GREMLIN Database
YGZD - Uncharacterized HTH-type transcriptional regulator YgzD
UniProt: C0H3X9 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 66 (60)
Sequences: 1922 (1236)
Seq/√Len: 159.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
17_E21_E2.7081.00
46_L62_L2.5211.00
22_T51_A2.4751.00
4_K7_E2.3431.00
55_K58_D1.9281.00
9_R34_E1.9061.00
14_Y51_A1.8811.00
46_L56_M1.8461.00
54_M58_D1.6041.00
8_L59_V1.5871.00
6_K10_A1.5771.00
8_L54_M1.5721.00
7_E10_A1.5701.00
7_E13_G1.4361.00
18_K22_T1.4081.00
15_S18_K1.4051.00
25_V30_V1.3931.00
23_V51_A1.3751.00
7_E11_R1.3461.00
48_I59_V1.3361.00
43_L47_K1.3111.00
31_A35_K1.2991.00
49_C56_M1.2431.00
33_I38_Y1.2371.00
19_L30_V1.1871.00
12_F53_S1.1621.00
45_A56_M1.1501.00
29_T38_Y1.1091.00
14_Y22_T1.0620.99
8_L11_R1.0510.99
4_K61_W1.0160.99
16_Q30_V1.0110.99
10_A13_G0.9990.99
39_V42_L0.9870.99
18_K21_E0.9710.99
43_L62_L0.9570.99
23_V52_F0.9460.99
14_Y18_K0.9370.98
26_T32_A0.9040.98
54_M59_V0.8980.98
50_K62_L0.8920.98
4_K8_L0.8810.98
28_Q32_A0.8760.98
6_K13_G0.8740.98
47_K62_L0.8720.98
39_V62_L0.8690.97
15_S31_A0.8460.97
11_R54_M0.8180.96
19_L52_F0.8080.96
12_F22_T0.8060.96
39_V43_L0.8050.96
37_D42_L0.7900.96
38_Y44_L0.7590.94
23_V30_V0.7440.94
47_K50_K0.7440.94
27_R60_F0.7380.94
25_V29_T0.7250.93
3_N26_T0.7200.93
4_K11_R0.7140.92
41_S44_L0.7090.92
16_Q27_R0.7060.92
3_N45_A0.7000.92
25_V33_I0.6980.92
5_V61_W0.6930.91
48_I54_M0.6630.89
8_L12_F0.6490.88
5_V48_I0.6470.88
5_V62_L0.6380.88
4_K55_K0.6200.86
19_L23_V0.6140.86
17_E27_R0.6010.84
3_N60_F0.5750.82
23_V44_L0.5670.81
33_I42_L0.5650.81
19_L51_A0.5560.79
40_P44_L0.5500.79
50_K53_S0.5470.78
32_A37_D0.5460.78
55_K61_W0.5460.78
44_L47_K0.5390.77
46_L50_K0.5380.77
33_I44_L0.5320.76
4_K22_T0.5200.75
6_K35_K0.5150.74
3_N28_Q0.5110.74
19_L48_I0.5090.73
52_F59_V0.5080.73
32_A35_K0.5020.72
6_K15_S0.5000.72
21_E53_S0.5000.72
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  
4yarA 2 1 99.5 0.228 Contact Map
3u3wA 2 0.9848 99.5 0.228 Contact Map
1y9qA 1 1 99.5 0.228 Contact Map
2p5tA 2 0.0606 99.5 0.231 Contact Map
4o8bA 2 1 99.4 0.243 Contact Map
4ichA 2 0 99.4 0.246 Contact Map
3mlfA 2 1 99.4 0.249 Contact Map
3tysA 2 0.9697 99.4 0.249 Contact Map
3ivpA 2 1 99.4 0.253 Contact Map
4ndwA 2 1 99.4 0.253 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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