GREMLIN Database
YODB - HTH-type transcriptional regulator YodB
UniProt: O34844 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 112 (98)
Sequences: 9837 (5894)
Seq/√Len: 595.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
39_T47_Q2.9181.00
64_E78_T2.7801.00
48_K52_E2.6621.00
85_A99_Q2.6501.00
70_E74_K2.5561.00
29_M87_Q2.5541.00
66_Q78_T2.4851.00
28_L63_V2.1831.00
27_V41_T2.1681.00
64_E80_T2.1041.00
68_L76_I1.9391.00
82_K100_F1.8441.00
28_L38_I1.7111.00
68_L74_K1.6961.00
89_V92_E1.6891.00
88_A92_E1.6821.00
92_E95_A1.6521.00
55_K58_E1.6101.00
32_P76_I1.5931.00
24_I53_R1.5911.00
79_L83_G1.5331.00
32_P78_T1.5301.00
33_K41_T1.5151.00
49_M52_E1.4781.00
21_N56_E1.3931.00
85_A96_W1.3761.00
84_T87_Q1.3721.00
62_I83_G1.3681.00
81_E84_T1.3651.00
82_K85_A1.3391.00
12_A93_M1.3051.00
21_N53_R1.2891.00
18_K56_E1.2581.00
65_R75_V1.2231.00
58_E63_V1.2121.00
82_K103_P1.1711.00
12_A97_A1.1471.00
47_Q51_A1.1391.00
15_L60_N1.1231.00
94_Q98_D1.1181.00
11_S101_C1.1151.00
33_K37_E1.1091.00
68_L72_P1.1011.00
36_K40_E1.0931.00
51_A55_K1.0911.00
21_N57_L1.0851.00
18_K53_R1.0691.00
34_R76_I1.0661.00
18_K21_N1.0651.00
28_L33_K1.0591.00
67_V72_P1.0491.00
67_V75_V1.0301.00
62_I86_L1.0251.00
68_L73_V0.9901.00
35_F51_A0.9891.00
78_T84_T0.9891.00
67_V73_V0.9881.00
66_Q76_I0.9751.00
68_L71_T0.9751.00
87_Q91_Q0.9621.00
69_P72_P0.9591.00
25_I79_L0.9541.00
85_A100_F0.9461.00
24_I42_I0.9461.00
49_M53_R0.9461.00
15_L62_I0.9421.00
22_G90_F0.9201.00
86_L96_W0.9071.00
45_I50_L0.8981.00
36_K39_T0.8871.00
37_E40_E0.8861.00
27_V38_I0.8821.00
61_E82_K0.8551.00
30_D33_K0.8521.00
95_A99_Q0.8211.00
88_A95_A0.8171.00
46_S49_M0.8091.00
21_N60_N0.7961.00
10_E14_S0.7951.00
29_M79_L0.7921.00
35_F47_Q0.7911.00
56_E60_N0.7661.00
91_Q95_A0.7591.00
42_I45_I0.7571.00
67_V71_T0.7501.00
33_K38_I0.7431.00
26_H94_Q0.7391.00
29_M91_Q0.7201.00
26_H29_M0.7171.00
7_P98_D0.7071.00
67_V70_E0.7041.00
20_W45_I0.6961.00
11_S100_F0.6881.00
24_I45_I0.6861.00
97_A101_C0.6731.00
89_V93_M0.6681.00
27_V30_D0.6611.00
95_A98_D0.6501.00
91_Q94_Q0.6461.00
52_E56_E0.6371.00
23_L27_V0.6281.00
31_G84_T0.6231.00
13_F93_M0.6071.00
58_E65_R0.6061.00
27_V33_K0.5991.00
88_A91_Q0.5981.00
71_T75_V0.5961.00
34_R37_E0.5961.00
70_E73_V0.5941.00
23_L42_I0.5921.00
13_F22_G0.5871.00
100_F103_P0.5861.00
98_D101_C0.5861.00
39_T50_L0.5851.00
28_L32_P0.5821.00
70_E76_I0.5801.00
9_M26_H0.5791.00
72_P75_V0.5761.00
36_K47_Q0.5681.00
9_M101_C0.5661.00
57_L62_I0.5641.00
12_A62_I0.5570.99
85_A88_A0.5540.99
10_E22_G0.5530.99
86_L89_V0.5510.99
96_W100_F0.5500.99
34_R68_L0.5470.99
6_C35_F0.5440.99
35_F39_T0.5410.99
28_L58_E0.5380.99
45_I75_V0.5360.99
25_I86_L0.5340.99
30_D41_T0.5250.99
58_E67_V0.5250.99
84_T88_A0.5240.99
37_E41_T0.5210.99
81_E85_A0.5190.99
89_V97_A0.5190.99
5_M11_S0.5180.99
70_E75_V0.5120.99
13_F86_L0.5060.99
82_K101_C0.5050.99
55_K65_R0.5030.99
47_Q53_R0.5020.99
11_S26_H0.5010.99
88_A99_Q0.5000.99
11_S14_S0.5000.99
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 0.9375 99.9 0.388 Contact Map
4a5nA 2 0.9375 99.7 0.465 Contact Map
1yyvA 2 0.9464 99.7 0.482 Contact Map
2hztA 2 0.8482 99.7 0.487 Contact Map
1z7uA 2 0.9554 99.7 0.492 Contact Map
2fswA 2 0.8929 99.7 0.492 Contact Map
2f2eA 4 0.9732 99.6 0.512 Contact Map
4hw0A 2 0.8393 99.6 0.529 Contact Map
3df8A 2 0.875 99.5 0.541 Contact Map
1xmaA 2 0.8482 99.3 0.6 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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