GREMLIN Database
YOBD - Uncharacterized HTH-type transcriptional regulator YobD
UniProt: O34647 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 112 (106)
Sequences: 1239 (1124)
Seq/√Len: 109.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
20_L31_Y3.6001.00
18_E22_E3.2001.00
18_E28_K3.0471.00
51_R63_L2.6061.00
15_L52_L2.4291.00
2_Y6_L2.3951.00
10_R35_E2.2941.00
3_C37_E2.2281.00
29_S33_G2.2231.00
12_A67_P2.1781.00
23_K52_L2.0961.00
57_V61_L2.0441.00
9_L53_Y2.0381.00
27_A30_S1.9971.00
40_K43_L1.9471.00
26_I31_Y1.9021.00
93_T96_I1.8891.00
20_L53_Y1.8091.00
103_I106_L1.7601.00
33_G38_S1.7051.00
29_S32_G1.6761.00
99_P106_L1.6421.00
30_S33_G1.6011.00
33_G39_K1.5951.00
58_D63_L1.4721.00
64_T67_P1.4661.00
28_K32_G1.4401.00
5_R59_Y1.4061.00
27_A33_G1.4001.00
20_L49_L1.3941.00
43_L46_L1.3771.00
50_A63_L1.3441.00
6_L31_Y1.3000.99
26_I30_S1.2880.99
102_K106_L1.2770.99
33_G36_A1.2700.99
99_P103_I1.2060.99
46_L61_L1.1820.99
103_I107_V1.1770.99
17_M28_K1.1750.99
100_I104_L1.1650.99
17_M21_A1.1400.98
24_I49_L1.0960.98
34_Y45_K1.0790.98
32_G36_A1.0670.98
46_L57_V1.0530.97
40_K45_K1.0510.97
87_W91_K1.0340.97
19_Q22_E1.0150.97
5_R62_G1.0150.97
86_H89_G1.0070.97
15_L19_Q1.0050.97
2_Y43_L1.0030.97
42_P45_K0.9850.96
99_P107_V0.9830.96
15_L23_K0.9640.96
19_Q23_K0.9530.95
5_R63_L0.9510.95
34_Y39_K0.9330.95
28_K36_A0.9270.95
92_L97_L0.9240.95
4_Q37_E0.9220.94
27_A32_G0.9220.94
5_R8_Q0.9120.94
32_G41_P0.9080.94
5_R65_D0.8920.93
96_I99_P0.8870.93
89_G93_T0.8820.93
28_K31_Y0.8810.93
13_H23_K0.8790.93
75_N79_F0.8750.93
45_K48_I0.8750.93
2_Y46_L0.8550.92
89_G97_L0.8510.92
89_G92_L0.8320.91
6_L20_L0.8260.91
34_Y41_P0.8250.90
8_Q12_A0.8140.90
41_P58_D0.8130.90
21_A31_Y0.7980.89
48_I51_R0.7760.88
99_P102_K0.7720.87
104_L107_V0.7690.87
17_M31_Y0.7600.86
101_R104_L0.7590.86
93_T99_P0.7560.86
92_L104_L0.7410.85
46_L58_D0.7340.85
98_D102_K0.7330.84
86_H92_L0.7250.84
2_Y53_Y0.7250.84
9_L55_V0.7240.84
96_I103_I0.7080.82
28_K38_S0.7060.82
16_T19_Q0.7040.82
64_T69_P0.6950.81
9_L52_L0.6850.80
27_A39_K0.6670.78
77_K80_L0.6600.78
25_G48_I0.6590.78
20_L52_L0.6570.77
28_K33_G0.6560.77
89_G104_L0.6560.77
101_R105_K0.6540.77
89_G101_R0.6470.76
29_S39_K0.6400.76
87_W94_P0.6400.76
43_L47_V0.6380.75
29_S36_A0.6370.75
88_D105_K0.6350.75
26_I34_Y0.6280.74
66_D69_P0.6260.74
100_I103_I0.6230.74
25_G29_S0.6200.73
26_I49_L0.6110.72
41_P46_L0.6080.72
85_I101_R0.6010.71
101_R107_V0.6000.71
17_M33_G0.5920.70
24_I52_L0.5910.70
36_A39_K0.5870.69
100_I107_V0.5840.69
36_A40_K0.5840.69
79_F83_P0.5820.68
28_K42_P0.5820.68
75_N80_L0.5760.68
79_F89_G0.5740.67
32_G49_L0.5730.67
31_Y34_Y0.5720.67
32_G42_P0.5680.67
55_V59_Y0.5660.66
21_A33_G0.5650.66
21_A28_K0.5560.65
20_L24_I0.5520.64
7_R10_R0.5490.64
80_L84_D0.5480.64
21_A29_S0.5440.63
88_D97_L0.5420.63
55_V60_I0.5410.63
2_Y60_I0.5380.62
39_K42_P0.5370.62
22_E25_G0.5370.62
7_R35_E0.5310.61
47_V63_L0.5300.61
34_Y42_P0.5300.61
32_G39_K0.5290.61
8_Q22_E0.5250.61
54_D68_D0.5150.59
16_T29_S0.5140.59
29_S38_S0.5130.59
26_I29_S0.5130.59
94_P98_D0.5100.58
43_L61_L0.5090.58
97_L101_R0.5080.58
27_A38_S0.5070.58
44_D48_I0.5060.58
100_I105_K0.5050.58
82_K90_Y0.5030.57
22_E26_I0.5000.57
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  
4ndwA 2 1 99.8 0.336 Contact Map
3r1fA 2 1 99.8 0.349 Contact Map
4o8bA 2 0.8661 99.8 0.361 Contact Map
3qwgA 2 0.7143 99.8 0.383 Contact Map
4jcyA 2 0.7857 99.8 0.385 Contact Map
1b0nA 2 0.9107 99.7 0.4 Contact Map
3op9A 4 0.9196 99.7 0.407 Contact Map
3ivpA 2 0.9196 99.7 0.407 Contact Map
2p5tA 2 0.3571 99.7 0.435 Contact Map
2ebyA 2 0.8661 99.7 0.439 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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