3770.25
30_E56_C1.3740.25
81_Y97_I1.3450.25
8_M29_R1.3240.24
11_E78_I1.3220.24
54_Q87_A1.3210.24
11_E50_L1.3160.24
7_K30_E1.2880.23
100_M117_I1.2770.23
51_V85_A1.2460.22
35_T114_R1.2360.22
42_K92_Q1.2330.22
35_T41_V1.2280.22
34_K79_A1.2040.21
62_T127_D1.1880.21
6_N84_G1.1820.21
51_V90_Y1.1790.20
35_T47_R1.1560.20
15_E61_N1.1460.20
42_K45_R1.1270.19
101_T118_R1.1230.19
29_R64_A1.1100.19
16_C108_V1.1090.19
5_R10_T1.1080.19
37_K58_F1.0980.19
74_A103_I1.0740.18
54_Q103_I1.0580.18
57_E128_E1.0460.18
39_P107_K1.0340.17
16_C120_F1.0340.17
17_L42_K1.0220.17
10_T26_R1.0200.17
17_L26_R1.0060.17
26_R42_K0.9990.17
77_R108_V0.9970.17
8_M32_G0.9930.17
34_K108_V0.9880.16
58_F85_A0.9590.16
19_V109_A0.9580.16
36_E120_F0.9380.16
29_R48_L0.9350.15
92_Q95_N0.9300.15
63_P93_I0.9270.15
10_T20_A0.9130.15
32_G54_Q0.9000.15
60_Q83_P0.8940.15
18_G46_A0.8920.15
45_R120_F0.8910.15
38_F92_Q0.8870.15
31_K93_I0.8840.15
78_I88_P0.8790.14
9_T126_I0.8780.14
51_V62_T0.8700.14
16_C49_I0.8620.14
34_K128_E0.8550.14
16_C32_G0.8550.14
77_R87_A0.8430.14
15_E94_I0.8350.14
25_N41_V0.8200.13
62_T98_D0.8100.13
82_A107_K0.8050.13
80_E83_P0.7940.13
95_N108_V0.7760.13
26_R93_I0.7730.13
25_N114_R0.7720.13
34_K76_E0.7620.13
91_R97_I0.7620.13
8_M34_K0.7600.13
43_G46_A0.7580.13
83_P103_I0.7530.12
13_L38_F0.7470.12
14_A25_N0.7400.12
49_I52_D0.7340.12
41_V114_R0.7280.12
17_L20_A0.7240.12
30_E36_E0.7230.12
112_L115_E0.7140.12
41_V112_L0.7130.12
109_A120_F0.7090.12
24_V102_D0.7080.12
30_E45_R0.7050.12
105_Q121_L0.6980.12
15_E49_I0.6910.12
28_I56_C0.6900.12
104_E115_E0.6760.11
82_A85_A0.6740.11
75_E80_E0.6640.11
118_R128_E0.6620.11
39_P47_R0.6580.11
102_D106_E0.6540.11
104_E112_L0.6510.11
51_V77_R0.6510.11
17_L92_Q0.6510.11
20_A38_F0.6460.11
114_R117_I0.6420.11
102_D115_E0.6380.11
99_N106_E0.6350.11
16_C57_E0.6340.11
25_N47_R0.6340.11
45_R63_P0.6280.11
54_Q77_R0.6270.11
17_L24_V0.6210.11
103_I128_E0.6110.10
56_C125_D0.6110.10
19_V26_R0.6050.10
78_I82_A0.6010.10
6_N10_T0.5990.10
38_F60_Q0.5970.10
105_Q126_I0.5910.10
24_V99_N0.5890.10
92_Q113_S0.5850.10
10_T99_N0.5670.10
52_D62_T0.5660.10
18_G44_G0.5560.10
18_G43_G0.5560.10
101_T107_K0.5540.10
8_M48_L0.5500.10
92_Q107_K0.5470.10
63_P76_E0.5470.10
99_N110_Q0.5430.10
54_Q125_D0.5430.10
50_L56_C0.5410.10
75_E125_D0.5410.10
20_A113_S0.5400.10
11_E21_K0.5390.10
49_I118_R0.5380.10
19_V59_I0.5330.09
11_E24_V0.5320.09
114_R124_L0.5280.09
61_N96_A0.5270.09
83_P119_N0.5250.09
61_N91_R0.5230.09
117_I122_A0.5220.09
12_E123_R0.5180.09
49_I99_N0.5160.09
79_A82_A0.5160.09
75_E97_I0.5060.09
51_V106_E0.5050.09
120_F128_E0.5030.09
31_K53_T0.5010.09
102_D122_A0.5000.09
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  
1g4dA 1 0.4923 98.9 0.812 Contact Map
1tnsA 1 0.5462 98.9 0.815 Contact Map
4j2nA 4 0.4231 97.5 0.871 Contact Map
1z4hA 1 0.4769 97.1 0.88 Contact Map
1j9iA 2 0.5231 96.6 0.888 Contact Map
2kfsA 1 0.8538 96.4 0.89 Contact Map
1y6uA 1 0.4308 96.3 0.891 Contact Map
1pdnC 1 0.7308 95.9 0.895 Contact Map
3kp7A 2 0.7154 95.7 0.896 Contact Map
2k27A 1 0.8 95.4 0.899 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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