GREMLIN Database
YPMB - Uncharacterized protein YpmB
UniProt: P54396 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 161 (150)
Sequences: 406 (347)
Seq/√Len: 28.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
99_G150_F6.5581.00
109_I134_V4.3891.00
149_D152_T3.8531.00
105_A121_V3.3081.00
102_E106_A3.2871.00
105_A148_V2.9451.00
100_I105_A2.9241.00
68_V82_W2.8041.00
73_D77_T2.3260.99
124_A145_L2.2930.99
80_Y96_A2.2530.98
51_L81_V2.2110.98
60_F133_E2.0410.97
62_G147_Y2.0380.97
37_G57_V1.9550.96
62_G133_E1.9390.96
129_V149_D1.9080.95
126_E147_Y1.8640.95
82_W94_K1.8570.95
51_L79_L1.8390.94
53_H72_T1.8140.94
123_L130_L1.7540.93
147_Y156_L1.6810.91
125_R130_L1.6720.91
81_V150_F1.5450.87
60_F126_E1.5180.86
44_E91_I1.5060.86
83_V91_I1.4540.84
58_E70_K1.3880.81
30_A123_L1.3760.80
64_E98_E1.3150.77
19_V134_V1.3130.77
41_A57_V1.3130.77
42_A69_V1.3100.76
73_D79_L1.3050.76
124_A133_E1.3020.76
76_G100_I1.2940.76
62_G82_W1.2860.75
62_G126_E1.2720.74
106_A110_K1.2570.73
52_A74_K1.2500.73
62_G131_L1.2420.73
9_T14_I1.2220.71
57_V83_V1.2120.71
48_E141_G1.1950.70
137_L145_L1.1850.69
82_W147_Y1.1660.68
7_I11_I1.1640.67
43_A47_K1.1620.67
99_G123_L1.1600.67
123_L150_F1.1600.67
126_E157_K1.1500.67
74_K90_K1.1360.66
57_V69_V1.1260.65
100_I104_K1.1150.64
74_K139_K1.1080.64
60_F66_Y1.0970.63
124_A131_L1.0890.62
135_T144_S1.0770.61
59_T82_W1.0650.60
60_F124_A1.0540.60
146_S158_N1.0510.59
138_D144_S1.0500.59
109_I150_F1.0490.59
113_G116_S1.0140.57
37_G65_K1.0060.56
102_E121_V1.0000.56
136_Y146_S0.9790.54
77_T95_E0.9640.53
21_L25_S0.9600.52
106_A118_Q0.9520.52
46_K61_V0.9490.52
54_V78_A0.9490.52
37_G67_Y0.9440.51
100_I148_V0.9430.51
137_L152_T0.9390.51
109_I116_S0.9370.51
70_K80_Y0.9350.51
103_D114_L0.9340.50
66_Y83_V0.9290.50
126_E131_L0.9260.50
27_Y46_K0.9200.49
18_A60_F0.9150.49
68_V124_A0.9080.48
138_D142_Q0.9050.48
49_T71_G0.8990.48
10_V47_K0.8930.47
15_I148_V0.8910.47
80_Y123_L0.8870.47
110_K118_Q0.8830.47
18_A74_K0.8770.46
106_A152_T0.8740.46
109_I113_G0.8710.46
11_I63_K0.8660.45
41_A83_V0.8600.45
136_Y143_Y0.8600.45
107_K110_K0.8550.44
120_E135_T0.8550.44
129_V156_L0.8500.44
82_W123_L0.8500.44
135_T143_Y0.8440.44
119_K143_Y0.8390.43
50_D73_D0.8370.43
39_E43_A0.8360.43
97_K134_V0.8340.43
8_F15_I0.8330.43
16_F95_E0.8290.42
52_A107_K0.8270.42
61_V142_Q0.8210.42
86_D139_K0.8160.41
103_D141_G0.8150.41
97_K101_S0.8140.41
51_L71_G0.8110.41
33_Q93_S0.7910.40
30_A150_F0.7880.39
79_L93_S0.7850.39
94_K123_L0.7700.38
20_L124_A0.7690.38
7_I148_V0.7680.38
92_L125_R0.7580.37
105_A134_V0.7530.37
104_K117_K0.7500.37
10_V16_F0.7480.36
138_D147_Y0.7420.36
66_Y119_K0.7420.36
62_G68_V0.7410.36
80_Y131_L0.7400.36
95_E98_E0.7390.36
58_E143_Y0.7380.36
122_H146_S0.7360.36
119_K137_L0.7330.35
42_A46_K0.7310.35
46_K49_T0.7310.35
61_V158_N0.7300.35
131_L156_L0.7290.35
62_G122_H0.7290.35
31_M35_E0.7260.35
22_V27_Y0.7250.35
51_L70_K0.7220.35
92_L103_D0.7220.35
73_D157_K0.7160.34
73_D116_S0.7060.34
155_I158_N0.7040.33
71_G81_V0.6970.33
45_A99_G0.6950.33
56_Q118_Q0.6900.32
56_Q151_T0.6890.32
137_L143_Y0.6860.32
9_T16_F0.6830.32
113_G136_Y0.6800.32
41_A45_A0.6780.32
104_K108_I0.6740.31
31_M80_Y0.6710.31
110_K117_K0.6680.31
131_L147_Y0.6670.31
27_Y104_K0.6610.30
9_T17_L0.6490.30
94_K137_L0.6470.30
16_F39_E0.6440.29
31_M125_R0.6410.29
57_V82_W0.6400.29
81_V93_S0.6360.29
7_I10_V0.6320.29
113_G158_N0.6320.29
46_K156_L0.6280.28
44_E48_E0.6260.28
30_A99_G0.6200.28
147_Y155_I0.6190.28
56_Q102_E0.6180.28
101_S121_V0.6180.28
21_L58_E0.6160.28
114_L137_L0.6110.27
10_V20_L0.6100.27
19_V95_E0.6100.27
33_Q99_G0.6070.27
116_S139_K0.6060.27
69_V128_N0.6050.27
55_D154_K0.6030.27
36_E72_T0.6030.27
44_E83_V0.6020.27
107_K141_G0.5990.27
52_A76_G0.5980.27
100_I108_I0.5970.26
90_K100_I0.5950.26
22_V26_I0.5870.26
52_A72_T0.5860.26
94_K151_T0.5850.26
78_A137_L0.5850.26
21_L120_E0.5830.26
67_Y122_H0.5770.25
10_V23_S0.5760.25
100_I134_V0.5760.25
94_K125_R0.5750.25
115_V137_L0.5730.25
66_Y91_I0.5710.25
133_E147_Y0.5680.25
43_A148_V0.5670.25
40_A55_D0.5590.24
27_Y136_Y0.5570.24
41_A157_K0.5530.24
92_L96_A0.5530.24
16_F75_K0.5490.24
32_A36_E0.5440.23
37_G158_N0.5420.23
38_H109_I0.5410.23
115_V136_Y0.5400.23
84_P87_K0.5400.23
143_Y157_K0.5390.23
122_H133_E0.5350.23
70_K78_A0.5350.23
16_F68_V0.5300.23
80_Y144_S0.5290.23
132_W153_G0.5280.23
81_V84_P0.5230.22
68_V94_K0.5230.22
38_H59_T0.5180.22
59_T67_Y0.5170.22
39_E72_T0.5120.22
61_V132_W0.5080.21
27_Y83_V0.5060.21
91_I107_K0.5040.21
124_A150_F0.5030.21
6_L10_V0.5020.21
112_E148_V0.5010.21
57_V67_Y0.5000.21
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  
2gu3A 1 0.795 100 0.246 Contact Map
4exrA 2 0.8199 99 0.745 Contact Map
2kgyA 1 0.5404 72.3 0.912 Contact Map
2o3oA 2 0.9503 56.7 0.921 Contact Map
4k90B 1 0.882 41 0.928 Contact Map
4ml1A 4 0.2795 34.3 0.931 Contact Map
3nqzA 1 0.8323 30.4 0.933 Contact Map
1rz2A 1 0.7578 19.8 0.939 Contact Map
1yr2A 1 0.6025 18.1 0.939 Contact Map
1t3bA 2 0.3416 15.8 0.941 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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