GREMLIN Database
YVAP - Uncharacterized HTH-type transcriptional regulator YvaP
UniProt: O32238 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 108 (97)
Sequences: 9592 (5667)
Seq/√Len: 575.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
40_E48_G2.8301.00
65_K79_S2.7431.00
49_R53_E2.6751.00
86_A100_E2.5921.00
30_L88_A2.5531.00
67_D79_S2.4501.00
71_E75_R2.4201.00
29_L64_V2.1851.00
28_Q42_A2.1551.00
65_K81_T2.1181.00
69_I77_E1.8551.00
83_K101_W1.7851.00
90_I93_E1.7241.00
69_I75_R1.6901.00
29_L39_I1.6871.00
89_P93_E1.6731.00
25_I54_R1.6371.00
93_E96_K1.6301.00
56_K59_E1.6031.00
33_S77_E1.5751.00
33_S79_S1.5381.00
50_V53_E1.5211.00
80_L84_G1.5151.00
34_Q42_A1.4821.00
86_A97_W1.4011.00
85_K88_A1.3751.00
22_V57_E1.3601.00
82_D85_K1.3511.00
63_V84_G1.3411.00
83_K86_A1.3011.00
13_A94_I1.2831.00
22_V54_R1.2821.00
19_K57_E1.2771.00
66_R76_I1.2461.00
59_E64_V1.1911.00
13_A98_A1.1781.00
12_K102_I1.1781.00
48_G52_S1.1751.00
34_Q38_E1.1741.00
37_S41_A1.1581.00
16_I61_E1.1391.00
29_L34_Q1.1251.00
68_V76_I1.1121.00
22_V58_L1.1101.00
52_S56_K1.0781.00
19_K54_R1.0781.00
95_S99_T1.0761.00
35_R77_E1.0671.00
69_I73_P1.0671.00
63_V87_L1.0531.00
19_K22_V1.0531.00
67_D77_E1.0331.00
79_S85_K0.9961.00
88_A92_G0.9891.00
68_V73_P0.9891.00
26_V80_L0.9821.00
69_I74_V0.9701.00
36_F52_S0.9641.00
25_I43_L0.9611.00
68_V74_V0.9561.00
70_P73_P0.9521.00
23_A91_L0.9301.00
86_A101_W0.9161.00
50_V54_R0.9151.00
16_I63_V0.9041.00
46_L51_L0.8981.00
89_P96_K0.8951.00
28_Q39_I0.8921.00
38_E41_A0.8891.00
96_K100_E0.8871.00
31_N34_Q0.8871.00
87_L97_W0.8871.00
69_I72_T0.8671.00
37_S40_E0.8651.00
47_S50_V0.8601.00
43_L46_L0.8361.00
62_G83_K0.8291.00
22_V61_E0.8231.00
36_F48_G0.8211.00
11_E15_D0.8041.00
30_L80_L0.7981.00
30_L92_G0.7791.00
8_P99_T0.7601.00
57_E61_E0.7581.00
12_K101_W0.7561.00
92_G96_K0.7481.00
21_W46_L0.7341.00
34_Q39_I0.7301.00
25_I46_L0.7191.00
72_T76_I0.7161.00
27_F30_L0.7151.00
68_V72_T0.7141.00
90_I94_I0.7131.00
96_K99_T0.7101.00
27_F95_S0.7101.00
68_V71_E0.7011.00
98_A102_I0.6821.00
28_Q31_N0.6791.00
59_E66_R0.6391.00
10_F102_I0.6311.00
14_V94_I0.6291.00
92_G95_S0.6261.00
35_R38_E0.6251.00
24_L43_L0.6201.00
71_E74_V0.6141.00
53_E57_E0.6071.00
29_L33_S0.6061.00
14_V23_A0.5951.00
89_P92_G0.5921.00
32_G85_K0.5911.00
87_L90_I0.5891.00
24_L28_Q0.5891.00
35_R69_I0.5811.00
37_S48_G0.5761.00
28_Q34_Q0.5640.99
26_V87_L0.5580.99
10_F27_F0.5540.99
11_E23_A0.5530.99
58_L63_V0.5510.99
46_L76_I0.5510.99
71_E77_E0.5510.99
99_T102_I0.5500.99
36_F40_E0.5490.99
73_P76_I0.5470.99
31_N42_A0.5450.99
33_S39_I0.5400.99
29_L59_E0.5380.99
40_E51_L0.5370.99
100_E103_D0.5340.99
7_C36_F0.5270.99
13_A63_V0.5260.99
71_E76_I0.5240.99
59_E68_V0.5190.99
48_G54_R0.5160.99
6_M12_K0.5140.99
33_S67_D0.5130.99
85_K89_P0.5100.99
86_A89_P0.5090.99
79_S82_D0.5090.99
98_A101_W0.5050.99
12_K27_F0.5040.99
83_K102_I0.5030.99
90_I98_A0.5030.99
29_L80_L0.5020.99
56_K66_R0.5000.99
12_K15_D0.5000.99
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 0.9259 99.8 0.385 Contact Map
4a5nA 2 0.9444 99.7 0.468 Contact Map
1z7uA 2 0.9907 99.7 0.482 Contact Map
2hztA 2 0.8796 99.7 0.483 Contact Map
1yyvA 2 0.963 99.7 0.488 Contact Map
2fswA 2 0.9352 99.7 0.494 Contact Map
2f2eA 4 0.9722 99.6 0.503 Contact Map
4hw0A 2 0.8148 99.6 0.518 Contact Map
3df8A 2 0.9167 99.5 0.547 Contact Map
1xmaA 2 0.8796 99.3 0.602 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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