GREMLIN Database
YQAF - Uncharacterized HTH-type transcriptional regulator YqaF
UniProt: P45903 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 76 (64)
Sequences: 964 (840)
Seq/√Len: 105.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
10_R35_E4.5071.00
20_V31_Y3.4521.00
18_E28_R2.9661.00
18_E22_K2.6131.00
23_A52_K2.1081.00
29_A33_M1.8391.00
33_M38_T1.8061.00
64_V67_E1.7181.00
5_W59_I1.6921.00
40_K43_V1.5911.00
12_E67_E1.5481.00
20_V53_L1.4611.00
45_V48_K1.4171.00
29_A32_T1.4151.00
51_E63_D1.4151.00
9_N53_L1.3831.00
17_Q28_R1.3350.99
46_S57_W1.3100.99
33_M36_N1.2840.99
30_Y33_M1.2650.99
50_G57_W1.2240.99
59_I62_E1.1980.99
57_W61_F1.1730.99
24_A53_L1.0900.98
5_W8_K1.0850.98
26_I31_Y1.0650.97
46_S61_F1.0410.97
16_T19_E1.0400.97
20_V49_I1.0250.97
33_M39_R1.0080.96
27_G30_Y0.9990.96
27_G33_M0.9920.96
58_T63_D0.9820.96
6_L31_Y0.9750.95
30_Y34_I0.9630.95
34_I45_V0.9610.95
32_T36_N0.9440.95
28_R32_T0.9400.94
24_A52_K0.9110.93
9_N55_F0.9060.93
17_Q35_E0.8980.93
13_K23_A0.8890.93
24_A34_I0.8850.92
47_K51_E0.8830.92
17_Q31_Y0.8500.91
19_E23_A0.8350.90
34_I39_R0.8310.90
13_K54_G0.8290.90
5_W63_D0.8120.89
28_R31_Y0.8070.89
7_K11_L0.8040.88
55_F59_I0.7940.88
43_V47_K0.7920.88
55_F60_F0.7920.88
26_I30_Y0.7520.85
4_K8_K0.7330.83
42_S47_K0.7170.82
9_N52_K0.7100.81
47_K65_C0.7100.81
21_A31_Y0.7080.81
19_E22_K0.7070.81
5_W65_C0.7000.80
21_A26_I0.6880.79
11_L16_T0.6870.79
10_R17_Q0.6870.79
8_K12_E0.6790.78
51_E54_G0.6780.78
21_A28_R0.6740.78
7_K35_E0.6720.78
41_P45_V0.6640.77
47_K54_G0.6630.77
9_N20_V0.6570.76
41_P46_S0.6500.75
15_F52_K0.6330.73
27_G32_T0.6090.70
50_G63_D0.5880.68
7_K10_R0.5770.66
16_T24_A0.5720.66
53_L57_W0.5710.65
40_K45_V0.5640.65
17_Q32_T0.5570.64
40_K44_I0.5520.63
47_K57_W0.5520.63
13_K53_L0.5520.63
4_K46_S0.5470.62
21_A24_A0.5460.62
50_G60_F0.5450.62
16_T20_V0.5200.58
26_I34_I0.5100.57
4_K40_K0.5080.57
10_R15_F0.5070.56
9_N13_K0.5060.56
4_K65_C0.5020.56
37_G44_I0.5010.56
9_N54_G0.5000.55
4_K36_N0.5000.55
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  
2p5tA 2 0.1842 99.5 0.254 Contact Map
4o8bA 2 1 99.5 0.269 Contact Map
4ndwA 2 1 99.5 0.286 Contact Map
3u3wA 2 0.9868 99.4 0.293 Contact Map
1b0nA 2 0.9342 99.4 0.296 Contact Map
4jcyA 2 1 99.4 0.296 Contact Map
3op9A 4 0.9737 99.4 0.297 Contact Map
3r1fA 2 1 99.4 0.297 Contact Map
1y9qA 1 1 99.4 0.298 Contact Map
3mlfA 2 1 99.4 0.298 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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