GREMLIN Database
YWIB - Uncharacterized beta-barrel protein YwiB
UniProt: O07624 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 142 (133)
Sequences: 743 (651)
Seq/√Len: 56.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
55_I66_M3.5841.00
78_V81_A3.3851.00
56_V65_V3.2431.00
40_Y57_K3.1721.00
82_S97_K3.0761.00
44_Y53_K3.0501.00
35_K40_Y2.8811.00
32_Y39_V2.4541.00
105_S114_I2.3341.00
82_S99_S2.1971.00
107_L112_G2.1781.00
63_V116_I2.0541.00
12_K133_T1.9161.00
67_R112_G1.7510.99
33_Y40_Y1.7400.99
41_L136_Y1.7200.99
97_K121_H1.7100.99
41_L58_V1.6980.99
115_S133_T1.6850.99
100_T103_I1.6760.99
77_F100_T1.6700.99
11_V134_I1.6610.99
13_S130_H1.6380.99
77_F116_I1.6260.99
11_V43_Y1.6250.99
9_L30_G1.6090.99
101_K119_D1.5200.98
12_K25_E1.5090.98
54_T67_R1.4970.98
75_Q98_T1.4860.98
113_R135_T1.4690.97
46_E51_K1.4610.97
120_M127_E1.4530.97
15_I130_H1.4450.97
14_V23_V1.3930.96
116_I132_M1.3830.96
62_E78_V1.3780.96
78_V83_T1.3530.96
117_A131_N1.3180.95
72_K88_K1.2690.94
112_G136_Y1.2660.94
108_D111_K1.2540.93
100_T116_I1.2270.93
10_H27_R1.2140.92
59_S62_E1.2100.92
64_L74_N1.2050.92
28_T46_E1.1970.92
36_Q40_Y1.1860.91
34_V39_V1.1840.91
5_T33_Y1.1580.90
35_K57_K1.1500.90
102_S117_A1.1420.90
119_D129_L1.1420.90
104_Q113_R1.1320.89
17_D20_N1.1300.89
13_S24_I1.1250.89
63_V92_G1.1230.89
120_M130_H1.1220.89
34_V109_E1.1170.89
120_M128_H1.1040.88
38_K59_S1.0930.88
34_V61_G1.0880.87
48_D52_V1.0790.87
54_T132_M1.0760.87
96_L122_V1.0740.87
7_I41_L1.0690.86
24_I103_I1.0660.86
102_S115_S1.0530.86
33_Y57_K1.0370.85
9_L82_S1.0340.85
105_S136_Y1.0080.83
122_V127_E1.0070.83
34_V37_N0.9680.80
43_Y92_G0.9600.80
45_E67_R0.9560.80
35_K38_K0.9550.80
77_F85_A0.9460.79
96_L124_D0.9420.79
58_V92_G0.9370.78
14_V21_Q0.9340.78
29_T46_E0.9300.78
73_M98_T0.9290.78
85_A98_T0.9190.77
101_K117_A0.9080.76
96_L121_H0.9030.76
77_F118_Y0.8970.75
45_E69_G0.8880.74
41_L56_V0.8700.73
63_V103_I0.8680.73
22_E128_H0.8670.73
64_L128_H0.8630.72
16_E114_I0.8500.71
13_S128_H0.8440.71
51_K70_A0.8380.70
112_G130_H0.8330.70
18_D137_E0.8300.69
105_S112_G0.8170.68
48_D51_K0.8060.67
42_S53_K0.7970.66
61_G78_V0.7950.66
16_E94_L0.7940.66
87_Y118_Y0.7930.66
22_E45_E0.7870.65
33_Y42_S0.7820.65
47_H52_V0.7760.64
21_Q94_L0.7750.64
8_T137_E0.7700.63
7_I110_E0.7660.63
50_G91_F0.7620.63
46_E49_L0.7600.62
15_I94_L0.7590.62
52_V71_V0.7510.61
79_T102_S0.7380.60
84_I97_K0.7320.60
43_Y75_Q0.7240.59
89_M132_M0.7240.59
7_I26_F0.7180.58
14_V103_I0.7150.58
8_T52_V0.7120.57
11_V30_G0.7080.57
20_N63_V0.7010.56
58_V63_V0.6990.56
106_D113_R0.6830.54
71_V136_Y0.6780.54
8_T29_T0.6750.53
32_Y48_D0.6660.52
68_S72_K0.6600.52
57_K105_S0.6520.51
85_A116_I0.6510.51
58_V111_K0.6500.51
49_L70_A0.6490.51
48_D65_V0.6460.50
41_L132_M0.6420.50
38_K60_E0.6420.50
93_E108_D0.6380.49
91_F104_Q0.6370.49
94_L98_T0.6330.49
94_L103_I0.6280.48
104_Q108_D0.6210.48
62_E76_R0.6200.47
104_Q109_E0.6170.47
14_V131_N0.6100.46
52_V70_A0.6080.46
63_V114_I0.6070.46
6_P29_T0.6050.46
13_S136_Y0.6050.46
37_N60_E0.6040.46
75_Q92_G0.6020.45
46_E50_G0.6000.45
123_G132_M0.6000.45
89_M92_G0.6000.45
13_S91_F0.5990.45
64_L76_R0.5970.45
10_H135_T0.5960.45
42_S55_I0.5950.45
33_Y36_Q0.5940.45
85_A128_H0.5920.44
10_H96_L0.5910.44
101_K129_L0.5910.44
94_L127_E0.5900.44
7_I111_K0.5820.43
22_E84_I0.5820.43
39_V111_K0.5770.43
8_T48_D0.5770.43
88_K93_E0.5760.43
74_N123_G0.5750.43
28_T43_Y0.5740.42
54_T64_L0.5730.42
13_S98_T0.5730.42
35_K66_M0.5680.42
72_K120_M0.5680.42
71_V93_E0.5670.42
67_R130_H0.5580.41
87_Y91_F0.5540.40
5_T13_S0.5530.40
63_V68_S0.5520.40
65_V137_E0.5490.40
95_E99_S0.5490.40
43_Y107_L0.5470.40
121_H125_E0.5470.40
75_Q110_E0.5390.39
61_G79_T0.5370.39
66_M127_E0.5340.38
58_V105_S0.5340.38
28_T112_G0.5340.38
30_G55_I0.5340.38
15_I68_S0.5290.38
37_N101_K0.5240.37
78_V82_S0.5240.37
12_K23_V0.5190.37
15_I82_S0.5160.36
50_G80_G0.5160.36
64_L112_G0.5130.36
84_I94_L0.5100.36
76_R84_I0.5080.36
24_I130_H0.5070.36
58_V114_I0.5060.35
54_T91_F0.5060.35
52_V82_S0.5010.35
25_E98_T0.5000.35
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  
1r0uA 1 0.9577 100 0.116 Contact Map
3mx7A 1 0.6338 7.4 0.936 Contact Map
2c1lA 2 0.7535 4.2 0.943 Contact Map
4a60A 1 0.7042 4.1 0.943 Contact Map
3zigA 2 0.4225 3.7 0.944 Contact Map
3wbgA 1 0.7113 3.7 0.945 Contact Map
1kmtA 1 0.7958 3.6 0.945 Contact Map
4aznA 1 0.7113 3.6 0.945 Contact Map
4l3aA 1 0.8732 3.5 0.945 Contact Map
3fyfA 2 0.8521 3.3 0.946 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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