GREMLIN Database
YDEP - Uncharacterized HTH-type transcriptional regulator YdeP
UniProt: P96673 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 128 (102)
Sequences: 9779 (5848)
Seq/√Len: 579.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
50_R58_Q2.7781.00
96_T110_K2.7761.00
75_H89_S2.7761.00
59_R63_L2.7151.00
40_I98_E2.5521.00
81_Q85_K2.5001.00
77_E89_S2.4781.00
39_L74_I2.3601.00
75_H91_T2.2671.00
38_H52_L2.0401.00
79_Y87_E1.9321.00
39_L49_F1.8591.00
93_F111_Y1.7941.00
103_H106_D1.7591.00
79_Y85_K1.7291.00
90_L94_G1.7111.00
100_V103_H1.6401.00
35_L64_Q1.6381.00
99_P103_H1.6361.00
66_R69_E1.5921.00
43_K89_S1.5791.00
44_K52_L1.5531.00
43_K87_E1.4601.00
95_R98_E1.4411.00
32_K67_E1.4331.00
60_M63_L1.4051.00
92_E95_R1.3551.00
76_R86_V1.3501.00
32_K64_Q1.3381.00
73_V94_G1.3321.00
23_T104_M1.3261.00
96_T107_W1.2731.00
29_G67_E1.2651.00
58_Q62_T1.2311.00
26_I71_D1.2211.00
105_K109_E1.2051.00
78_V83_P1.1921.00
93_F96_T1.1761.00
23_T108_G1.1701.00
79_Y83_P1.1591.00
22_T112_K1.1591.00
39_L44_K1.1491.00
47_N51_K1.1351.00
29_G64_Q1.1281.00
36_L90_L1.1161.00
93_F114_R1.1061.00
69_E74_I1.1021.00
44_K48_E1.0791.00
77_E87_E1.0721.00
46_F62_T1.0661.00
80_K83_P1.0591.00
62_T66_R1.0541.00
73_V97_L1.0501.00
78_V86_V1.0281.00
32_K68_L1.0241.00
26_I73_V1.0001.00
96_T111_Y0.9981.00
33_G101_I0.9801.00
35_L53_Y0.9771.00
78_V84_P0.9671.00
60_M64_Q0.9641.00
57_T60_M0.9501.00
45_R87_E0.9491.00
89_S95_R0.9411.00
29_G32_K0.9341.00
56_I61_L0.9301.00
79_Y84_P0.9281.00
79_Y82_V0.9221.00
97_L107_W0.9071.00
40_I90_L0.9061.00
48_E51_K0.8941.00
106_D110_K0.8791.00
46_F58_Q0.8721.00
41_D44_K0.8701.00
98_E102_L0.8671.00
99_P106_D0.8471.00
32_K71_D0.8341.00
72_G93_F0.8231.00
44_K49_F0.8061.00
38_H49_F0.7991.00
47_N50_R0.7991.00
21_E25_D0.7951.00
67_E71_D0.7931.00
40_I102_L0.7811.00
37_Y105_K0.7761.00
100_V104_M0.7731.00
78_V82_V0.7611.00
19_P109_E0.7531.00
102_L106_D0.7511.00
22_T111_Y0.7281.00
31_W56_I0.7211.00
63_L67_E0.7101.00
16_E21_E0.6921.00
78_V81_Q0.6881.00
53_Y56_I0.6861.00
35_L56_I0.6861.00
37_Y40_I0.6771.00
102_L105_K0.6731.00
31_W61_L0.6711.00
24_L104_M0.6651.00
38_H41_D0.6601.00
36_L97_L0.6561.00
16_E25_D0.6531.00
106_D109_E0.6501.00
69_E78_V0.6471.00
50_R61_L0.6461.00
45_R79_Y0.6371.00
24_L33_G0.6371.00
111_Y114_R0.6261.00
97_L100_V0.6201.00
68_L73_V0.6201.00
108_G112_K0.6161.00
39_L43_K0.6161.00
56_I86_V0.6141.00
107_W111_Y0.6141.00
41_D52_L0.6091.00
109_E112_K0.6091.00
83_P86_V0.6051.00
43_K49_F0.6011.00
24_L97_L0.5861.00
81_Q87_E0.5861.00
82_V86_V0.5831.00
42_G95_R0.5751.00
58_Q64_Q0.5721.00
45_R48_E0.5640.99
93_F115_I0.5630.99
34_I53_Y0.5630.99
81_Q84_P0.5610.99
110_K113_D0.5600.99
14_D20_V0.5580.99
22_T115_I0.5560.99
48_E52_L0.5540.99
43_K48_E0.5510.99
39_L69_E0.5500.99
81_Q86_V0.5440.99
96_T99_P0.5440.99
20_V112_K0.5430.99
16_E22_T0.5420.99
100_V108_G0.5390.99
77_E80_K0.5370.99
69_E76_R0.5360.99
20_V37_Y0.5330.99
18_C46_F0.5290.99
82_V85_K0.5210.99
90_L95_R0.5180.99
36_L73_V0.5140.99
39_L90_L0.5110.99
34_I38_H0.5110.99
27_I104_M0.5070.99
93_F112_K0.5030.99
92_E96_T0.5020.99
31_W60_M0.5020.99
23_T27_I0.5000.99
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 0.8594 99.9 0.428 Contact Map
4a5nA 2 0.8203 99.7 0.501 Contact Map
1yyvA 2 0.875 99.7 0.507 Contact Map
2fswA 2 0.8047 99.7 0.517 Contact Map
2hztA 2 0.7422 99.7 0.518 Contact Map
1z7uA 2 0.8672 99.7 0.524 Contact Map
2f2eA 4 0.9062 99.6 0.544 Contact Map
4hw0A 2 0.7656 99.6 0.562 Contact Map
3df8A 2 0.8203 99.6 0.566 Contact Map
4hqeA 2 0.8281 99.4 0.609 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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