GREMLIN Database
YDDM - Uncharacterized HTH-type transcriptional regulator YddM
UniProt: P67699 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13784
Length: 94 (84)
Sequences: 1686 (1196)
Seq/√Len: 130.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
30_A59_V2.6651.00
57_S64_P2.3501.00
37_T52_M2.3431.00
25_R29_R2.1481.00
26_E30_A2.0081.00
25_R35_P1.9611.00
40_R46_A1.9321.00
24_L39_S1.9241.00
69_N73_A1.9161.00
36_S39_S1.8821.00
4_A77_A1.8151.00
36_S40_R1.7581.00
15_E18_D1.7261.00
27_F38_A1.6761.00
14_Q18_D1.6581.00
17_L27_F1.6571.00
57_S63_S1.5941.00
57_S62_S1.5921.00
77_A81_K1.5451.00
39_S43_T1.5191.00
40_R45_K1.4851.00
41_L48_L1.4671.00
54_I79_A1.4271.00
53_A65_Q1.4161.00
74_W78_E1.3931.00
6_H78_E1.2711.00
51_E55_K1.2591.00
24_L36_S1.2040.99
4_A7_P1.2030.99
35_P39_S1.1940.99
68_L72_N1.1810.99
65_Q80_E1.1800.99
64_P80_E1.1690.99
24_L42_L1.1620.99
53_A64_P1.1590.99
64_P76_L1.1580.99
62_S66_M1.1570.99
11_D15_E1.1360.99
83_V88_L1.1260.99
12_I70_L1.0990.99
27_F56_L1.0740.99
22_V27_F1.0310.98
6_H77_A1.0220.98
34_A37_T1.0210.98
49_T52_M1.0150.98
24_L38_A1.0040.98
33_I52_M0.9960.98
8_R44_G0.9870.98
7_P77_A0.9770.98
16_S19_E0.9760.98
41_L52_M0.9760.98
69_N72_N0.9680.98
16_S66_M0.9410.97
7_P12_I0.9400.97
5_N78_E0.9350.97
11_D44_G0.9260.97
14_Q42_L0.9210.97
47_A75_S0.9160.97
19_E66_M0.9070.96
66_M70_L0.9000.96
14_Q44_G0.8860.96
73_A77_A0.8850.96
37_T46_A0.8670.95
63_S66_M0.8410.94
11_D16_S0.8390.94
53_A57_S0.8340.94
65_Q69_N0.8320.94
26_E29_R0.8190.94
12_I62_S0.8080.93
29_R43_T0.8000.93
17_L22_V0.7990.93
33_I55_K0.7930.93
71_Q75_S0.7890.92
13_I41_L0.7810.92
12_I16_S0.7800.92
17_L20_L0.7750.92
56_L60_I0.7420.90
33_I37_T0.7400.90
30_A58_V0.7380.90
8_R47_A0.7330.89
24_L40_R0.7230.89
65_Q72_N0.7230.89
16_S20_L0.7180.88
53_A69_N0.7030.87
83_V86_S0.7020.87
24_L35_P0.6940.87
8_R74_W0.6770.85
33_I38_A0.6730.85
25_R36_S0.6730.85
36_S43_T0.6660.84
14_Q19_E0.6650.84
59_V88_L0.6650.84
30_A60_I0.6630.84
16_S60_I0.6550.83
46_A52_M0.6500.83
53_A68_L0.6450.82
65_Q73_A0.6380.82
50_P68_L0.6360.81
23_S29_R0.6340.81
79_A83_V0.6300.81
9_P74_W0.6190.80
7_P11_D0.6160.79
29_R32_E0.6080.78
83_V87_R0.6010.78
23_S26_E0.6010.78
72_N75_S0.5980.77
58_V87_R0.5940.77
32_E87_R0.5930.77
40_R60_I0.5820.75
78_E81_K0.5800.75
68_L76_L0.5800.75
14_Q20_L0.5730.74
66_M69_N0.5690.74
54_I80_E0.5630.73
31_M59_V0.5490.71
14_Q43_T0.5460.71
21_N61_G0.5440.70
5_N81_K0.5370.69
34_A52_M0.5320.69
81_K87_R0.5200.67
62_S67_W0.5160.66
37_T51_E0.5060.65
14_Q24_L0.5050.65
58_V86_S0.5040.65
18_D59_V0.5000.64
34_A46_A0.5000.64
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  
4mctA 2 0.9894 99.7 0.539 Contact Map
2ictA 2 1 99.6 0.563 Contact Map
4mcxA 2 0.9894 99.6 0.568 Contact Map
3trbA 3 0.9574 99.5 0.588 Contact Map
3cecA 1 0.9468 99.5 0.595 Contact Map
2ebyA 2 0.9574 99.5 0.607 Contact Map
3fmyA 2 0.6809 98.9 0.694 Contact Map
4rykA 2 0.9362 98.9 0.695 Contact Map
4yarA 2 1 98.9 0.695 Contact Map
4y42A 6 0.9787 98.9 0.699 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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