GREMLIN Database
YDEM - Uncharacterized protein YdeM
UniProt: P96670 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 141 (130)
Sequences: 6405 (4159)
Seq/√Len: 364.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
50_G92_Y3.1341.00
11_V100_I2.8781.00
18_K96_E2.5271.00
105_D117_T2.4701.00
84_H134_E2.4471.00
104_L119_L2.3741.00
11_V102_E2.3541.00
7_T10_Q2.3201.00
24_I93_P2.2431.00
89_K128_V2.1641.00
102_E119_L2.0961.00
17_L23_D2.0071.00
21_K40_E1.8921.00
40_E44_S1.8831.00
102_E121_S1.8321.00
58_T91_V1.8001.00
29_G33_P1.7781.00
62_S122_T1.7531.00
123_Y129_K1.7441.00
41_E44_S1.7291.00
100_I121_S1.6971.00
13_K100_I1.6771.00
20_S23_D1.6601.00
59_L85_M1.6381.00
40_E51_I1.6291.00
119_L134_E1.6231.00
21_K51_I1.6221.00
19_V61_I1.5621.00
100_I123_Y1.5311.00
25_M29_G1.5111.00
107_Q115_I1.4821.00
96_E124_N1.4721.00
121_S129_K1.4381.00
8_I105_D1.4281.00
95_D125_Q1.4251.00
91_V130_V1.4191.00
8_I106_K1.3951.00
40_E50_G1.3941.00
124_N128_V1.3801.00
57_Q61_I1.3741.00
7_T106_K1.3731.00
104_L134_E1.3691.00
119_L132_E1.3451.00
21_K25_M1.2921.00
65_L99_T1.2761.00
110_R113_L1.2741.00
115_I136_S1.2481.00
117_T134_E1.2351.00
106_K116_L1.2121.00
86_T132_E1.2011.00
83_N117_T1.1941.00
35_Y42_K1.1891.00
19_V57_Q1.1751.00
99_T120_L1.1611.00
11_V14_T1.1601.00
22_D26_R1.1511.00
28_A54_S1.1491.00
64_K68_E1.1361.00
92_Y95_D1.1251.00
62_S99_T1.1191.00
117_T136_S1.1181.00
37_H55_G1.1111.00
58_T131_F1.1101.00
83_N134_E1.1061.00
14_T100_I1.0871.00
88_I132_E1.0761.00
122_T131_F1.0691.00
42_K45_K1.0671.00
22_D25_M1.0621.00
28_A38_V1.0501.00
26_R29_G1.0271.00
95_D124_N1.0201.00
123_Y130_V1.0031.00
91_V97_L0.9831.00
39_D42_K0.9801.00
22_D29_G0.9751.00
104_L117_T0.9691.00
6_F116_L0.9611.00
13_K98_F0.9431.00
33_P38_V0.9341.00
56_I59_L0.9171.00
99_T122_T0.9101.00
24_I53_A0.9001.00
95_D126_K0.9001.00
16_S96_E0.8961.00
58_T122_T0.8861.00
118_V137_V0.8831.00
101_V118_V0.8811.00
74_D77_I0.8771.00
82_M135_L0.8721.00
85_M133_G0.8581.00
92_Y126_K0.8541.00
50_G93_P0.8541.00
9_G102_E0.8461.00
41_E45_K0.8441.00
56_I82_M0.8391.00
56_I63_F0.8341.00
42_K46_G0.8301.00
16_S98_F0.8121.00
17_L61_I0.8071.00
30_E54_S0.7981.00
18_K94_D0.7971.00
98_F127_E0.7761.00
25_M38_V0.7711.00
124_N130_V0.7691.00
69_E101_V0.7681.00
82_M85_M0.7681.00
106_K114_G0.7671.00
83_N86_T0.7431.00
77_I80_T0.7291.00
94_D97_L0.7291.00
107_Q117_T0.7231.00
51_I93_P0.7181.00
103_V118_V0.7150.99
37_H54_S0.7110.99
23_D31_F0.7100.99
52_I92_Y0.7070.99
46_G49_N0.7060.99
103_V116_L0.7050.99
54_S57_Q0.7040.99
23_D26_R0.6970.99
121_S132_E0.6950.99
35_Y46_G0.6950.99
44_S50_G0.6910.99
44_S49_N0.6900.99
98_F123_Y0.6890.99
88_I131_F0.6860.99
62_S120_L0.6850.99
10_Q106_K0.6780.99
78_A81_E0.6760.99
6_F10_Q0.6730.99
129_K132_E0.6720.99
32_D37_H0.6660.99
66_W118_V0.6610.99
31_F64_K0.6560.99
56_I87_F0.6520.99
67_I70_G0.6460.99
62_S131_F0.6450.99
101_V120_L0.6450.99
88_I129_K0.6430.99
32_D54_S0.6390.99
63_F67_I0.6340.99
62_S133_G0.6290.99
56_I135_L0.6220.99
35_Y39_D0.6210.99
31_F57_Q0.6190.99
18_K23_D0.6140.98
24_I28_A0.6140.98
6_F103_V0.6060.98
49_N92_Y0.6040.98
6_F106_K0.6000.98
30_E57_Q0.5960.98
66_W135_L0.5940.98
34_Q42_K0.5930.98
17_L57_Q0.5920.98
123_Y127_E0.5880.98
25_M40_E0.5770.98
27_F60_A0.5730.98
26_R30_E0.5720.98
97_L122_T0.5700.97
17_L64_K0.5630.97
89_K124_N0.5620.97
97_L124_N0.5600.97
62_S135_L0.5600.97
76_I79_G0.5520.97
56_I60_A0.5520.97
59_L87_F0.5500.97
48_F90_P0.5480.97
89_K130_V0.5470.97
20_S25_M0.5460.97
44_S47_R0.5460.97
110_R115_I0.5430.97
111_N114_G0.5390.97
66_W101_V0.5390.97
124_N127_E0.5380.96
15_K98_F0.5350.96
83_N136_S0.5350.96
25_M51_I0.5340.96
53_A91_V0.5330.96
89_K126_K0.5300.96
53_A57_Q0.5270.96
67_I71_F0.5190.96
66_W120_L0.5180.96
47_R50_G0.5180.96
28_A32_D0.5160.96
25_M33_P0.5130.95
55_G58_T0.5120.95
59_L82_M0.5110.95
120_L133_G0.5060.95
70_G118_V0.5050.95
108_P112_E0.5030.95
47_R52_I0.5030.95
59_L131_F0.5020.95
27_F56_I0.5010.95
52_I90_P0.5000.95
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  
3exzA 2 0.9787 100 0.222 Contact Map
1q6wA 6 0.9858 100 0.229 Contact Map
4e3eA 3 0.9787 100 0.242 Contact Map
2bi0A 3 0.9787 100 0.242 Contact Map
4ffuA 6 0.9787 100 0.246 Contact Map
4rv2B 2 0.9433 100 0.285 Contact Map
4v12A 2 0.9433 100 0.285 Contact Map
3ir3A 2 0.8723 100 0.292 Contact Map
2c2iA 2 0.9929 99.9 0.295 Contact Map
4w78B 2 0.8936 99.9 0.3 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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