GREMLIN Database
YPBD - Uncharacterized protein YpbD
UniProt: P50730 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 189 (157)
Sequences: 2348 (2073)
Seq/√Len: 165.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
145_N148_V3.9151.00
84_T158_A3.8021.00
100_Q141_E3.3401.00
88_A154_F3.3381.00
139_M152_A3.3041.00
109_S134_F3.2771.00
113_A130_T3.2641.00
105_L137_G3.0321.00
100_Q137_G2.9491.00
105_L141_E2.8001.00
156_I160_F2.7641.00
110_L130_T2.7491.00
122_K125_L2.5891.00
113_A129_V2.5211.00
125_L129_V2.5171.00
147_F150_M2.4411.00
87_I154_F2.3941.00
140_Y149_P2.1431.00
95_F115_L2.1261.00
105_L134_F2.1241.00
138_L142_W2.1161.00
109_S130_T2.1111.00
38_Y42_I1.8551.00
89_F150_M1.8391.00
140_Y143_T1.7661.00
108_A137_G1.7441.00
69_K73_S1.6901.00
106_W134_F1.6401.00
100_Q108_A1.5941.00
139_M148_V1.4921.00
113_A133_S1.4771.00
136_L152_A1.4561.00
122_K129_V1.4401.00
109_S137_G1.4331.00
84_T87_I1.4271.00
125_L128_M1.4021.00
88_A157_D1.3721.00
128_M156_I1.3591.00
43_A47_I1.3101.00
145_N149_P1.3011.00
108_A133_S1.2901.00
98_V102_H1.2861.00
136_L149_P1.2751.00
25_L28_W1.2691.00
155_I158_A1.2681.00
84_T88_A1.2471.00
35_I39_G1.2071.00
130_T134_F1.2061.00
134_F138_L1.1931.00
19_E22_R1.1891.00
139_M149_P1.1771.00
83_L87_I1.1741.00
97_G101_T1.1261.00
39_G43_A1.1111.00
36_I40_V1.1081.00
126_F129_V1.1071.00
84_T161_A1.1071.00
103_I107_T1.0871.00
64_D68_N1.0700.99
99_L111_I1.0690.99
58_P67_I1.0680.99
25_L29_D1.0530.99
132_I136_L1.0510.99
79_H83_L1.0410.99
59_S62_Y1.0370.99
27_L30_I1.0170.99
87_I150_M1.0160.99
57_F60_H0.9900.99
100_Q105_L0.9900.99
50_D53_V0.9720.99
104_G108_A0.9690.99
122_K126_F0.9660.99
65_G68_N0.9600.99
14_G18_F0.9560.99
30_I41_S0.9560.99
97_G145_N0.9530.99
58_P61_L0.9470.99
138_L148_V0.9460.99
66_G69_K0.9440.99
6_I9_A0.9400.99
85_L154_F0.9240.98
41_S45_I0.9080.98
97_G146_L0.9060.98
108_A140_Y0.8950.98
132_I152_A0.8890.98
109_S133_S0.8880.98
37_W41_S0.8850.98
57_F62_Y0.8830.98
85_L89_F0.8820.98
113_A125_L0.8660.98
37_W51_M0.8550.97
47_I54_M0.8550.97
55_K58_P0.8470.97
51_M58_P0.8440.97
66_G70_K0.8420.97
103_I145_N0.8410.97
115_L122_K0.8390.97
6_I10_A0.8370.97
9_A12_A0.8340.97
65_G69_K0.8220.97
25_L144_G0.8180.97
154_F158_A0.8170.97
77_I81_I0.8090.97
69_K110_L0.8010.96
51_M54_M0.7980.96
29_D32_D0.7860.96
51_M55_K0.7840.96
128_M160_F0.7840.96
137_G141_E0.7820.96
109_S113_A0.7810.96
36_I43_A0.7780.96
24_V31_R0.7760.96
117_F122_K0.7700.95
65_G70_K0.7690.95
67_I75_R0.7600.95
15_L19_E0.7570.95
137_G149_P0.7550.95
44_V48_L0.7510.95
67_I71_I0.7470.95
94_L98_V0.7440.94
52_A55_K0.7430.94
47_I50_D0.7410.94
101_T104_G0.7400.94
113_A126_F0.7360.94
50_D54_M0.7320.94
57_F61_L0.7320.94
104_G129_V0.7320.94
39_G46_V0.7310.94
102_H128_M0.7290.94
7_I13_A0.7280.94
80_I154_F0.7260.94
108_A126_F0.7240.94
63_D70_K0.7240.94
58_P62_Y0.7230.94
151_T154_F0.7220.94
117_F126_F0.7220.94
144_G149_P0.7160.93
90_A132_I0.7140.93
10_A13_A0.7120.93
40_V151_T0.7060.93
80_I161_A0.6890.92
34_R40_V0.6880.92
129_V145_N0.6850.92
33_M36_I0.6840.92
150_M154_F0.6840.92
101_T140_Y0.6830.92
86_L90_A0.6790.91
99_L108_A0.6770.91
9_A13_A0.6630.90
69_K72_F0.6590.90
31_R44_V0.6580.90
98_V115_L0.6570.90
133_S137_G0.6560.90
20_D23_D0.6540.90
126_F130_T0.6500.89
33_M44_V0.6430.89
28_W31_R0.6420.89
13_A17_F0.6410.89
104_G132_I0.6380.89
93_M150_M0.6320.88
101_T142_W0.6290.88
36_I39_G0.6270.88
100_Q140_Y0.6240.87
82_F86_L0.6230.87
151_T155_I0.6230.87
48_L51_M0.6210.87
10_A16_F0.6200.87
81_I85_L0.6150.87
28_W40_V0.6150.87
74_K126_F0.6150.87
88_A165_R0.6120.86
99_L109_S0.6070.86
159_V163_Q0.6070.86
15_L21_V0.6060.86
114_A144_G0.5990.85
18_F23_D0.5980.85
72_F76_S0.5950.85
124_L128_M0.5930.85
102_H148_V0.5910.84
9_A17_F0.5890.84
7_I11_A0.5880.84
87_I157_D0.5870.84
129_V156_I0.5870.84
23_D27_L0.5860.84
125_L145_N0.5810.83
110_L151_T0.5800.83
21_V24_V0.5800.83
46_V50_D0.5760.83
10_A14_G0.5750.83
132_I156_I0.5740.83
157_D161_A0.5710.82
34_R39_G0.5700.82
40_V43_A0.5680.82
147_F151_T0.5670.82
48_L52_A0.5670.82
146_L149_P0.5630.82
11_A106_W0.5630.82
104_G125_L0.5610.81
140_Y145_N0.5600.81
74_K159_V0.5580.81
45_I49_A0.5550.81
148_V151_T0.5530.80
105_L109_S0.5520.80
128_M143_T0.5510.80
20_D24_V0.5510.80
93_M98_V0.5510.80
98_V146_L0.5500.80
88_A108_A0.5480.80
13_A18_F0.5440.79
70_K73_S0.5410.79
7_I20_D0.5380.79
24_V37_W0.5380.79
33_M47_I0.5360.78
94_L99_L0.5330.78
36_I73_S0.5320.78
39_G47_I0.5310.78
78_P83_L0.5310.78
88_A113_A0.5300.78
114_A129_V0.5300.78
66_G72_F0.5290.77
83_L88_A0.5290.77
122_K128_M0.5280.77
33_M42_I0.5250.77
7_I93_M0.5240.77
59_S63_D0.5240.77
17_F46_V0.5230.77
100_Q129_V0.5150.75
11_A35_I0.5150.75
44_V162_C0.5150.75
65_G76_S0.5130.75
97_G156_I0.5130.75
100_Q104_G0.5100.75
12_A134_F0.5080.75
33_M38_Y0.5050.74
105_L156_I0.5020.74
42_I46_V0.5000.73
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  
4cadC 1 0.8942 99.8 0.545 Contact Map
4n7wA 2 0.8571 16.9 0.933 Contact Map
4w6vA 1 0.7619 12.8 0.936 Contact Map
3zuxA 1 0.8466 11.4 0.937 Contact Map
3w4tA 1 0.8201 7.7 0.942 Contact Map
4rp9A 2 0.9788 4.7 0.948 Contact Map
4j05A 3 0.7884 4.6 0.948 Contact Map
2wswA 3 0.8042 3.8 0.95 Contact Map
4c7rA 3 0.8571 3.8 0.95 Contact Map
4eneA 2 0.9418 3.5 0.951 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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