GREMLIN Database
YRRD - Uncharacterized protein YrrD
UniProt: O34402 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 174 (150)
Sequences: 268 (223)
Seq/√Len: 18.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
41_L88_A5.8261.00
74_R77_D4.3031.00
128_Y140_E3.9741.00
44_I58_F2.5710.97
93_E96_L2.2600.94
115_S155_Q2.1840.92
75_A134_G2.0590.90
108_M114_K2.0260.89
44_I104_T1.9940.88
82_F85_R1.9890.88
55_C89_S1.9450.87
138_A155_Q1.9430.87
108_M165_V1.8840.85
48_C58_F1.8590.85
148_D167_K1.7570.81
63_K108_M1.7480.81
138_A152_S1.7130.79
142_S152_S1.7070.79
164_E169_E1.6510.77
149_L172_L1.6400.76
124_L129_F1.5730.73
50_S56_L1.5730.73
90_V98_L1.5570.72
25_H109_K1.5180.70
32_V128_Y1.5050.70
142_S153_K1.4780.68
23_T26_E1.4720.68
85_R115_S1.4510.67
82_F115_S1.4360.66
58_F86_I1.4350.66
38_S110_M1.4150.65
30_F82_F1.3980.64
103_F141_L1.3960.64
44_I172_L1.3940.63
139_Y170_I1.3870.63
28_E109_K1.3790.63
50_S76_C1.3710.62
60_L108_M1.3550.61
23_T28_E1.3450.61
129_F171_V1.3440.61
60_L142_S1.3240.59
46_D140_E1.3210.59
139_Y168_D1.3030.58
73_L95_L1.2660.56
31_P82_F1.2570.55
88_A109_K1.2560.55
144_G148_D1.2560.55
47_I58_F1.2540.55
58_F73_L1.2520.55
58_F100_K1.2520.55
77_D113_V1.2390.54
127_V148_D1.2180.53
65_F132_D1.2150.53
78_I151_G1.2120.52
52_K92_S1.2060.52
126_D139_Y1.2050.52
28_E137_V1.2040.52
113_V141_L1.1910.51
31_P65_F1.1860.51
63_K86_I1.1850.51
40_Y74_R1.1690.50
40_Y146_F1.1680.50
123_M142_S1.1620.49
23_T123_M1.1520.49
166_R172_L1.1460.48
73_L79_S1.1370.48
45_S132_D1.1350.48
49_F166_R1.1300.47
71_A167_K1.1190.47
84_D143_D1.1080.46
73_L169_E1.1070.46
57_G156_I1.0960.45
145_F169_E1.0840.45
126_D148_D1.0790.44
46_D127_V1.0700.44
47_I127_V1.0680.44
30_F42_G1.0670.44
45_S71_A1.0670.44
32_V74_R1.0580.43
39_S91_S1.0560.43
39_S61_A1.0510.43
158_R172_L1.0440.42
112_L127_V1.0340.42
149_L152_S1.0190.41
135_I163_V1.0080.40
141_L149_L1.0010.40
138_A153_K0.9970.39
44_I63_K0.9890.39
111_K169_E0.9600.37
59_I114_K0.9590.37
86_I124_L0.9570.37
148_D152_S0.9530.37
102_C105_Y0.9510.37
24_C126_D0.9510.37
40_Y170_I0.9330.36
115_S166_R0.9120.34
130_C157_Q0.9100.34
32_V150_A0.9000.34
59_I119_D0.8950.34
35_E83_D0.8940.33
151_G155_Q0.8790.33
23_T65_F0.8700.32
46_D144_G0.8700.32
117_E120_I0.8610.32
46_D153_K0.8580.31
38_S82_F0.8390.30
78_I101_S0.8340.30
127_V143_D0.8330.30
47_I164_E0.8310.30
64_R69_H0.8220.30
32_V77_D0.8210.30
129_F162_L0.8210.30
25_H28_E0.8200.29
32_V64_R0.8170.29
58_F90_V0.8100.29
30_F79_S0.8100.29
47_I151_G0.8080.29
22_R74_R0.8030.29
117_E146_F0.7960.28
138_A147_S0.7870.28
99_P114_K0.7800.27
81_I170_I0.7790.27
77_D84_D0.7780.27
156_I161_S0.7740.27
37_T139_Y0.7700.27
111_K165_V0.7690.27
44_I136_I0.7690.27
107_Q113_V0.7620.27
82_F166_R0.7570.26
30_F107_Q0.7520.26
113_V164_E0.7510.26
26_E80_S0.7480.26
49_F153_K0.7440.26
87_L137_V0.7430.26
135_I157_Q0.7380.25
58_F87_L0.7340.25
23_T132_D0.7330.25
120_I123_M0.7180.25
165_V170_I0.7120.24
64_R67_H0.7110.24
86_I156_I0.7040.24
135_I151_G0.7040.24
81_I106_E0.7000.24
58_F63_K0.6930.23
47_I86_I0.6920.23
47_I146_F0.6840.23
121_L152_S0.6830.23
110_M136_I0.6820.23
50_S65_F0.6740.23
124_L146_F0.6730.23
121_L153_K0.6730.23
150_A156_I0.6720.22
64_R73_L0.6710.22
21_L131_L0.6640.22
129_F139_Y0.6610.22
57_G142_S0.6570.22
51_L89_S0.6550.22
49_F159_A0.6530.22
121_L166_R0.6520.22
81_I117_E0.6520.22
142_S169_E0.6510.22
62_Q70_H0.6510.22
88_A103_F0.6470.21
31_P91_S0.6440.21
61_A115_S0.6440.21
146_F158_R0.6430.21
121_L155_Q0.6410.21
51_L56_L0.6400.21
43_T168_D0.6380.21
38_S138_A0.6350.21
118_G122_G0.6320.21
60_L141_L0.6280.21
125_E171_V0.6260.21
26_E156_I0.6240.20
82_F87_L0.6240.20
54_D119_D0.6240.20
113_V165_V0.6190.20
128_Y137_V0.6160.20
49_F87_L0.6140.20
48_C97_P0.6070.20
149_L153_K0.6050.20
22_R30_F0.6050.20
45_S170_I0.6040.20
44_I100_K0.6030.20
48_C130_C0.6020.20
153_K159_A0.5990.19
82_F113_V0.5980.19
67_H139_Y0.5960.19
46_D108_M0.5960.19
25_H125_E0.5940.19
131_L171_V0.5930.19
21_L67_H0.5920.19
128_Y154_R0.5850.19
64_R68_H0.5830.19
57_G136_I0.5830.19
39_S172_L0.5770.19
60_L80_S0.5730.18
95_L132_D0.5700.18
52_K55_C0.5700.18
32_V125_E0.5670.18
33_Y44_I0.5660.18
37_T70_H0.5660.18
30_F148_D0.5640.18
27_V129_F0.5590.18
31_P85_R0.5570.18
113_V145_F0.5470.18
143_D155_Q0.5440.17
138_A144_G0.5430.17
37_T126_D0.5420.17
127_V140_E0.5410.17
121_L127_V0.5370.17
127_V170_I0.5330.17
75_A156_I0.5300.17
121_L139_Y0.5290.17
128_Y138_A0.5290.17
27_V131_L0.5250.17
145_F148_D0.5210.17
113_V170_I0.5210.17
27_V163_V0.5190.17
126_D152_S0.5180.17
26_E157_Q0.5160.16
95_L116_Q0.5130.16
37_T71_A0.5100.16
76_C104_T0.5030.16
27_V100_K0.5000.16
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  
1pm3A 2 0.3908 99.2 0.769 Contact Map
3htrA 2 0.4483 98.2 0.835 Contact Map
1eysH 1 0.7586 96.5 0.878 Contact Map
2wjnH 1 0.7529 95.9 0.883 Contact Map
1rzhH 1 0.7241 95.6 0.886 Contact Map
3h9nA 3 0.8851 73 0.924 Contact Map
2f1lA 2 0.8506 68 0.927 Contact Map
1vrdA 3 0.3103 62.9 0.929 Contact Map
2dyiA 1 0.4943 56.1 0.932 Contact Map
1jcnA 6 0.7299 46.6 0.936 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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