GREMLIN Database
YVDD - LOG family protein YvdD
UniProt: O06986 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 191 (176)
Sequences: 4280 (2750)
Seq/√Len: 207.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
147_K160_L3.0301.00
3_T35_G2.8901.00
27_V31_E2.3991.00
134_N140_E2.3541.00
143_M165_S2.3101.00
19_K48_T2.2781.00
67_G125_I2.2211.00
5_C98_A2.1751.00
66_S70_S2.1671.00
82_I93_K2.1661.00
28_Y170_D2.1141.00
88_H120_W2.0941.00
32_Q177_Q2.0601.00
100_G176_M2.0401.00
166_S175_Q1.9411.00
168_R171_E1.9371.00
174_E178_N1.9161.00
93_K97_L1.8851.00
21_K24_E1.8771.00
85_N89_E1.8491.00
35_G59_T1.8421.00
51_D75_H1.8201.00
108_F118_L1.8181.00
137_G140_E1.7951.00
141_P145_M1.7931.00
166_S171_E1.7721.00
164_H175_Q1.7601.00
103_S114_L1.7391.00
66_S85_N1.7061.00
30_A58_G1.6791.00
54_M79_T1.6691.00
25_L102_I1.6591.00
17_A136_N1.6281.00
28_Y32_Q1.6051.00
114_L132_L1.5951.00
86_G89_E1.5771.00
28_Y31_E1.5741.00
131_G172_L1.5611.00
15_N136_N1.5551.00
111_Y149_S1.5211.00
48_T52_A1.4821.00
148_Y152_E1.4521.00
11_N156_N1.4371.00
31_E56_N1.4251.00
29_M34_I1.4151.00
35_G61_I1.4071.00
27_V56_N1.4061.00
23_A52_A1.4051.00
28_Y169_P1.3841.00
20_R23_A1.3661.00
23_A51_D1.3631.00
23_A48_T1.3631.00
141_P144_K1.3571.00
149_S155_S1.3401.00
30_A56_N1.3371.00
115_F146_V1.3341.00
18_Y152_E1.3321.00
92_A96_E1.3291.00
59_T79_T1.3291.00
23_A55_E1.2981.00
157_E161_K1.2801.00
16_E20_R1.2631.00
53_I58_G1.2591.00
19_K23_A1.2051.00
166_S172_L1.2021.00
61_I82_I1.1951.00
6_V26_G1.1891.00
17_A21_K1.1731.00
115_F142_M1.1701.00
61_I97_L1.1701.00
12_P19_K1.1611.00
24_E27_V1.1561.00
52_A56_N1.1491.00
22_A104_M1.1471.00
6_V49_I1.1391.00
26_G30_A1.1381.00
23_A27_V1.1301.00
15_N152_E1.1251.00
21_K135_V1.1161.00
4_I29_M1.1101.00
102_I172_L1.1101.00
59_T80_E1.1071.00
138_Y149_S1.0941.00
32_Q174_E1.0931.00
21_K134_N1.0901.00
141_P148_Y1.0821.00
93_K96_E1.0731.00
150_I155_S1.0731.00
22_A26_G1.0651.00
24_E28_Y1.0611.00
69_F74_V1.0471.00
24_E170_D1.0461.00
36_L53_I1.0271.00
20_R24_E1.0221.00
150_I160_L1.0161.00
5_C94_M1.0121.00
51_D55_E1.0081.00
4_I34_I1.0031.00
8_A41_S1.0001.00
51_D77_N0.9981.00
140_E144_K0.9961.00
91_K112_E0.9941.00
47_G51_D0.9941.00
63_V93_K0.9801.00
133_Y172_L0.9721.00
64_M71_G0.9550.99
53_I56_N0.9510.99
29_M36_L0.9360.99
75_H78_L0.9310.99
144_K147_K0.9300.99
8_A49_I0.9290.99
132_L143_M0.9270.99
26_G52_A0.9190.99
22_A45_L0.9110.99
53_I60_A0.9040.99
30_A53_I0.8990.99
147_K151_Q0.8980.99
28_Y173_I0.8970.99
25_L104_M0.8910.99
147_K157_E0.8830.99
4_I100_G0.8760.99
27_V55_E0.8750.99
88_H95_S0.8740.99
171_E175_Q0.8650.99
131_G166_S0.8530.99
5_C101_F0.8440.99
66_S69_F0.8430.99
12_P48_T0.8410.99
29_M53_I0.8400.99
26_G36_L0.8360.99
114_L130_I0.8360.99
17_A20_R0.8220.98
121_A131_G0.8180.98
18_Y154_F0.8160.98
108_F146_V0.8140.98
86_G92_A0.8140.98
95_S101_F0.8130.98
121_A126_H0.8120.98
121_A162_L0.8060.98
139_F145_M0.8060.98
104_M134_N0.8030.98
14_G152_E0.8030.98
82_I97_L0.8010.98
61_I80_E0.8000.98
121_A179_Y0.7990.98
111_Y115_F0.7990.98
108_F155_S0.7980.98
145_M149_S0.7970.98
35_G58_G0.7870.98
114_L163_I0.7840.98
95_S117_V0.7780.98
15_N20_R0.7760.98
95_S120_W0.7740.98
12_P154_F0.7680.98
122_Q159_H0.7660.98
174_E177_Q0.7600.97
143_M163_I0.7570.97
52_A55_E0.7560.97
26_G53_I0.7550.97
144_K148_Y0.7500.97
38_Y60_A0.7500.97
64_M83_E0.7490.97
119_C122_Q0.7440.97
118_L162_L0.7390.97
3_T97_L0.7370.97
136_N140_E0.7210.97
13_G16_E0.7180.96
169_P173_I0.7150.96
54_M60_A0.7120.96
88_H92_A0.7100.96
9_G154_F0.7030.96
63_V94_M0.6990.96
145_M148_Y0.6990.96
54_M75_H0.6960.96
158_S161_K0.6950.96
64_M73_V0.6940.96
138_Y141_P0.6910.96
146_V149_S0.6900.96
148_Y151_Q0.6890.95
50_A60_A0.6880.95
118_L163_I0.6830.95
14_G153_G0.6760.95
159_H162_L0.6730.95
111_Y139_F0.6720.95
68_L72_E0.6680.95
112_E116_E0.6680.95
101_F117_V0.6670.95
118_L146_V0.6650.95
18_Y135_V0.6640.95
117_V121_A0.6630.94
41_S64_M0.6630.94
131_G176_M0.6620.94
108_F159_H0.6620.94
34_I177_Q0.6610.94
126_H129_P0.6560.94
27_V52_A0.6540.94
9_G13_G0.6510.94
166_S169_P0.6480.94
134_N169_P0.6470.94
25_L29_M0.6460.94
73_V78_L0.6460.94
6_V36_L0.6380.93
42_R47_G0.6360.93
112_E119_C0.6350.93
88_H116_E0.6330.93
25_L134_N0.6330.93
80_E97_L0.6330.93
167_S171_E0.6280.93
24_E168_R0.6260.93
48_T51_D0.6250.93
6_V25_L0.6200.92
45_L104_M0.6190.92
54_M77_N0.6170.92
115_F119_C0.6150.92
91_K116_E0.6120.92
146_V160_L0.6030.91
103_S110_T0.6020.91
54_M78_L0.6010.91
66_S83_E0.6000.91
171_E174_E0.5940.91
64_M81_L0.5900.90
101_F129_P0.5840.90
9_G14_G0.5800.90
150_I157_E0.5800.90
13_G153_G0.5790.89
65_P87_M0.5770.89
30_A52_A0.5720.89
117_V129_P0.5670.88
98_A101_F0.5630.88
64_M72_E0.5610.88
170_D174_E0.5570.88
21_K104_M0.5560.87
60_A78_L0.5550.87
162_L179_Y0.5530.87
38_Y50_A0.5520.87
95_S112_E0.5460.87
140_E147_K0.5450.86
131_G173_I0.5450.86
119_C123_I0.5440.86
21_K25_L0.5400.86
78_L81_L0.5390.86
120_W125_I0.5380.86
18_Y45_L0.5360.86
94_M103_S0.5350.85
16_E19_K0.5330.85
84_V93_K0.5320.85
143_M147_K0.5300.85
19_K45_L0.5250.84
121_A127_Q0.5230.84
63_V84_V0.5170.83
38_Y44_G0.5140.83
22_A49_I0.5130.83
89_E92_A0.5130.83
116_E120_W0.5120.83
136_N152_E0.5100.83
4_I102_I0.5080.82
3_T37_V0.5050.82
8_A64_M0.5050.82
51_D54_M0.5040.82
114_L118_L0.5020.82
88_H112_E0.5020.82
18_Y105_P0.5010.82
147_K150_I0.5010.82
134_N172_L0.5000.81
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  
5ajtA 2 0.9948 100 0.151 Contact Map
1ydhA 2 0.9424 100 0.192 Contact Map
1t35A 5 0.9634 100 0.205 Contact Map
2a33A 2 0.9058 100 0.209 Contact Map
3bq9A 3 0.9634 100 0.233 Contact Map
3gh1A 3 0.9686 100 0.24 Contact Map
3sbxA 2 0.9267 100 0.245 Contact Map
1wekA 5 0.9319 100 0.271 Contact Map
3quaA 2 0.9319 100 0.295 Contact Map
1wehA 1 0.8901 100 0.332 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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