GREMLIN Database
YYBR - Uncharacterized HTH-type transcriptional regulator YybR
UniProt: P37486 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 125 (102)
Sequences: 9971 (5994)
Seq/√Len: 593.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
46_R54_Q2.8461.00
92_T106_S2.8101.00
71_H85_S2.7971.00
55_R59_L2.7221.00
73_E85_S2.4991.00
77_Q81_K2.4791.00
35_M70_V2.3591.00
71_H87_T2.2291.00
34_H48_I2.1041.00
75_Y83_E1.9911.00
35_M45_F1.8531.00
89_F107_N1.8241.00
36_I94_E1.7421.00
99_Q102_E1.7281.00
75_Y81_K1.6891.00
96_I99_Q1.6651.00
86_L90_G1.6651.00
95_P99_Q1.6391.00
62_R65_E1.6241.00
40_K48_I1.6091.00
31_L60_Q1.5621.00
39_K85_S1.5551.00
56_M59_L1.5401.00
39_K83_E1.4541.00
28_K63_E1.4431.00
69_I90_G1.4231.00
91_R94_E1.3981.00
72_R82_V1.3791.00
19_T100_M1.3631.00
28_K60_Q1.3511.00
92_T103_W1.2991.00
88_E91_R1.2951.00
25_G63_E1.2741.00
54_Q58_T1.2401.00
22_V67_D1.2401.00
19_T104_G1.2051.00
89_F92_T1.2051.00
35_M40_K1.2021.00
43_N47_R1.1911.00
74_V79_P1.1671.00
101_K105_E1.1621.00
18_F108_R1.1541.00
25_G60_Q1.1511.00
65_E70_V1.1181.00
58_T62_R1.1141.00
89_F110_V1.1101.00
73_E83_E1.1021.00
32_F86_L1.0961.00
69_I93_L1.0841.00
75_Y79_P1.0771.00
42_F58_T1.0721.00
40_K44_E1.0621.00
28_K64_L1.0581.00
92_T107_N1.0521.00
74_V82_V1.0401.00
56_M60_Q1.0321.00
75_Y78_V1.0031.00
41_R83_E0.9881.00
74_V80_P0.9851.00
31_L49_C0.9791.00
22_V69_I0.9751.00
76_H79_P0.9741.00
94_E98_L0.9711.00
25_G28_K0.9631.00
85_S91_R0.9521.00
93_L103_W0.9451.00
29_G97_V0.9331.00
53_T56_M0.9251.00
75_Y80_P0.9161.00
44_E47_R0.8991.00
52_I57_L0.8971.00
28_K67_D0.8821.00
37_D40_K0.8771.00
68_G89_F0.8721.00
34_H45_F0.8651.00
42_F54_Q0.8631.00
95_P102_E0.8501.00
102_E106_S0.8461.00
43_N46_R0.8461.00
17_E21_D0.8321.00
33_Y101_K0.8021.00
96_I100_M0.8001.00
31_L52_I0.7891.00
98_L102_E0.7881.00
63_E67_D0.7821.00
33_Y36_I0.7821.00
40_K45_F0.7771.00
15_P105_E0.7591.00
74_V78_V0.7391.00
49_C52_I0.7371.00
18_F107_N0.7321.00
98_L101_K0.7041.00
27_W52_I0.6861.00
74_V77_Q0.6791.00
52_I82_V0.6771.00
59_L63_E0.6711.00
104_G108_R0.6691.00
36_I98_L0.6681.00
46_R57_L0.6581.00
34_H37_D0.6561.00
107_N110_V0.6531.00
20_L29_G0.6491.00
36_I86_L0.6381.00
65_E74_V0.6321.00
41_R44_E0.6311.00
77_Q80_P0.6291.00
12_E17_E0.6271.00
38_G91_R0.6261.00
41_R75_Y0.6231.00
35_M39_K0.6181.00
78_V82_V0.6161.00
32_F93_L0.6141.00
20_L100_M0.6081.00
77_Q83_E0.6061.00
93_L96_I0.6041.00
18_F111_L0.5961.00
34_H40_K0.5931.00
105_E108_R0.5901.00
89_F111_L0.5891.00
12_E21_D0.5881.00
65_E72_R0.5871.00
20_L93_L0.5831.00
103_W107_N0.5801.00
14_C42_F0.5791.00
30_I49_C0.5771.00
10_N16_V0.5731.00
30_I34_H0.5731.00
102_E105_E0.5721.00
89_F108_R0.5671.00
54_Q60_Q0.5651.00
37_D48_I0.5641.00
36_I40_K0.5611.00
27_W57_L0.5590.99
12_E18_F0.5580.99
77_Q82_V0.5550.99
17_E29_G0.5420.99
79_P82_V0.5370.99
44_E48_I0.5360.99
35_M65_E0.5350.99
43_N54_Q0.5310.99
16_V108_R0.5300.99
39_K45_F0.5290.99
96_I104_G0.5260.99
88_E92_T0.5220.99
106_S109_D0.5210.99
64_L69_I0.5200.99
11_K50_P0.5180.99
86_L91_R0.5100.99
16_V33_Y0.5070.99
23_I100_M0.5070.99
31_L45_F0.5060.99
18_F21_D0.5010.99
95_P98_L0.5000.99
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 0.888 99.9 0.417 Contact Map
4a5nA 2 0.84 99.8 0.441 Contact Map
1yyvA 2 0.888 99.7 0.496 Contact Map
2hztA 2 0.76 99.7 0.516 Contact Map
2fswA 2 0.824 99.7 0.518 Contact Map
1z7uA 2 0.888 99.7 0.521 Contact Map
2f2eA 4 0.936 99.6 0.533 Contact Map
4hw0A 2 0.784 99.6 0.557 Contact Map
3df8A 2 0.84 99.6 0.563 Contact Map
4hqeA 2 0.848 99.4 0.605 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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