GREMLIN Database
YTRA - HTH-type transcriptional repressor YtrA
UniProt: O34712 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 130 (109)
Sequences: 9772 (7358)
Seq/√Len: 704.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
30_K33_D4.0671.00
23_L28_I3.0991.00
21_K62_E3.0161.00
68_L71_R2.8551.00
38_V49_P2.7051.00
67_T73_T2.4981.00
66_E76_S2.4601.00
10_T18_Q2.4541.00
17_I58_E2.1491.00
19_Q23_L2.0831.00
34_K74_Y1.8951.00
31_P77_E1.8491.00
17_I62_E1.8441.00
35_L65_I1.8261.00
17_I21_K1.8181.00
40_E44_I1.7851.00
71_R74_Y1.7731.00
58_E61_R1.7521.00
21_K64_I1.7361.00
22_E26_K1.6721.00
32_G66_E1.6061.00
53_S57_K1.6041.00
60_E65_I1.5441.00
14_E18_Q1.5381.00
32_G77_E1.5371.00
65_I73_T1.5131.00
16_I47_A1.5051.00
29_M75_I1.4981.00
94_Q97_Q1.4751.00
108_E111_K1.4271.00
57_K60_E1.4021.00
60_E67_T1.3891.00
24_C75_I1.3051.00
57_K61_R1.2991.00
23_L29_M1.2921.00
10_T14_E1.2761.00
13_Y58_E1.2631.00
89_T93_E1.2531.00
95_L98_L1.2241.00
94_Q101_D1.1811.00
40_E43_T1.1521.00
13_Y54_K1.1471.00
45_I56_Y1.1401.00
16_I55_A1.1251.00
50_N53_S1.1151.00
56_Y65_I1.0831.00
19_Q22_E1.0721.00
109_L113_H1.0681.00
95_L112_L1.0631.00
19_Q45_I1.0581.00
37_S40_E1.0561.00
47_A52_V1.0511.00
24_C64_I1.0311.00
90_M94_Q1.0311.00
31_P78_N1.0221.00
98_L102_A1.0191.00
93_E97_Q0.9981.00
54_K58_E0.9921.00
94_Q98_L0.9831.00
21_K25_L0.9701.00
18_Q22_E0.9621.00
16_I45_I0.9411.00
54_K57_K0.9321.00
107_V111_K0.9301.00
58_E62_E0.9211.00
39_R42_A0.9101.00
97_Q101_D0.8921.00
96_K109_L0.8911.00
12_I48_N0.8721.00
66_E77_E0.8661.00
12_I15_Q0.8501.00
50_N54_K0.8431.00
56_Y73_T0.8401.00
25_L64_I0.8361.00
103_H109_L0.8331.00
99_I112_L0.8281.00
20_M35_L0.8151.00
38_V53_S0.7991.00
20_M29_M0.7981.00
41_L56_Y0.7771.00
51_T54_K0.7721.00
41_L52_V0.7711.00
68_L74_Y0.7651.00
97_Q100_I0.7521.00
22_E25_L0.7471.00
29_M35_L0.7401.00
38_V56_Y0.7391.00
27_G30_K0.7371.00
31_P76_S0.7311.00
66_E74_Y0.7241.00
18_Q21_K0.7231.00
48_N51_T0.7181.00
14_E58_E0.7181.00
70_G73_T0.7141.00
15_Q19_Q0.7061.00
20_M24_C0.7051.00
83_L88_M0.7041.00
12_I51_T0.7001.00
37_S69_R0.6991.00
107_V112_L0.6911.00
34_K72_G0.6881.00
53_S67_T0.6861.00
89_T92_K0.6791.00
91_I102_A0.6631.00
38_V82_T0.6561.00
93_E96_K0.6481.00
96_K103_H0.6481.00
11_P14_E0.6481.00
38_V70_G0.6471.00
99_I103_H0.6441.00
38_V73_T0.6421.00
23_L26_K0.6391.00
91_I98_L0.6331.00
49_P54_K0.6321.00
34_K37_S0.6321.00
11_P15_Q0.6291.00
101_D104_Y0.6271.00
100_I106_G0.6261.00
100_I104_Y0.6251.00
60_E73_T0.6161.00
111_K114_E0.6161.00
102_A107_V0.6141.00
14_E17_I0.6141.00
48_N53_S0.6141.00
87_K90_M0.6131.00
42_A52_V0.6111.00
38_V67_T0.6111.00
76_S79_A0.6091.00
16_I52_V0.6091.00
88_M92_K0.6061.00
39_R56_Y0.6031.00
17_I55_A0.5971.00
52_V56_Y0.5921.00
17_I64_I0.5831.00
37_S70_G0.5781.00
53_S56_Y0.5781.00
95_L114_E0.5711.00
65_I75_I0.5691.00
110_E113_H0.5691.00
12_I47_A0.5681.00
32_G68_L0.5681.00
91_I94_Q0.5651.00
20_M59_L0.5651.00
35_L52_V0.5651.00
10_T15_Q0.5521.00
87_K92_K0.5481.00
84_V88_M0.5401.00
37_S73_T0.5371.00
82_T85_E0.5251.00
80_K84_V0.5241.00
23_L44_I0.5191.00
101_D105_A0.5191.00
108_E112_L0.5191.00
86_G89_T0.5191.00
85_E89_T0.5120.99
82_T87_K0.5110.99
50_N67_T0.5090.99
93_E109_L0.5090.99
56_Y60_E0.5060.99
42_A49_P0.5050.99
96_K100_I0.5050.99
92_K96_K0.5050.99
84_V87_K0.5020.99
34_K40_E0.5000.99
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 0.9154 99.9 0.335 Contact Map
3ic7A 2 0.8692 99.9 0.34 Contact Map
3by6A 2 0.9615 99.9 0.35 Contact Map
4r1hA 2 0.8923 99.9 0.358 Contact Map
2ek5A 4 0.9 99.9 0.366 Contact Map
4u0wA 2 0.9385 99.9 0.369 Contact Map
2ra5A 2 0.2385 99.9 0.376 Contact Map
3tqnA 2 0.8308 99.9 0.391 Contact Map
3f8mA 2 0.8308 99.8 0.41 Contact Map
3eetA 2 0.9154 99.8 0.413 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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