GREMLIN Database
YRKF - UPF0033 protein YrkF
UniProt: P54433 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 185 (145)
Sequences: 1156 (911)
Seq/√Len: 75.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
53_K56_G3.3921.00
129_L158_A3.3191.00
91_S94_A3.3001.00
52_A56_G3.1021.00
59_Y62_T3.0781.00
107_I148_I2.9321.00
135_R138_E2.8761.00
95_F146_Y2.8281.00
119_A177_M2.5951.00
59_Y63_E2.4821.00
51_W54_S2.3691.00
115_E150_H2.3591.00
141_E167_F2.3081.00
113_I117_E2.2281.00
51_W55_T2.2071.00
88_P98_K2.0991.00
112_E115_E2.0801.00
105_L146_Y1.9141.00
110_V150_H1.8871.00
145_I167_F1.8861.00
66_G69_L1.8731.00
51_W56_G1.8411.00
140_N143_D1.7421.00
94_A97_Q1.7331.00
59_Y64_A1.6901.00
61_G65_E1.6771.00
124_V177_M1.6761.00
60_L63_E1.6351.00
44_S48_L1.6101.00
67_E70_R1.6061.00
110_V158_A1.6041.00
45_T50_A1.5600.99
44_S47_D1.5600.99
62_T65_E1.5520.99
52_A57_H1.5340.99
75_K79_H1.5260.99
99_V107_I1.4570.99
149_C155_S1.4470.99
116_Y126_H1.4290.99
147_I158_A1.3160.98
38_H42_K1.3130.98
130_G154_R1.3070.98
94_A98_K1.2920.98
127_I135_R1.2820.98
72_F75_K1.2700.97
99_V103_E1.2490.97
116_Y120_H1.2320.97
152_G155_S1.2270.97
90_I95_F1.2000.96
70_R80_S1.1880.96
77_G80_S1.1860.96
134_K138_E1.1660.96
66_G70_R1.1470.95
113_I126_H1.1420.95
99_V105_L1.1410.95
38_H45_T1.1400.95
177_M181_T1.1240.95
133_E165_Q1.1160.95
42_K46_A1.1020.94
150_H158_A1.0890.94
53_K57_H1.0870.94
137_N164_K1.0870.94
70_R77_G1.0850.94
82_E142_N1.0610.93
121_I173_V1.0410.92
72_F141_E1.0390.92
59_Y69_L1.0230.92
133_E161_T1.0220.91
121_I148_I1.0210.91
52_A55_T1.0170.91
117_E126_H1.0140.91
178_R182_G1.0120.91
110_V139_L0.9970.90
139_L145_I0.9960.90
37_I40_T0.9670.89
96_K99_V0.9660.89
40_T44_S0.9610.89
88_P94_A0.9610.89
60_L64_A0.9480.88
159_A172_N0.9340.87
92_L179_D0.9280.87
54_S57_H0.9110.86
175_P179_D0.9090.86
144_E168_K0.9070.86
71_H74_R0.9030.86
98_K105_L0.9020.85
70_R168_K0.8930.85
108_L127_I0.8890.85
116_Y161_T0.8860.84
160_R164_K0.8860.84
126_H150_H0.8790.84
110_V115_E0.8770.84
112_E150_H0.8750.84
46_A49_E0.8710.83
64_A69_L0.8680.83
50_A78_E0.8680.83
115_E179_D0.8650.83
60_L65_E0.8590.83
108_L173_V0.8580.82
58_E63_E0.8560.82
69_L77_G0.8480.82
37_I121_I0.8410.81
79_H93_E0.8400.81
58_E61_G0.8390.81
164_K168_K0.8270.80
82_E85_S0.8230.80
128_P135_R0.8200.80
47_D151_S0.8090.79
41_D45_T0.7930.77
92_L99_V0.7860.77
47_D112_E0.7760.76
112_E126_H0.7680.75
161_T165_Q0.7630.74
90_I105_L0.7490.73
91_S97_Q0.7430.72
69_L80_S0.7380.72
89_E174_V0.7360.72
86_S170_V0.7280.71
127_I137_N0.7260.71
90_I107_I0.7170.70
67_E77_G0.7120.69
73_L80_S0.7090.69
144_E163_K0.7060.69
61_G69_L0.7040.68
82_E169_K0.7040.68
134_K165_Q0.7030.68
41_D46_A0.6980.68
61_G142_N0.6950.67
44_S112_E0.6820.66
157_M161_T0.6780.65
119_A181_T0.6780.65
97_Q100_D0.6760.65
62_T69_L0.6730.65
104_S143_D0.6680.64
136_A167_F0.6660.64
108_L162_M0.6640.64
115_E118_K0.6590.63
82_E93_E0.6560.63
61_G68_I0.6500.62
61_G66_G0.6490.62
150_H179_D0.6480.62
120_H150_H0.6450.62
61_G64_A0.6390.61
150_H154_R0.6360.61
173_V180_W0.6350.60
110_V126_H0.6340.60
67_E137_N0.6240.59
41_D47_D0.6200.59
58_E62_T0.6170.58
73_L133_E0.6110.57
149_C158_A0.6100.57
91_S99_V0.6090.57
65_E69_L0.6060.57
89_E182_G0.6060.57
77_G81_S0.6030.56
67_E164_K0.6030.56
38_H41_D0.6020.56
163_K168_K0.6000.56
62_T66_G0.5970.56
103_E107_I0.5930.55
64_A67_E0.5880.55
144_E169_K0.5870.54
124_V150_H0.5860.54
152_G178_R0.5850.54
120_H170_V0.5810.54
100_D104_S0.5800.54
148_I151_S0.5790.53
110_V120_H0.5780.53
110_V149_C0.5780.53
70_R137_N0.5770.53
72_F167_F0.5760.53
51_W130_G0.5730.53
68_I72_F0.5700.52
96_K100_D0.5640.52
69_L74_R0.5610.51
157_M160_R0.5580.51
43_G148_I0.5550.50
60_L70_R0.5520.50
72_F77_G0.5520.50
92_L137_N0.5510.50
37_I42_K0.5500.50
159_A170_V0.5470.49
92_L96_K0.5470.49
133_E164_K0.5390.48
43_G154_R0.5380.48
175_P180_W0.5360.48
114_E118_K0.5340.48
110_V176_G0.5340.48
137_N165_Q0.5320.48
151_S155_S0.5300.47
38_H43_G0.5290.47
111_R126_H0.5270.47
97_Q102_D0.5260.47
62_T145_I0.5250.47
89_E172_N0.5210.46
37_I167_F0.5210.46
81_S84_A0.5190.46
59_Y74_R0.5180.46
46_A77_G0.5170.46
95_F98_K0.5170.46
127_I152_G0.5160.46
136_A144_E0.5150.45
64_A70_R0.5140.45
39_A42_K0.5140.45
58_E64_A0.5140.45
96_K147_I0.5130.45
42_K49_E0.5120.45
90_I146_Y0.5120.45
98_K144_E0.5110.45
115_E151_S0.5110.45
112_E158_A0.5110.45
42_K47_D0.5100.45
93_E96_K0.5080.45
48_L152_G0.5070.44
112_E147_I0.5050.44
62_T67_E0.5020.44
59_Y70_R0.5000.44
96_K123_G0.5000.44
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  
3tp9A 2 0.9784 99.9 0.557 Contact Map
1gmxA 1 0.5459 99.9 0.568 Contact Map
3r2uA 4 0.5081 99.9 0.568 Contact Map
3iwhA 1 0.5297 99.9 0.575 Contact Map
3fojA 1 0.5297 99.9 0.578 Contact Map
1yt8A 1 0.5351 99.9 0.579 Contact Map
3ilmA 2 0.5189 99.9 0.582 Contact Map
3gk5A 1 0.5135 99.9 0.584 Contact Map
3icsA 2 0.9676 99.9 0.586 Contact Map
3d1pA 1 0.5351 99.9 0.587 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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