GREMLIN Database
YGDD - UPF0382 inner membrane protein YgdD
UniProt: P0ADR2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11793
Length: 131 (118)
Sequences: 1605 (1180)
Seq/√Len: 108.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
15_F110_L4.5071.00
41_Q45_E3.1131.00
6_M73_S2.5211.00
76_L112_G2.4371.00
13_S51_T2.3781.00
19_A110_L2.3711.00
14_G51_T2.1791.00
14_G53_A2.1521.00
32_M91_A2.0141.00
53_A76_L2.0121.00
15_F114_A2.0041.00
24_G40_I1.9751.00
75_F108_S1.9241.00
10_A55_L1.8401.00
8_I117_L1.7971.00
39_W87_L1.7831.00
97_L100_F1.7641.00
47_Q88_Y1.7401.00
75_F111_A1.7291.00
29_S35_V1.7161.00
68_W115_L1.6811.00
86_S102_T1.6451.00
80_T109_F1.6341.00
9_F77_A1.6111.00
10_A51_T1.5931.00
45_E49_F1.5901.00
48_A52_L1.5891.00
114_A118_V1.5281.00
90_L99_A1.5041.00
57_L76_L1.4561.00
49_F52_L1.4491.00
40_I43_G1.4391.00
17_F48_A1.4261.00
13_S77_A1.4251.00
32_M37_M1.3961.00
21_G46_Y1.3871.00
10_A14_G1.2990.99
11_A117_L1.2640.99
71_W115_L1.2580.99
35_V38_G1.2440.99
8_I121_I1.2340.99
71_W74_V1.2330.99
100_F104_V1.2180.99
82_L100_F1.2160.99
38_G41_Q1.2120.99
9_F13_S1.1880.99
78_L108_S1.1870.99
36_E39_W1.1840.99
36_E91_A1.1740.99
44_L47_Q1.1660.99
75_F112_G1.1450.98
25_A42_T1.1440.98
117_L121_I1.1250.98
33_G36_E1.1040.98
68_W119_G1.0960.98
12_I16_I1.0670.98
50_H113_W1.0380.97
24_G47_Q1.0320.97
10_A58_A1.0290.97
35_V39_W1.0110.97
50_H109_F1.0040.97
8_I120_A0.9910.96
98_W101_V0.9870.96
51_T80_T0.9820.96
107_V111_A0.9810.96
104_V108_S0.9780.96
39_W90_L0.9670.96
4_R8_I0.9600.95
52_L56_G0.9560.95
11_A116_M0.9520.95
40_I45_E0.9490.95
24_G27_V0.9180.94
34_A38_G0.9160.94
12_I117_L0.9070.94
23_F27_V0.8920.93
86_S90_L0.8870.93
18_V50_H0.8810.93
28_L40_I0.8690.92
40_I47_Q0.8380.91
53_A112_G0.8300.91
111_A115_L0.8280.90
17_F49_F0.8250.90
82_L104_V0.8240.90
90_L100_F0.8170.90
27_V32_M0.8130.90
89_C93_S0.8030.89
7_L58_A0.8020.89
66_S69_F0.7960.89
50_H80_T0.7880.88
43_G85_G0.7830.88
6_M74_V0.7830.88
31_T67_I0.7830.88
36_E94_H0.7730.87
15_F19_A0.7690.87
14_G48_A0.7670.87
69_F119_G0.7640.87
61_M69_F0.7640.87
17_F51_T0.7440.85
74_V78_L0.7370.85
15_F117_L0.7350.84
23_F87_L0.7330.84
6_M10_A0.7310.84
72_S119_G0.7270.84
89_C100_F0.7230.83
13_S80_T0.7190.83
16_I20_L0.7170.83
68_W118_V0.7130.83
57_L69_F0.7090.82
4_R120_A0.6990.81
39_W91_A0.6940.81
7_L120_A0.6910.81
72_S116_M0.6850.80
6_M9_F0.6840.80
10_A56_G0.6780.79
67_I71_W0.6670.78
118_V122_R0.6650.78
71_W75_F0.6590.77
76_L109_F0.6520.77
59_V63_R0.6500.76
18_V22_A0.6460.76
82_L86_S0.6400.75
87_L100_F0.6390.75
54_I73_S0.6380.75
55_L59_V0.6370.75
20_L40_I0.6320.74
38_G42_T0.6310.74
95_L101_V0.6180.73
26_H103_P0.6180.73
14_G49_F0.6170.73
90_L102_T0.6170.73
28_L92_L0.6160.73
57_L60_A0.6140.72
72_S112_G0.6090.72
67_I70_Y0.6070.71
87_L93_S0.6010.71
68_W71_W0.6010.71
29_S84_S0.5990.70
40_I44_L0.5990.70
5_F31_T0.5970.70
40_I52_L0.5940.70
86_S101_V0.5940.70
44_L48_A0.5930.70
10_A48_A0.5890.69
43_G84_S0.5860.69
60_A116_M0.5810.68
13_S47_Q0.5810.68
100_F108_S0.5790.68
44_L51_T0.5780.68
45_E116_M0.5780.68
104_V107_V0.5730.67
102_T107_V0.5690.67
39_W44_L0.5680.66
23_F28_L0.5670.66
20_L27_V0.5640.66
13_S17_F0.5630.66
57_L73_S0.5620.66
23_F46_Y0.5610.65
43_G91_A0.5560.65
85_G118_V0.5510.64
15_F18_V0.5420.63
55_L58_A0.5420.63
56_G59_V0.5410.63
23_F29_S0.5400.63
11_A37_M0.5400.63
82_L108_S0.5360.62
54_I84_S0.5290.61
36_E96_R0.5270.61
9_F73_S0.5250.60
75_F115_L0.5240.60
58_A120_A0.5240.60
44_L49_F0.5130.59
90_L96_R0.5130.59
58_A62_Q0.5100.58
7_L60_A0.5090.58
99_A107_V0.5080.58
90_L93_S0.5010.57
6_M58_A0.5000.57
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  
2gsmA 1 0.9847 38.2 0.919 Contact Map
2yevA 1 0.9847 31.2 0.923 Contact Map
3ayfA 2 0.9924 27 0.926 Contact Map
1v54A 1 0.9847 25.5 0.926 Contact Map
3mk7A 1 0.9847 22.9 0.928 Contact Map
1fftA 1 0.9466 18.7 0.931 Contact Map
3s8fA 1 0.9847 17.8 0.931 Contact Map
3wfdB 1 0.8931 8 0.941 Contact Map
2kluA 1 0.2824 4.9 0.947 Contact Map
4p6vD 1 0.7405 4.8 0.947 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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