GREMLIN Database
DEF1 - Peptide deformylase 1
UniProt: P94462 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 160 (149)
Sequences: 6110 (3852)
Seq/√Len: 315.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
57_R138_D3.4661.00
110_A118_F2.8431.00
109_R117_P2.4711.00
59_A134_M2.4661.00
112_N116_K2.4271.00
36_Y69_R2.3241.00
76_E109_R2.3191.00
107_K119_I2.2321.00
15_E144_S2.2021.00
109_R119_I2.1911.00
122_A130_V1.9531.00
32_L71_D1.9081.00
86_G128_R1.8861.00
111_F117_P1.8471.00
50_P55_L1.8471.00
33_D113_R1.8131.00
24_F28_L1.8021.00
40_L62_E1.7781.00
7_V13_V1.7071.00
78_L109_R1.6981.00
85_T101_T1.6641.00
105_Y121_E1.6581.00
103_A131_Q1.6511.00
107_K121_E1.6341.00
18_A55_L1.6101.00
18_A50_P1.6081.00
6_V42_M1.5791.00
71_D113_R1.5761.00
32_L113_R1.5511.00
85_T99_D1.5391.00
87_I99_D1.5371.00
45_V125_F1.5351.00
112_N118_F1.5111.00
7_V11_A1.5081.00
105_Y123_R1.5031.00
80_K103_A1.4681.00
31_L54_I1.4671.00
4_K52_I1.4461.00
81_S105_Y1.4441.00
40_L69_R1.4401.00
79_E107_K1.4311.00
7_V53_G1.4241.00
122_A126_L1.4141.00
63_I129_A1.3851.00
59_A72_L1.3661.00
134_M138_D1.3531.00
29_K114_Q1.3411.00
29_K113_R1.3261.00
17_P20_T1.3161.00
104_D124_G1.3091.00
24_F111_F1.3091.00
32_L58_A1.2911.00
20_T57_R1.2841.00
4_K34_D1.2801.00
32_L73_V1.2741.00
70_I120_L1.2601.00
30_K34_D1.2581.00
8_T94_P1.2571.00
31_L58_A1.2521.00
72_L110_A1.2461.00
16_T55_L1.2141.00
26_K29_K1.2061.00
25_D28_L1.1741.00
72_L130_V1.1701.00
31_L52_I1.1701.00
20_T76_E1.1501.00
98_G142_F1.1481.00
34_D38_T1.1461.00
19_E55_L1.1381.00
140_V145_K1.1351.00
36_Y71_D1.1331.00
62_E69_R1.1321.00
17_P138_D1.1301.00
120_L130_V1.1161.00
84_Q103_A1.0801.00
32_L36_Y1.0741.00
36_Y40_L1.0691.00
13_V55_L1.0531.00
58_A73_V1.0271.00
36_Y60_V1.0211.00
93_F141_L1.0171.00
21_V58_A1.0091.00
27_K56_K1.0051.00
61_V70_I1.0051.00
3_V38_T1.0041.00
64_G67_R1.0011.00
78_L107_K0.9971.00
64_G68_G0.9621.00
110_A120_L0.9431.00
45_V129_A0.9371.00
9_H93_F0.9311.00
84_Q101_T0.9261.00
72_L118_F0.9251.00
125_F129_A0.9201.00
13_V53_G0.9161.00
147_S150_Y0.9111.00
84_Q104_D0.9071.00
18_A57_R0.9071.00
101_T147_S0.9021.00
78_L119_I0.8971.00
79_E82_G0.8791.00
135_D145_K0.8781.00
126_L130_V0.8701.00
75_P137_L0.8691.00
9_H143_T0.8681.00
135_D140_V0.8661.00
38_T52_I0.8631.00
77_I80_K0.8601.00
111_F115_G0.8461.00
97_Y142_F0.8331.00
65_D68_G0.8251.00
61_V129_A0.8221.00
140_V144_S0.8191.00
130_V134_M0.8171.00
24_F29_K0.8141.00
22_T74_N0.8081.00
77_I134_M0.8021.00
11_A53_G0.7951.00
108_V120_L0.7861.00
87_I97_Y0.7861.00
70_I126_L0.7841.00
83_E101_T0.7821.00
4_K54_I0.7811.00
28_L58_A0.7771.00
9_H141_L0.7690.99
33_D37_D0.7650.99
106_V122_A0.7600.99
120_L126_L0.7590.99
3_V34_D0.7470.99
96_V142_F0.7460.99
17_P57_R0.7390.99
108_V130_V0.7340.99
72_L108_V0.7330.99
4_K30_K0.7310.99
29_K32_L0.7300.99
19_E22_T0.7290.99
98_G146_I0.7290.99
3_V41_E0.7260.99
45_V63_I0.7250.99
63_I125_F0.7240.99
28_L56_K0.7230.99
63_I126_L0.7200.99
9_H15_E0.7170.99
147_S151_T0.7120.99
104_D123_R0.7080.99
3_V37_D0.7060.99
34_D37_D0.6980.99
89_G97_Y0.6950.99
24_F115_G0.6950.99
100_V142_F0.6930.99
39_M46_G0.6880.99
19_E56_K0.6860.99
5_K8_T0.6840.99
16_T19_E0.6840.99
83_E104_D0.6840.99
44_G91_L0.6800.99
108_V122_A0.6750.99
57_R76_E0.6730.99
26_K30_K0.6720.99
93_F143_T0.6720.99
90_C136_H0.6670.99
59_A130_V0.6550.98
72_L120_L0.6520.98
39_M60_V0.6430.98
32_L60_V0.6390.98
59_A110_A0.6350.98
31_L35_M0.6350.98
61_V130_V0.6330.98
39_M44_G0.6280.98
24_F73_V0.6260.98
47_L60_V0.6200.98
36_Y39_M0.6200.98
23_V26_K0.6190.98
30_K33_D0.6190.98
116_K119_I0.6160.98
28_L31_L0.6140.97
77_I103_A0.6130.97
39_M42_M0.6070.97
73_V111_F0.6040.97
77_I106_V0.6020.97
35_M47_L0.5960.97
61_V126_L0.5960.97
38_T41_E0.5880.97
9_H96_V0.5870.97
84_Q128_R0.5850.97
106_V130_V0.5810.97
39_M62_E0.5810.97
49_A58_A0.5780.96
79_E105_Y0.5770.96
22_T25_D0.5770.96
51_Q136_H0.5770.96
35_M58_A0.5730.96
48_A90_C0.5720.96
86_G99_D0.5630.96
4_K38_T0.5580.96
48_A91_L0.5570.96
77_I131_Q0.5560.96
15_E141_L0.5480.95
60_V71_D0.5460.95
61_V72_L0.5400.95
146_I150_Y0.5380.95
146_I149_Y0.5380.95
15_E143_T0.5300.94
12_E16_T0.5290.94
81_S84_Q0.5260.94
51_Q90_C0.5260.94
35_M91_L0.5240.94
142_F146_I0.5240.94
18_A59_A0.5240.94
61_V110_A0.5220.94
39_M45_V0.5220.94
108_V134_M0.5210.94
78_L81_S0.5210.94
33_D71_D0.5210.94
9_H151_T0.5200.94
46_G133_E0.5180.94
17_P140_V0.5180.94
13_V16_T0.5150.93
9_H146_I0.5140.93
110_A122_A0.5100.93
78_L117_P0.5090.93
31_L34_D0.5070.93
13_V18_A0.5060.93
98_G147_S0.5000.92
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  
3u04A 2 1 100 0.013 Contact Map
3e3uA 1 0.9938 100 0.027 Contact Map
1n5nA 1 0.9938 100 0.032 Contact Map
4e9aA 1 0.9812 100 0.034 Contact Map
1rl4A 1 0.9313 100 0.035 Contact Map
2w3tA 1 0.9938 100 0.039 Contact Map
3qu1A 2 0.9938 100 0.039 Contact Map
1xeoA 1 0.9938 100 0.04 Contact Map
4dr8A 1 0.9875 100 0.042 Contact Map
1y6hA 3 0.9938 100 0.044 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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