GREMLIN Database
YDBS - UPF0699 transmembrane protein YdbS
UniProt: P96615 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 159 (141)
Sequences: 4423 (3726)
Seq/√Len: 313.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
110_Q138_M3.3161.00
140_E143_R3.2601.00
108_T120_A3.0401.00
87_Q95_R2.8271.00
120_A141_A2.6881.00
137_E140_E2.6151.00
13_G17_W2.5191.00
13_G16_V2.5071.00
104_Q127_A2.2021.00
114_L135_A2.1791.00
80_H83_E2.0021.00
143_R147_S1.9961.00
105_H125_S1.9821.00
85_D95_R1.9501.00
14_L17_W1.9471.00
120_A138_M1.9171.00
12_D15_K1.9161.00
110_Q120_A1.7941.00
138_M142_D1.7771.00
66_I70_V1.7721.00
103_V124_I1.7371.00
80_H85_D1.6831.00
78_E85_D1.6751.00
110_Q115_K1.6731.00
118_N138_M1.6611.00
111_G114_L1.6521.00
79_V100_M1.6421.00
67_I71_R1.6421.00
136_L141_A1.5381.00
17_W20_Q1.4831.00
76_R87_Q1.4671.00
109_S123_K1.4631.00
70_V90_I1.4541.00
121_T132_S1.4231.00
75_W86_I1.3971.00
17_W21_E1.3971.00
28_C32_V1.3831.00
69_K73_K1.3691.00
75_W134_P1.3631.00
114_L121_T1.3441.00
108_T145_R1.3371.00
37_V40_Y1.3121.00
84_I124_I1.3081.00
51_V55_V1.2851.00
74_V93_V1.2471.00
147_S151_L1.2411.00
23_I27_V1.2381.00
88_S96_V1.2321.00
121_T134_P1.2261.00
12_D17_W1.2151.00
52_L56_W1.2131.00
16_V19_L1.2091.00
35_V39_S1.2051.00
83_E97_I1.2021.00
67_I90_I1.1931.00
28_C31_I1.1891.00
55_V59_G1.1721.00
70_V74_V1.1621.00
86_I131_H1.1561.00
142_D146_D1.1511.00
13_G19_L1.1301.00
62_V66_I1.1131.00
113_L116_K1.1021.00
74_V90_I1.0871.00
33_I37_V1.0791.00
13_G18_R1.0651.00
47_W51_V1.0491.00
98_V126_T1.0421.00
145_R150_R1.0351.00
108_T142_D1.0261.00
67_I70_V1.0211.00
84_I133_I1.0201.00
16_V20_Q1.0111.00
107_D123_K1.0071.00
139_E143_R1.0061.00
112_P116_K1.0021.00
18_R69_K0.9961.00
107_D125_S0.9921.00
114_L119_L0.9831.00
79_V147_S0.9791.00
25_S28_C0.9771.00
96_V105_H0.9681.00
99_P102_R0.9521.00
14_L69_K0.9401.00
34_A38_L0.9361.00
87_Q93_V0.9241.00
14_L21_E0.9181.00
13_G20_Q0.9131.00
18_R65_F0.9061.00
21_E24_I0.8911.00
119_L135_A0.8901.00
98_V131_H0.8831.00
15_K18_R0.8821.00
140_E147_S0.8791.00
85_D97_I0.8781.00
12_D16_V0.8711.00
72_H88_S0.8701.00
32_V39_S0.8691.00
125_S129_T0.8631.00
146_D150_R0.8611.00
77_Y86_I0.8581.00
55_V58_L0.8581.00
106_V145_R0.8571.00
106_V141_A0.8551.00
20_Q23_I0.8521.00
100_M151_L0.8461.00
103_V148_I0.8441.00
122_V141_A0.8421.00
24_I27_V0.8371.00
21_E37_V0.8331.00
29_L32_V0.8241.00
65_F69_K0.8161.00
38_L41_Y0.8061.00
75_W115_K0.7941.00
58_L62_V0.7911.00
16_V23_I0.7831.00
12_D23_I0.7821.00
16_V119_L0.7640.99
119_L136_L0.7600.99
88_S94_T0.7600.99
70_V91_F0.7490.99
108_T141_A0.7480.99
50_G54_A0.7470.99
71_R88_S0.7430.99
14_L18_R0.7420.99
102_R127_A0.7340.99
15_K23_I0.7320.99
83_E102_R0.7270.99
14_L19_L0.7210.99
38_L42_F0.7190.99
46_Y49_S0.7160.99
16_V21_E0.7120.99
139_E142_D0.7080.99
100_M148_I0.7070.99
109_S121_T0.7050.99
104_Q125_S0.7040.99
125_S130_V0.7000.99
71_R98_V0.6890.99
18_R21_E0.6870.99
82_H100_M0.6870.99
45_P48_I0.6860.99
25_S32_V0.6810.99
49_S53_G0.6810.99
105_H129_T0.6800.99
148_I151_L0.6730.99
25_S61_I0.6710.99
103_V129_T0.6610.98
142_D145_R0.6490.98
55_V62_V0.6460.98
26_A29_L0.6390.98
126_T136_L0.6300.98
144_L148_I0.6300.98
63_T66_I0.6130.97
89_G148_I0.6110.97
80_H100_M0.6110.97
46_Y52_L0.6070.97
64_V68_P0.6030.97
133_I136_L0.5930.97
36_A40_Y0.5900.97
63_T67_I0.5890.97
100_M104_Q0.5880.97
78_E108_T0.5880.97
103_V152_A0.5870.97
108_T122_V0.5850.97
103_V131_H0.5850.97
17_W23_I0.5840.97
128_A131_H0.5830.97
100_M131_H0.5800.96
27_V30_L0.5790.96
37_V41_Y0.5760.96
104_Q110_Q0.5760.96
79_V144_L0.5760.96
25_S29_L0.5760.96
33_I36_A0.5740.96
81_E100_M0.5730.96
82_H99_P0.5730.96
105_H124_I0.5710.96
45_P53_G0.5700.96
145_R149_S0.5700.96
127_A141_A0.5680.96
49_S61_I0.5680.96
53_G57_L0.5660.96
12_D19_L0.5640.96
73_K76_R0.5610.96
104_Q126_T0.5600.96
106_V148_I0.5550.95
125_S131_H0.5520.95
34_A41_Y0.5490.95
94_T129_T0.5420.95
31_I35_V0.5400.95
35_V40_Y0.5370.95
126_T144_L0.5350.94
77_Y90_I0.5330.94
84_I101_V0.5330.94
77_Y119_L0.5320.94
110_Q124_I0.5300.94
79_V84_I0.5290.94
99_P111_G0.5280.94
97_I100_M0.5280.94
75_W88_S0.5280.94
86_I96_V0.5260.94
127_A133_I0.5230.94
71_R90_I0.5220.94
13_G135_A0.5160.93
54_A58_L0.5140.93
83_E100_M0.5130.93
47_W52_L0.5060.93
75_W85_D0.5050.93
68_P71_R0.5010.92
77_Y136_L0.5010.92
96_V129_T0.5000.92
34_A42_F0.5000.92
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  
4i0uA 4 0.4717 5.1 0.925 Contact Map
4ev6A 3 0.4654 4.1 0.928 Contact Map
3hsaA 3 0.6792 3.8 0.929 Contact Map
4khbD 1 0.6101 3.1 0.932 Contact Map
4ix7A 1 0.5094 3 0.933 Contact Map
4wxaA 1 0.2327 2.7 0.934 Contact Map
4e6zA 1 0.3145 2.5 0.936 Contact Map
2zqeA 1 0.2013 2.2 0.938 Contact Map
4y93A 1 0.6604 2.1 0.938 Contact Map
3encA 2 0.2327 2.1 0.938 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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