GREMLIN Database
YTCD - Uncharacterized HTH-type transcriptional regulator YtcD
UniProt: O34533 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 126 (101)
Sequences: 9617 (5637)
Seq/√Len: 560.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
65_N79_E2.9181.00
86_S100_N2.8811.00
40_K48_Q2.8501.00
49_K53_Q2.7061.00
71_Q75_K2.6021.00
67_I79_E2.5511.00
29_L64_I2.3231.00
28_H42_L2.2081.00
65_N81_S2.1691.00
69_Y77_E1.9661.00
83_Y101_H1.8941.00
69_Y75_K1.8251.00
29_L39_L1.7701.00
30_T88_E1.7681.00
93_M96_A1.7571.00
25_I54_Q1.7551.00
90_I93_M1.7031.00
80_L84_G1.6921.00
89_G93_M1.6921.00
56_R59_E1.6111.00
33_K79_E1.5811.00
34_K42_L1.5541.00
33_K77_E1.4631.00
13_T94_L1.4551.00
85_R88_E1.4261.00
66_R76_V1.4131.00
22_K57_E1.3771.00
50_M53_Q1.3591.00
19_G57_E1.3181.00
82_E85_R1.3051.00
63_V84_G1.2741.00
22_K54_Q1.2731.00
48_Q52_T1.2481.00
13_T98_G1.2411.00
86_S97_W1.2371.00
16_V61_D1.2281.00
95_C99_A1.1931.00
68_V76_V1.1801.00
83_Y104_R1.1731.00
37_S41_R1.1631.00
83_Y86_S1.1591.00
52_T56_R1.1421.00
12_A102_I1.1391.00
34_K38_E1.1351.00
59_E64_I1.1301.00
26_L80_L1.1221.00
69_Y73_P1.1171.00
67_I77_E1.0991.00
35_R77_E1.0991.00
19_G54_Q1.0851.00
23_C91_L1.0731.00
68_V73_P1.0621.00
36_T52_T1.0581.00
86_S101_H1.0491.00
63_V87_L1.0481.00
29_L34_K1.0451.00
22_K58_L1.0201.00
16_V63_V1.0171.00
19_G22_K1.0141.00
70_N73_P0.9921.00
68_V74_P0.9831.00
69_Y72_V0.9781.00
79_E85_R0.9691.00
25_I43_M0.9631.00
38_E41_R0.9221.00
69_Y74_P0.9201.00
87_L97_W0.9071.00
47_T50_M0.8981.00
50_M54_Q0.8951.00
88_E92_D0.8841.00
36_T48_Q0.8711.00
46_I51_L0.8591.00
96_A100_N0.8521.00
37_S40_K0.8461.00
9_S99_A0.8311.00
27_C95_C0.8201.00
28_H39_L0.8191.00
31_H34_K0.8111.00
11_E15_E0.8081.00
89_G96_A0.8041.00
34_K39_L0.7881.00
62_G83_Y0.7841.00
27_C30_T0.7711.00
90_I94_L0.7621.00
43_M46_I0.7521.00
68_V72_V0.7461.00
25_I46_I0.7401.00
22_K61_D0.7221.00
6_Y11_E0.7201.00
12_A101_H0.7091.00
53_Q57_E0.7001.00
92_D96_A0.6991.00
57_E61_D0.6941.00
68_V71_Q0.6841.00
12_A105_V0.6691.00
40_K51_L0.6661.00
99_A102_I0.6611.00
28_H31_H0.6601.00
14_L94_L0.6581.00
6_Y15_E0.6561.00
26_L87_L0.6521.00
10_V27_C0.6441.00
101_H104_R0.6401.00
29_L33_K0.6381.00
71_Q74_P0.6351.00
46_I76_V0.6281.00
24_V28_H0.6121.00
58_L63_V0.6121.00
92_D95_C0.6121.00
6_Y12_A0.6091.00
32_G85_R0.6061.00
21_W46_I0.6021.00
59_E68_V0.6011.00
72_V76_V0.5961.00
98_G102_I0.5931.00
71_Q77_E0.5891.00
90_I98_G0.5861.00
24_V43_M0.5821.00
103_N106_Y0.5791.00
83_Y105_V0.5771.00
21_W51_L0.5771.00
71_Q76_V0.5760.99
14_L23_C0.5710.99
38_E42_L0.5680.99
35_R69_Y0.5660.99
10_V102_I0.5650.99
83_Y102_I0.5640.99
30_T80_L0.5630.99
59_E66_R0.5580.99
30_T34_K0.5580.99
28_H34_K0.5530.99
30_T92_D0.5520.99
73_P77_E0.5460.99
29_L59_E0.5440.99
37_S48_Q0.5440.99
87_L90_I0.5360.99
96_A99_A0.5320.99
89_G92_D0.5310.99
86_S89_G0.5310.99
26_L63_V0.5210.99
100_N103_N0.5210.99
11_E23_C0.5210.99
14_L87_L0.5210.99
97_W101_H0.5200.99
73_P76_V0.5180.99
17_I94_L0.5160.99
11_E44_P0.5150.99
79_E82_E0.5150.99
11_E24_V0.5070.99
33_K39_L0.5040.99
80_L85_R0.5030.99
56_R66_R0.5000.99
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  
4gcvA 3 0.9365 99.8 0.44 Contact Map
4a5nA 2 0.8333 99.7 0.503 Contact Map
1yyvA 2 0.8413 99.7 0.506 Contact Map
2hztA 2 0.754 99.7 0.52 Contact Map
1z7uA 2 0.8571 99.7 0.52 Contact Map
2fswA 2 0.8095 99.7 0.535 Contact Map
2f2eA 4 0.9762 99.6 0.548 Contact Map
4hw0A 2 0.7778 99.6 0.554 Contact Map
3df8A 2 0.7937 99.5 0.578 Contact Map
4hqeA 2 0.8413 99.3 0.624 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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