GREMLIN Database
YYBD - UPF0039 protein YybD
UniProt: P37500 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 147 (130)
Sequences: 3330 (2555)
Seq/√Len: 224.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
94_E122_Y2.9311.00
60_A93_L2.8891.00
114_A124_T2.6481.00
108_H129_F2.3751.00
20_K34_E2.1561.00
92_A95_R2.1051.00
18_I75_C1.9671.00
87_K120_L1.9161.00
14_T51_Y1.8381.00
128_E135_P1.8071.00
94_E141_K1.7801.00
18_I77_L1.7721.00
57_V80_Y1.7651.00
111_T128_E1.7461.00
114_A137_V1.7411.00
63_R72_E1.7281.00
90_V120_L1.7201.00
50_A85_L1.7181.00
49_L56_P1.6941.00
125_A138_L1.6561.00
12_L16_F1.6261.00
104_A140_T1.6251.00
21_A77_L1.6221.00
71_L90_V1.6201.00
51_Y56_P1.5801.00
58_G76_I1.5781.00
59_T75_C1.5701.00
21_A25_E1.5531.00
50_A58_G1.5411.00
125_A140_T1.5121.00
118_E124_T1.5041.00
96_I100_Q1.5001.00
94_E105_F1.4931.00
87_K119_K1.4731.00
114_A118_E1.4431.00
130_M133_G1.4271.00
129_F138_L1.4131.00
115_G118_E1.3751.00
87_K91_D1.3461.00
33_D132_D1.3251.00
108_H138_L1.3251.00
130_M135_P1.3221.00
17_E21_A1.3211.00
55_V79_S1.3121.00
126_S138_L1.2981.00
29_C134_I1.2971.00
15_A49_L1.2901.00
29_C132_D1.2761.00
27_Q110_Q1.2721.00
48_I93_L1.2601.00
96_I99_E1.2591.00
48_I96_I1.2521.00
60_A74_I1.2501.00
74_I90_V1.2371.00
20_K31_I1.2231.00
52_H80_Y1.2191.00
68_T106_K1.2091.00
108_H131_L1.2081.00
106_K138_L1.2001.00
46_Q96_I1.1971.00
16_F35_F1.1841.00
65_V70_K1.1801.00
124_T137_V1.1461.00
88_V92_A1.1451.00
52_H57_V1.1401.00
15_A59_T1.1141.00
20_K24_V1.1111.00
21_A33_D1.0741.00
70_K106_K1.0241.00
106_K140_T1.0231.00
98_K141_K1.0201.00
46_Q100_Q0.9991.00
62_V97_V0.9961.00
68_T104_A0.9801.00
37_E40_T0.9781.00
111_T114_A0.9761.00
110_Q136_H0.9701.00
69_G102_I0.9701.00
71_L74_I0.9681.00
20_K35_F0.9661.00
91_D95_R0.9641.00
80_Y83_F0.9551.00
14_T17_E0.9461.00
10_Q14_T0.9391.00
24_V31_I0.9371.00
13_H16_F0.9361.00
40_T45_C0.9291.00
26_E81_R0.9221.00
20_K25_E0.9140.99
104_A142_Q0.9110.99
97_V105_F0.8940.99
95_R99_E0.8890.99
109_G139_M0.8780.99
38_F63_R0.8610.99
51_Y54_N0.8610.99
64_I102_I0.8570.99
52_H83_F0.8510.99
58_G89_I0.8510.99
48_I60_A0.8380.99
113_A116_F0.8350.99
30_P33_D0.8310.99
92_A96_I0.8270.99
9_E13_H0.8250.99
60_A89_I0.8190.99
86_G116_F0.8100.99
71_L93_L0.8090.99
63_R70_K0.8020.99
25_E30_P0.8010.99
70_K108_H0.7980.99
70_K107_L0.7850.98
55_V77_L0.7760.98
57_V85_L0.7750.98
58_G85_L0.7700.98
52_H55_V0.7610.98
91_D120_L0.7540.98
88_V91_D0.7520.98
111_T135_P0.7440.98
122_Y141_K0.7440.98
45_C63_R0.7430.98
123_R142_Q0.7430.98
16_F20_K0.7420.98
18_I56_P0.7380.98
77_L80_Y0.7290.97
17_E37_E0.7200.97
10_Q40_T0.7100.97
21_A79_S0.7100.97
11_D49_L0.7030.97
62_V96_I0.7000.97
84_G87_K0.6920.96
105_F122_Y0.6910.96
85_L88_V0.6910.96
111_T137_V0.6730.96
29_C131_L0.6720.96
30_P34_E0.6690.96
40_T44_D0.6680.96
45_C64_I0.6660.96
124_T128_E0.6650.96
48_I92_A0.6640.96
50_A88_V0.6620.96
11_D15_A0.6570.95
23_F26_E0.6530.95
71_L122_Y0.6530.95
26_E78_K0.6500.95
47_H59_T0.6500.95
39_D72_E0.6490.95
71_L105_F0.6470.95
18_I59_T0.6460.95
23_F110_Q0.6440.95
20_K30_P0.6310.94
69_G97_V0.6280.94
94_E120_L0.6280.94
24_V34_E0.6270.94
107_L117_Y0.6270.94
95_R98_K0.6260.94
83_F86_G0.6100.93
89_I92_A0.6060.93
48_I62_V0.6030.93
58_G86_G0.6000.93
71_L107_L0.6000.93
50_A57_V0.6000.93
13_H35_F0.5820.91
131_L134_I0.5780.91
118_E123_R0.5720.91
72_E110_Q0.5690.90
76_I85_L0.5590.90
13_H37_E0.5580.90
23_F27_Q0.5560.89
12_L39_D0.5550.89
33_D131_L0.5500.89
80_Y85_L0.5500.89
107_L113_A0.5490.89
107_L139_M0.5480.89
26_E110_Q0.5450.88
22_V81_R0.5390.88
112_Q134_I0.5380.88
66_G70_K0.5350.88
86_G113_A0.5340.87
38_F44_D0.5340.87
82_K87_K0.5320.87
61_R73_R0.5310.87
24_V30_P0.5300.87
37_E44_D0.5260.87
63_R69_G0.5200.86
91_D119_K0.5160.86
26_E73_R0.5160.86
73_R110_Q0.5140.85
109_G117_Y0.5130.85
27_Q73_R0.5120.85
69_G101_G0.5110.85
13_H17_E0.5070.85
13_H40_T0.5040.84
27_Q136_H0.5040.84
14_T56_P0.5020.84
101_G104_A0.5000.84
23_F73_R0.5000.84
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  
2g0bA 4 0.9864 100 0.407 Contact Map
1q2yA 1 0.9456 99.9 0.427 Contact Map
1kzfA 1 0.9048 99.9 0.436 Contact Map
3p2hA 1 0.932 99.9 0.443 Contact Map
2jdcA 1 0.932 99.9 0.45 Contact Map
1xebA 2 0.9524 99.9 0.452 Contact Map
1ro5A 5 0.9864 99.9 0.455 Contact Map
3efaA 2 0.9592 99.9 0.458 Contact Map
1y9wA 2 0.9388 99.8 0.572 Contact Map
1yvkA 3 0.9252 99.7 0.591 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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