GREMLIN Database
YPDP - Uncharacterized protein YpdP
UniProt: P54163 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 229 (200)
Sequences: 1637 (1016)
Seq/√Len: 71.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
142_L174_F5.0811.00
134_L182_V4.3031.00
161_W216_Y3.4721.00
73_L85_A2.9501.00
149_A152_R2.9001.00
131_G182_V2.8111.00
178_I182_V2.6881.00
117_A120_T2.5681.00
127_R186_G2.3611.00
134_L178_I2.3361.00
31_F85_A2.2641.00
71_D167_S2.2321.00
87_W141_T2.1981.00
176_T204_K2.1931.00
49_V106_F2.1421.00
173_L201_Y2.1181.00
189_P192_V2.1071.00
116_T119_E2.0961.00
127_R184_F2.0641.00
177_F197_F2.0111.00
89_G136_F1.9971.00
115_Q119_E1.9761.00
149_A153_I1.9271.00
74_N148_S1.9191.00
80_A83_R1.8941.00
173_L177_F1.8391.00
87_W91_S1.8251.00
146_V150_I1.8031.00
37_A66_I1.7991.00
169_A201_Y1.7931.00
142_L170_V1.7811.00
42_N132_S1.7741.00
165_G212_L1.7681.00
138_F174_F1.6931.00
139_S171_S1.6761.00
179_F183_A1.6731.00
35_G39_V1.6410.99
138_F178_I1.6260.99
39_V96_L1.6020.99
142_L146_V1.5470.99
104_L119_E1.5400.99
57_T200_T1.5290.99
70_T143_D1.4990.99
143_D171_S1.4870.99
169_A205_F1.4810.99
159_L162_L1.4690.99
63_Y139_S1.4650.99
45_V57_T1.4340.99
193_W197_F1.4180.98
164_N212_L1.4160.98
140_Q144_V1.3900.98
68_F215_A1.3890.98
32_V88_L1.3640.98
57_T180_T1.3500.98
58_L106_F1.3400.98
192_V195_H1.3350.98
150_I157_D1.3280.98
145_Y149_A1.3160.98
75_E163_R1.3110.97
212_L216_Y1.2930.97
45_V60_N1.2870.97
143_D147_Y1.2640.97
50_E53_G1.2570.97
195_H199_S1.2540.97
51_L56_A1.2470.97
164_N211_S1.2430.97
128_V183_A1.2420.97
132_S175_D1.2410.96
72_V218_A1.2130.96
161_W212_L1.2020.96
94_L133_L1.1970.96
172_Q208_S1.1880.95
33_W95_T1.1810.95
60_N200_T1.1810.95
27_K81_E1.1770.95
217_A221_M1.1640.95
211_S214_Y1.1420.94
71_D168_T1.1420.94
97_T129_A1.1350.94
181_A193_W1.1230.94
90_F182_V1.1220.94
40_C96_L1.1220.94
30_L69_A1.1210.94
185_L190_A1.1190.94
103_V118_L1.0910.93
94_L98_F1.0890.93
55_T109_A1.0890.93
112_D118_L1.0830.93
153_I158_R1.0740.92
25_F29_G1.0730.92
93_L97_T1.0670.92
160_L215_A1.0540.92
181_A185_L1.0360.91
140_Q147_Y1.0360.91
45_V200_T1.0360.91
79_P83_R1.0360.91
47_K115_Q1.0360.91
175_D179_F1.0340.91
44_Q59_G1.0260.91
202_L206_A1.0250.90
152_R214_Y1.0160.90
208_S211_S0.9940.89
104_L118_L0.9910.89
29_G33_W0.9800.88
56_A203_I0.9710.88
68_F211_S0.9680.88
63_Y67_F0.9670.88
70_T208_S0.9660.88
190_A194_L0.9470.87
44_Q100_M0.9440.86
34_I89_G0.9410.86
160_L164_N0.9400.86
188_Y196_I0.9360.86
36_F39_V0.9350.86
58_L103_V0.9260.85
36_F92_T0.9150.85
102_G138_F0.9100.84
114_S120_T0.9080.84
112_D115_Q0.9060.84
104_L122_F0.9050.84
176_T201_Y0.8980.84
143_D167_S0.8950.83
80_A152_R0.8930.83
80_A84_K0.8910.83
146_V149_A0.8910.83
155_P160_L0.8830.83
71_D216_Y0.8820.82
79_P144_V0.8720.82
140_Q143_D0.8710.82
104_L123_G0.8680.81
90_F133_L0.8670.81
43_L122_F0.8570.81
177_F181_A0.8530.80
168_T216_Y0.8510.80
153_I156_S0.8490.80
118_L121_I0.8470.80
206_A209_L0.8450.80
111_S192_V0.8440.80
191_D194_L0.8380.79
71_D143_D0.8320.79
128_V179_F0.8310.79
98_F102_G0.8270.78
63_Y164_N0.8230.78
42_N175_D0.8180.77
153_I198_I0.8180.77
160_L219_K0.8120.77
140_Q176_T0.8070.77
101_Q105_L0.8040.76
135_A175_D0.8020.76
100_M122_F0.7990.76
90_F137_I0.7940.75
103_V174_F0.7930.75
134_L138_F0.7900.75
207_V211_S0.7890.75
101_Q104_L0.7890.75
112_D121_I0.7860.75
79_P148_S0.7840.74
136_F175_D0.7830.74
63_Y143_D0.7740.73
63_Y204_K0.7700.73
146_V170_V0.7660.73
76_K222_I0.7630.72
30_L73_L0.7560.72
68_F214_Y0.7540.72
95_T99_V0.7540.72
48_T184_F0.7500.71
75_E151_R0.7410.70
196_I200_T0.7400.70
75_E160_L0.7350.70
83_R87_W0.7330.69
63_Y132_S0.7230.68
175_D204_K0.7200.68
150_I166_G0.7160.68
167_S208_S0.7130.67
48_T111_S0.7120.67
151_R223_P0.7120.67
97_T125_L0.7100.67
38_T66_I0.7050.66
147_Y164_N0.7010.66
126_P129_A0.6990.66
71_D183_A0.6930.65
58_L200_T0.6910.65
59_G93_L0.6880.64
35_G144_V0.6880.64
143_D208_S0.6850.64
142_L145_Y0.6840.64
55_T111_S0.6830.64
160_L212_L0.6800.64
165_G211_S0.6800.64
124_F178_I0.6740.63
155_P216_Y0.6730.63
96_L100_M0.6650.62
148_S211_S0.6630.62
157_D223_P0.6610.61
60_N199_S0.6610.61
79_P152_R0.6580.61
151_R163_R0.6570.61
172_Q211_S0.6560.61
90_F136_F0.6550.61
54_L92_T0.6540.61
217_A220_K0.6530.60
180_T200_T0.6500.60
142_L150_I0.6490.60
173_L197_F0.6480.60
81_E84_K0.6480.60
57_T196_I0.6470.60
39_V121_I0.6440.59
59_G141_T0.6420.59
128_V132_S0.6410.59
144_V147_Y0.6410.59
63_Y205_F0.6390.59
51_L106_F0.6380.59
168_T208_S0.6370.59
40_C95_T0.6360.58
110_S131_G0.6340.58
53_G196_I0.6310.58
45_V51_L0.6310.58
104_L115_Q0.6270.57
214_Y218_A0.6240.57
92_T118_L0.6240.57
121_I130_L0.6230.57
127_R193_W0.6210.57
188_Y192_V0.6190.56
62_M99_V0.6180.56
135_A178_I0.6170.56
128_V131_G0.6140.56
59_G170_V0.6120.56
108_P125_L0.6120.56
143_D165_G0.6120.56
41_A63_Y0.6080.55
82_A140_Q0.6070.55
33_W37_A0.6050.55
179_F184_F0.6010.54
98_F152_R0.6010.54
34_I38_T0.5980.54
160_L163_R0.5940.53
29_G88_L0.5930.53
188_Y193_W0.5930.53
34_I61_V0.5890.53
83_R151_R0.5870.52
165_G169_A0.5850.52
48_T196_I0.5830.52
215_A219_K0.5820.52
88_L92_T0.5820.52
91_S177_F0.5820.52
33_W65_T0.5770.51
125_L156_S0.5750.51
38_T136_F0.5730.51
125_L129_A0.5730.51
86_V144_V0.5730.51
79_P151_R0.5710.51
67_F71_D0.5700.50
89_G172_Q0.5670.50
186_G189_P0.5650.50
148_S152_R0.5640.50
176_T200_T0.5640.50
132_S179_F0.5630.50
151_R204_K0.5630.50
50_E110_S0.5630.50
122_F136_F0.5590.49
35_G182_V0.5580.49
63_Y211_S0.5550.49
73_L222_I0.5540.48
79_P145_Y0.5540.48
206_A210_I0.5530.48
76_K223_P0.5510.48
57_T100_M0.5510.48
46_V100_M0.5490.48
27_K73_L0.5490.48
50_E220_K0.5470.48
95_T178_I0.5470.48
187_I191_D0.5450.47
55_T93_L0.5450.47
128_V184_F0.5450.47
142_L149_A0.5430.47
144_V208_S0.5430.47
198_I202_L0.5410.47
85_A219_K0.5370.46
136_F203_I0.5350.46
180_T197_F0.5340.46
63_Y175_D0.5320.46
109_A112_D0.5300.45
60_N203_I0.5290.45
153_I159_L0.5290.45
68_F139_S0.5280.45
156_S221_M0.5280.45
46_V124_F0.5250.45
82_A86_V0.5220.45
188_Y199_S0.5210.44
34_I168_T0.5200.44
79_P147_Y0.5160.44
155_P159_L0.5120.43
201_Y205_F0.5100.43
26_G77_Y0.5090.43
40_C103_V0.5070.43
70_T147_Y0.5050.42
48_T112_D0.5030.42
72_V122_F0.5020.42
138_F198_I0.5010.42
65_T105_L0.5000.42
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  
4rfsS 1 0.7598 40.6 0.942 Contact Map
4huqS 1 0.6332 21 0.95 Contact Map
3o7qA 1 0.5764 8.6 0.958 Contact Map
4pypA 1 0.5808 8.5 0.958 Contact Map
2gfpA 2 0.5415 6.3 0.96 Contact Map
4ldsA 2 0.5415 4.6 0.963 Contact Map
4xnjA 1 0.5983 4.3 0.963 Contact Map
2k1eA 3 0.4192 3.9 0.964 Contact Map
3p5nA 2 0.5852 3.4 0.965 Contact Map
3mktA 1 0.9039 3.3 0.965 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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