GREMLIN Database
YGGD - Uncharacterized protein YggD
UniProt: P11663 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11162
Length: 169 (162)
Sequences: 118 (66)
Seq/√Len: 5.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
56_P73_L2.9870.72
112_T116_I2.9550.71
101_Q105_P2.8910.69
14_D105_P2.8350.67
46_D56_P2.6490.62
9_V152_V2.6290.61
53_A74_I2.5780.60
46_D58_L2.4480.55
58_L73_L2.4010.54
73_L150_G2.2070.47
37_F72_R2.2060.47
6_E11_E2.2010.47
46_D54_V2.1850.47
14_D109_D2.1510.46
48_E52_Y2.1260.45
102_D130_D2.1240.45
66_D113_W2.0730.43
71_L119_V2.0500.42
116_I152_V2.0250.41
44_D72_R2.0180.41
71_L98_L1.9810.40
46_D73_L1.9300.38
81_D90_H1.8270.35
131_A163_T1.7670.34
24_K95_W1.7550.33
20_F104_T1.7160.32
92_S152_V1.6730.31
107_F158_L1.5840.28
66_D106_G1.5550.28
50_V70_A1.5440.27
46_D85_Y1.5190.27
105_P119_V1.5080.26
34_I161_T1.5070.26
40_S119_V1.4960.26
47_E86_A1.4260.24
76_A95_W1.3930.24
22_F98_L1.3570.23
17_D103_E1.3550.23
135_M140_F1.3510.23
47_E51_E1.3390.22
9_V74_I1.3290.22
128_L156_L1.3170.22
69_V108_A1.3130.22
26_A122_I1.2910.21
99_N104_T1.2700.21
17_D21_S1.2630.21
84_L129_Y1.2560.20
108_A150_G1.2540.20
69_V106_G1.2500.20
91_F146_A1.2490.20
101_Q119_V1.2370.20
132_L136_K1.2350.20
8_D153_K1.2270.20
53_A76_A1.2270.20
48_E53_A1.2220.20
9_V88_I1.2200.20
121_S159_A1.2180.20
98_L120_N1.2180.20
70_A154_T1.2060.19
51_E55_K1.1860.19
53_A110_D1.1820.19
50_V109_D1.1790.19
114_D122_I1.1770.19
30_L163_T1.1640.19
26_A156_L1.1550.18
16_Q76_A1.1500.18
159_A166_E1.1480.18
24_K104_T1.1330.18
21_S167_L1.1290.18
11_E112_T1.1030.17
56_P85_Y1.1010.17
34_I134_A1.1000.17
54_V96_H1.0910.17
39_P85_Y1.0830.17
98_L105_P1.0750.17
44_D47_E1.0700.17
23_M95_W1.0650.17
43_V71_L1.0560.16
69_V100_E1.0460.16
22_F67_I1.0450.16
82_K86_A1.0430.16
51_E114_D1.0370.16
91_F115_F1.0290.16
17_D100_E1.0280.16
93_Q114_D1.0130.16
73_L85_Y1.0100.16
142_V163_T0.9940.15
34_I133_K0.9910.15
7_D115_F0.9750.15
48_E72_R0.9670.15
37_F48_E0.9670.15
140_F153_K0.9620.15
34_I90_H0.9620.15
134_A163_T0.9610.15
153_K162_T0.9530.15
137_F154_T0.9520.15
37_F67_I0.9490.15
28_T102_D0.9390.14
132_L145_E0.9300.14
19_L108_A0.9300.14
14_D104_T0.9290.14
49_I154_T0.9070.14
80_M166_E0.9040.14
163_T167_L0.9010.14
14_D43_V0.9000.14
54_V153_K0.8990.14
17_D152_V0.8960.14
41_L138_A0.8890.14
81_D127_M0.8880.14
75_Y85_Y0.8840.14
80_M96_H0.8790.14
146_A162_T0.8620.13
66_D80_M0.8600.13
26_A86_A0.8600.13
51_E154_T0.8580.13
44_D70_A0.8580.13
52_Y110_D0.8540.13
131_A146_A0.8470.13
8_D25_T0.8430.13
19_L33_G0.8310.13
12_Q19_L0.8260.13
130_D162_T0.8240.13
106_G166_E0.8190.13
157_T161_T0.8180.13
83_W160_V0.8160.13
23_M103_E0.8140.13
111_M114_D0.8120.13
95_W145_E0.8100.12
40_S141_S0.8090.12
41_L74_I0.7880.12
14_D101_Q0.7810.12
48_E70_A0.7760.12
84_L105_P0.7730.12
90_H145_E0.7720.12
125_N128_L0.7710.12
10_L73_L0.7700.12
59_A65_D0.7680.12
5_T8_D0.7650.12
18_N125_N0.7640.12
18_N104_T0.7580.12
74_I160_V0.7550.12
42_F72_R0.7510.12
79_K156_L0.7460.12
22_F29_I0.7410.12
102_D106_G0.7240.11
88_I116_I0.7150.11
37_F44_D0.7140.11
12_Q166_E0.7110.11
41_L53_A0.7010.11
43_V154_T0.7000.11
90_H161_T0.7000.11
100_E152_V0.6950.11
9_V106_G0.6950.11
118_N140_F0.6910.11
109_D147_R0.6870.11
61_S97_Y0.6870.11
29_I93_Q0.6860.11
25_T31_L0.6850.11
56_P150_G0.6830.11
80_M90_H0.6820.11
96_H167_L0.6810.11
98_L119_V0.6810.11
15_A75_Y0.6780.11
93_Q115_F0.6760.11
49_I72_R0.6750.11
68_D159_A0.6730.11
143_W155_A0.6710.11
122_I126_A0.6680.11
34_I96_H0.6680.11
26_A82_K0.6680.11
24_K76_A0.6670.11
22_F144_S0.6640.11
27_H137_F0.6600.10
52_Y76_A0.6580.10
114_D152_V0.6570.10
41_L72_R0.6470.10
70_A144_S0.6430.10
11_E50_V0.6420.10
18_N99_N0.6410.10
86_A114_D0.6310.10
49_I131_A0.6300.10
58_L85_Y0.6300.10
25_T102_D0.6280.10
6_E108_A0.6230.10
63_P78_G0.6230.10
57_L87_D0.6230.10
62_G78_G0.6230.10
64_L87_D0.6230.10
57_L78_G0.6230.10
57_L64_L0.6230.10
57_L63_P0.6230.10
62_G87_D0.6230.10
57_L62_G0.6230.10
64_L78_G0.6230.10
63_P87_D0.6230.10
78_G87_D0.6230.10
6_E147_R0.6180.10
13_L41_L0.6150.10
116_I133_K0.6070.10
19_L128_L0.6040.10
15_A83_W0.6040.10
13_L167_L0.6030.10
115_F149_S0.6030.10
49_I149_S0.5990.10
93_Q132_L0.5930.10
22_F71_L0.5910.10
159_A164_L0.5890.10
12_Q56_P0.5870.10
11_E167_L0.5860.10
29_I113_W0.5750.09
23_M69_V0.5730.09
93_Q140_F0.5720.09
47_E76_A0.5700.09
16_Q162_T0.5690.09
19_L69_V0.5670.09
25_T162_T0.5660.09
80_M161_T0.5500.09
27_H50_V0.5490.09
16_Q160_V0.5480.09
89_T94_F0.5450.09
22_F156_L0.5440.09
36_Q106_G0.5440.09
83_W126_A0.5430.09
55_K166_E0.5420.09
53_A56_P0.5350.09
30_L157_T0.5340.09
66_D96_H0.5330.09
51_E86_A0.5330.09
33_G43_V0.5330.09
26_A160_V0.5320.09
19_L101_Q0.5310.09
38_L143_W0.5310.09
34_I81_D0.5310.09
9_V116_I0.5300.09
21_S35_R0.5260.09
32_Q104_T0.5200.09
44_D154_T0.5160.09
21_S96_H0.5150.09
24_K99_N0.5090.09
105_P153_K0.5060.09
23_M26_A0.5060.09
132_L143_W0.5040.09
127_M143_W0.5000.09
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  
3c8gA 2 0.9586 100 0.171 Contact Map
3brjA 2 0.9822 100 0.206 Contact Map
2fnaA 1 0.645 12.5 0.96 Contact Map
2ftxA 1 0.2012 9.5 0.962 Contact Map
1ylmA 2 0.716 8.6 0.963 Contact Map
1wwpA 2 0.6509 6 0.966 Contact Map
4hatC 1 0.929 5 0.967 Contact Map
4f7rA 2 0.5917 4.9 0.967 Contact Map
2qenA 1 0.6272 4.5 0.968 Contact Map
4gc8A 1 0.3373 4.3 0.968 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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