GREMLIN Database
YHCF - Uncharacterized HTH-type transcriptional regulator YhcF
UniProt: P54590 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 121 (107)
Sequences: 8247 (6196)
Seq/√Len: 599.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
29_L32_D3.9701.00
22_R27_E3.0301.00
67_R70_Q2.8951.00
20_F61_L2.7261.00
37_V48_P2.7101.00
9_K17_D2.4911.00
16_A57_E2.4601.00
66_T72_T2.2891.00
65_E75_A2.2071.00
34_L64_V2.0191.00
20_F63_I1.9221.00
18_Q22_R1.9051.00
16_A61_L1.9011.00
57_E60_R1.8541.00
92_V95_G1.8021.00
16_A20_F1.7961.00
30_P76_E1.7681.00
33_K73_F1.7621.00
52_Q56_S1.7571.00
39_E43_Q1.7531.00
64_V72_T1.6601.00
31_G65_E1.6001.00
28_L74_I1.5991.00
59_E64_V1.5691.00
21_Y25_R1.5361.00
106_T109_E1.5001.00
15_I46_V1.4951.00
70_Q73_F1.4881.00
13_L17_D1.4811.00
22_R28_L1.4071.00
31_G76_E1.3851.00
87_K91_E1.3481.00
92_V99_Q1.3411.00
49_N52_Q1.2801.00
23_L74_I1.2761.00
18_Q44_T1.2101.00
107_K111_L1.2001.00
59_E66_T1.1941.00
56_S60_R1.1891.00
9_K13_L1.1711.00
93_L96_F1.1451.00
93_L110_M1.1431.00
23_L63_I1.1421.00
20_F24_V1.1401.00
56_S59_E1.1191.00
30_P77_K1.1091.00
39_E42_I1.0881.00
15_I54_T1.0871.00
44_T55_Y1.0361.00
96_F100_M1.0141.00
12_Y53_R0.9751.00
95_G99_Q0.9721.00
46_V51_I0.9531.00
53_R57_E0.9481.00
105_L109_E0.9431.00
57_E61_L0.9381.00
97_V110_M0.9381.00
36_S39_E0.9381.00
38_R41_A0.9261.00
12_Y57_E0.9151.00
92_V96_F0.9131.00
18_Q21_Y0.9131.00
88_L92_V0.9121.00
65_E76_E0.9011.00
19_I23_L0.8861.00
79_E82_D0.8771.00
101_K107_K0.8731.00
91_E95_G0.8731.00
67_R73_F0.8491.00
47_N52_Q0.8491.00
11_I47_N0.8451.00
19_I34_L0.8271.00
55_Y64_V0.8251.00
85_K90_R0.8181.00
28_L34_L0.8171.00
49_N66_T0.8111.00
40_M51_I0.8091.00
15_I51_I0.8071.00
94_E107_K0.7941.00
37_V52_Q0.7941.00
47_N50_T0.7941.00
50_T53_R0.7881.00
16_A63_I0.7761.00
17_D21_Y0.7731.00
40_M55_Y0.7721.00
55_Y72_T0.7671.00
14_Q18_Q0.7651.00
38_R55_Y0.7611.00
52_Q66_T0.7411.00
69_G72_T0.7411.00
80_I83_E0.7391.00
89_T92_V0.7371.00
36_S68_R0.7371.00
98_K102_E0.7371.00
65_E73_F0.7231.00
95_G98_K0.7181.00
15_I44_T0.7131.00
7_S14_Q0.7091.00
59_E72_T0.7071.00
49_N53_R0.7031.00
37_V69_G0.7011.00
89_T97_V0.6991.00
26_K29_L0.6971.00
19_I28_L0.6921.00
85_K89_T0.6801.00
33_K36_S0.6771.00
87_K90_R0.6651.00
53_R56_S0.6581.00
28_L43_Q0.6501.00
99_Q102_E0.6481.00
37_V72_T0.6441.00
108_E111_L0.6331.00
10_P14_Q0.6321.00
89_T100_M0.6261.00
36_S69_G0.6191.00
97_V101_K0.6161.00
90_R94_E0.6151.00
13_L16_A0.6091.00
89_T96_F0.6091.00
33_K71_G0.6021.00
88_L91_E0.6001.00
11_I14_Q0.6001.00
89_T105_L0.5941.00
20_F58_M0.5921.00
91_E94_E0.5881.00
101_K111_L0.5751.00
53_R99_Q0.5751.00
52_Q55_Y0.5741.00
64_V74_I0.5721.00
86_D90_R0.5691.00
19_I40_M0.5671.00
24_V63_I0.5671.00
37_V66_T0.5651.00
11_I46_V0.5611.00
24_V27_E0.5581.00
17_D20_F0.5510.99
30_P75_A0.5500.99
94_E98_K0.5490.99
55_Y59_E0.5480.99
22_R25_R0.5430.99
35_P40_M0.5370.99
12_Y50_T0.5340.99
78_A83_E0.5340.99
31_G67_R0.5320.99
28_L32_D0.5260.99
94_E101_K0.5260.99
37_V55_Y0.5260.99
105_L110_M0.5250.99
11_I50_T0.5180.99
51_I54_T0.5130.99
85_K103_L0.5130.99
100_M105_L0.5090.99
21_Y24_V0.5080.99
37_V56_S0.5080.99
80_I88_L0.5060.99
98_K104_G0.5040.99
38_R42_I0.5020.99
91_E107_K0.5010.99
96_F101_K0.5010.99
68_R73_F0.5000.99
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  
3neuA 2 0.9835 99.9 0.301 Contact Map
4r1hA 2 0.9587 99.9 0.319 Contact Map
4u0wA 2 1 99.9 0.319 Contact Map
3ic7A 2 0.9174 99.9 0.324 Contact Map
3by6A 2 1 99.9 0.324 Contact Map
2ra5A 2 0.2397 99.9 0.341 Contact Map
2ek5A 4 0.9339 99.9 0.342 Contact Map
3tqnA 2 0.8843 99.9 0.36 Contact Map
3bwgA 2 0.9091 99.9 0.378 Contact Map
3edpA 2 0.8926 99.9 0.381 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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