GREMLIN Database
YRDD - Uncharacterized protein YrdD
UniProt: P45771 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12841
Length: 180 (147)
Sequences: 977 (577)
Seq/√Len: 47.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
69_A86_N6.6451.00
108_Q135_Q5.3581.00
141_K157_E5.3011.00
101_E113_H3.5211.00
87_Y91_E3.2421.00
125_F131_Y2.7101.00
71_L92_H2.5751.00
65_P92_H2.5511.00
143_I166_H2.4711.00
112_G130_R2.4111.00
65_P71_L2.2921.00
35_C41_C2.2631.00
63_V70_N2.2611.00
70_N85_I2.1101.00
41_C44_V2.1091.00
147_C150_C2.0210.99
148_P175_K1.9420.99
155_L175_K1.9210.99
71_L82_I1.9080.99
113_H129_D1.8490.99
27_G30_G1.7950.99
147_C168_C1.6780.98
150_C168_C1.6700.98
45_R48_K1.6630.98
60_E82_I1.6620.98
65_P82_I1.6440.98
130_R133_E1.6300.98
160_T163_G1.5970.97
145_G155_L1.5640.97
41_C45_R1.5250.96
67_C90_C1.5240.96
105_T113_H1.5040.96
69_A85_I1.3690.93
145_G166_H1.3660.93
59_L70_N1.3570.93
111_T130_R1.3530.93
62_Q94_E1.3380.93
152_Y169_A1.3240.92
66_A92_H1.3080.92
66_A91_E1.3000.92
171_K175_K1.2990.92
30_G35_C1.2930.91
110_R151_H1.2550.90
98_K116_Q1.1820.87
157_E164_V1.1690.87
30_G41_C1.1530.86
36_S41_C1.1470.85
74_R93_T1.1420.85
125_F132_P1.1400.85
54_H74_R1.1360.85
33_L36_S1.1350.85
61_G70_N1.1150.84
69_A89_E1.1140.84
105_T111_T1.1010.83
117_R164_V1.0960.83
142_P150_C1.0870.82
126_H141_K1.0820.82
62_Q82_I1.0240.78
67_C71_L1.0230.78
152_Y170_S1.0200.78
115_V129_D1.0200.78
72_V85_I1.0190.78
41_C48_K1.0090.77
71_L90_C1.0030.77
170_S174_G1.0010.77
37_Q40_A0.9860.76
162_Q165_K0.9800.75
154_L169_A0.9730.75
81_F88_P0.9620.74
65_P94_E0.9520.73
33_L47_L0.9510.73
34_G44_V0.9430.72
170_S173_C0.9420.72
86_N89_E0.9400.72
125_F129_D0.9300.71
138_I156_I0.9260.71
78_F126_H0.9250.71
162_Q176_P0.9160.70
147_C173_C0.9130.70
168_C173_C0.9030.69
128_C134_C0.8970.68
146_E169_A0.8940.68
167_F174_G0.8940.68
160_T167_F0.8900.68
106_C128_C0.8840.67
142_P147_C0.8560.65
68_G151_H0.8550.65
33_L44_V0.8470.64
105_T108_Q0.8440.64
149_E174_G0.8350.63
114_L138_I0.8320.62
60_E65_P0.8230.62
136_F152_Y0.8210.61
125_F137_A0.8150.61
119_S139_N0.8140.61
53_G56_V0.8140.61
127_S132_P0.8120.61
33_L41_C0.7950.59
90_C128_C0.7860.58
145_G175_K0.7840.58
60_E71_L0.7820.58
58_V80_M0.7780.57
128_C150_C0.7740.57
83_G93_T0.7680.56
43_Y46_P0.7610.56
47_L53_G0.7580.55
32_F41_C0.7540.55
121_Y139_N0.7520.55
72_V83_G0.7510.55
171_K174_G0.7450.54
46_P50_S0.7450.54
138_I154_L0.7340.53
109_C142_P0.7300.53
155_L166_H0.7280.52
150_C173_C0.7280.52
165_K176_P0.7250.52
75_Q118_R0.7250.52
103_A113_H0.7220.52
93_T133_E0.7220.52
28_K31_P0.7170.51
136_F169_A0.7150.51
68_G86_N0.6940.49
75_Q176_P0.6940.49
80_M95_L0.6940.49
67_C128_C0.6940.49
40_A46_P0.6910.49
82_I95_L0.6890.48
82_I92_H0.6830.48
61_G82_I0.6810.48
41_C47_L0.6780.47
105_T110_R0.6770.47
131_Y137_A0.6740.47
78_F162_Q0.6730.47
125_F128_C0.6700.47
36_S121_Y0.6680.46
84_C90_C0.6670.46
147_C155_L0.6610.46
75_Q80_M0.6560.45
35_C39_P0.6560.45
106_C134_C0.6540.45
33_L38_Y0.6500.45
38_Y44_V0.6460.44
122_G145_G0.6450.44
27_G31_P0.6440.44
69_A90_C0.6420.44
121_Y135_Q0.6400.44
60_E63_V0.6360.43
147_C151_H0.6310.43
116_Q141_K0.6270.42
119_S160_T0.6270.42
152_Y171_K0.6240.42
136_F170_S0.6220.42
60_E92_H0.6180.41
104_I154_L0.6140.41
71_L89_E0.6130.41
67_C84_C0.6110.41
158_K163_G0.6100.41
38_Y41_C0.6090.41
159_K164_V0.6070.40
166_H169_A0.6060.40
77_R137_A0.6050.40
37_Q41_C0.5970.39
95_L117_R0.5960.39
36_S44_V0.5910.39
159_K163_G0.5910.39
35_C43_Y0.5900.39
90_C134_C0.5860.38
106_C110_R0.5850.38
27_G48_K0.5760.37
37_Q42_D0.5750.37
102_T113_H0.5740.37
67_C142_P0.5740.37
128_C147_C0.5720.37
101_E107_P0.5700.37
53_G87_Y0.5700.37
118_R137_A0.5680.37
90_C142_P0.5680.37
56_V59_L0.5650.36
44_V48_K0.5630.36
52_D55_I0.5610.36
155_L173_C0.5580.36
149_E175_K0.5540.35
73_L96_I0.5530.35
43_Y47_L0.5490.35
58_V67_C0.5480.35
61_G69_A0.5480.35
62_Q92_H0.5460.35
61_G92_H0.5430.34
143_I163_G0.5430.34
74_R80_M0.5430.34
124_T140_F0.5410.34
60_E70_N0.5390.34
86_N90_C0.5360.34
109_C128_C0.5360.34
128_C142_P0.5330.33
77_R145_G0.5320.33
163_G166_H0.5320.33
170_S175_K0.5300.33
61_G85_I0.5300.33
120_R140_F0.5300.33
126_H130_R0.5300.33
110_R129_D0.5290.33
28_K35_C0.5260.33
159_K166_H0.5240.33
67_C86_N0.5210.32
84_C128_C0.5200.32
31_P35_C0.5180.32
140_F156_I0.5180.32
34_G42_D0.5170.32
128_C132_P0.5140.32
122_G128_C0.5130.32
159_K165_K0.5100.31
112_G128_C0.5100.31
35_C44_V0.5070.31
112_G129_D0.5060.31
42_D46_P0.5060.31
84_C134_C0.5040.31
163_G169_A0.5040.31
105_T144_A0.5010.31
146_E152_Y0.5000.31
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  
2gaiA 1 0.5389 99.8 0.703 Contact Map
4cgyA 1 0.0167 99.6 0.742 Contact Map
1yuaA 1 0.5667 97.4 0.882 Contact Map
3h0gI 1 0.4222 90.6 0.92 Contact Map
1twfI 1 0.6278 85.4 0.927 Contact Map
3qt1I 1 0.2278 83 0.929 Contact Map
4c2mI 1 0.4778 80.2 0.931 Contact Map
3h0gL 1 0.25 48.1 0.945 Contact Map
1qypA 1 0.2833 47.3 0.945 Contact Map
2jrpA 1 0.3667 43 0.946 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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