GREMLIN Database
YGAV - Probable HTH-type transcriptional regulator YgaV
UniProt: P77295 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13524
Length: 99 (83)
Sequences: 5270 (3360)
Seq/√Len: 368.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_G71_Q3.7741.00
70_S77_I3.0391.00
69_D80_S2.9301.00
72_R77_I2.5401.00
69_D82_K2.4651.00
12_E24_P2.1271.00
20_A65_E2.1121.00
36_S39_T1.7011.00
50_L55_T1.6891.00
38_G80_S1.6731.00
60_A64_D1.6551.00
32_M47_I1.5921.00
39_T43_E1.5281.00
40_S76_R1.4731.00
32_M39_T1.4561.00
34_S87_N1.4441.00
63_R70_S1.4421.00
51_S54_A1.4301.00
30_L67_L1.3931.00
16_A64_D1.3881.00
40_S43_E1.3791.00
15_A24_P1.3411.00
45_T52_A1.3331.00
39_T47_I1.3331.00
61_R65_E1.3211.00
59_L68_I1.2921.00
88_A92_T1.2871.00
38_G78_L1.2381.00
29_I44_L1.2321.00
23_H57_Q1.2091.00
30_L81_I1.2081.00
50_L54_A1.2061.00
84_E87_N1.1851.00
11_A28_L1.1821.00
10_S13_Q1.1521.00
41_A59_L1.1441.00
11_A31_C1.1331.00
12_E16_A1.0911.00
73_D76_R1.0561.00
20_A61_R1.0121.00
29_I33_L1.0111.00
54_A57_Q0.9961.00
38_G73_D0.9821.00
40_S78_L0.9691.00
25_K50_L0.9671.00
34_S91_A0.9601.00
45_T55_T0.9521.00
25_K55_T0.9401.00
43_E46_R0.9371.00
61_R64_D0.9261.00
66_G82_K0.9181.00
87_N91_A0.9131.00
88_A91_A0.9001.00
33_L39_T0.9001.00
59_L63_R0.8951.00
44_L55_T0.8791.00
54_A58_H0.8741.00
15_A27_L0.8731.00
57_Q75_Q0.8571.00
41_A63_R0.8561.00
63_R77_I0.8511.00
33_L68_I0.8491.00
42_G76_R0.8341.00
33_L36_S0.8261.00
48_T55_T0.8101.00
57_Q60_A0.8031.00
36_S43_E0.7961.00
51_S58_H0.7941.00
73_D78_L0.7941.00
17_L67_L0.7931.00
62_M68_I0.7781.00
18_L21_M0.7761.00
57_Q61_R0.7711.00
25_K28_L0.7691.00
18_L89_I0.7671.00
18_L22_S0.7661.00
89_I93_L0.7561.00
45_T49_G0.7471.00
17_L89_I0.7351.00
13_Q16_A0.7291.00
82_K85_A0.7251.00
31_C34_S0.6970.99
18_L93_L0.6940.99
23_H51_S0.6880.99
72_R75_Q0.6840.99
60_A63_R0.6840.99
59_L79_Y0.6810.99
32_M44_L0.6800.99
83_N86_V0.6750.99
13_Q85_A0.6650.99
43_E47_I0.6590.99
28_L32_M0.6530.99
35_G39_T0.6450.99
51_S75_Q0.6420.99
85_A89_I0.6250.99
85_A90_I0.6240.99
45_T51_S0.6240.99
54_A75_Q0.6210.99
39_T44_L0.6160.99
53_S74_A0.6120.98
20_A67_L0.6070.98
21_M89_I0.6060.98
84_E88_A0.6050.98
14_A93_L0.6000.98
85_A88_A0.5960.98
50_L53_S0.5880.98
21_M30_L0.5860.98
28_L31_C0.5860.98
29_I55_T0.5840.98
25_K58_H0.5820.98
11_A15_A0.5800.98
42_G46_R0.5680.98
31_C90_I0.5470.97
71_Q80_S0.5400.97
14_A90_I0.5390.97
30_L90_I0.5350.96
15_A22_S0.5280.96
23_H54_A0.5240.96
52_A55_T0.5220.96
17_L85_A0.5220.96
51_S57_Q0.5140.96
85_A92_T0.5130.96
23_H45_T0.5030.95
19_K22_S0.5000.95
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  
3cuoA 2 0.9899 99.7 0.484 Contact Map
2kkoA 2 0.9899 99.7 0.497 Contact Map
3pqkA 2 0.9697 99.7 0.516 Contact Map
4k2eA 2 0.9596 99.7 0.521 Contact Map
1r1tA 2 0.9899 99.6 0.528 Contact Map
1u2wA 2 1 99.6 0.539 Contact Map
2jscA 2 0.8687 99.6 0.542 Contact Map
1r1uA 2 0.9495 99.6 0.544 Contact Map
2zkzA 2 0.899 99.6 0.545 Contact Map
3f6vA 2 0.8586 99.6 0.554 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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