GREMLIN Database
YVKB - Uncharacterized HTH-type transcriptional regulator YvkB
UniProt: O34643 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 189 (173)
Sequences: 41209 (32298)
Seq/√Len: 2455.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
27_K37_E3.9161.00
19_K28_E3.8051.00
14_Q32_K3.4201.00
45_K49_G2.6321.00
16_L24_T2.3641.00
124_V142_A2.2251.00
46_N49_G2.1421.00
30_A40_I2.0051.00
11_A32_K1.9501.00
15_L28_E1.9111.00
15_L32_K1.9101.00
15_L24_T1.9021.00
124_V128_K1.8841.00
18_K32_K1.8671.00
6_K57_Q1.8161.00
76_D129_T1.8051.00
4_T7_R1.8021.00
7_R11_A1.8001.00
128_K141_E1.7781.00
15_L19_K1.7721.00
72_D75_K1.7191.00
27_K31_E1.7141.00
128_K132_E1.7141.00
11_A14_Q1.7121.00
13_M57_Q1.6521.00
36_S39_T1.6201.00
5_N53_A1.6151.00
26_T41_F1.6141.00
9_L53_A1.5931.00
78_L176_E1.5721.00
26_T37_E1.5641.00
12_A16_L1.5091.00
131_G138_T1.4991.00
6_K10_D1.4911.00
128_K131_G1.4801.00
53_A56_S1.4581.00
82_T172_E1.4521.00
63_G67_E1.4451.00
13_M58_H1.4311.00
129_T133_K1.4161.00
28_E31_E1.4131.00
147_V151_I1.3961.00
13_M54_L1.3931.00
14_Q18_K1.3861.00
28_E32_K1.3781.00
44_F53_A1.3701.00
12_A50_L1.3431.00
20_G24_T1.3391.00
24_T29_I1.3361.00
52_E56_S1.3321.00
39_T42_R1.3251.00
20_G23_A1.3181.00
57_Q61_N1.3181.00
130_M135_V1.3141.00
25_T28_E1.2801.00
52_E111_H1.2711.00
26_T40_I1.2331.00
19_K23_A1.2181.00
11_A15_L1.2151.00
131_G139_G1.2071.00
82_T176_E1.1951.00
78_L82_T1.1921.00
10_D57_Q1.1871.00
130_M136_I1.1851.00
56_S111_H1.1791.00
120_K146_D1.1791.00
75_K79_H1.1761.00
140_N143_E1.1641.00
37_E41_F1.1501.00
143_E177_H1.1491.00
41_F46_N1.1471.00
35_V39_T1.1451.00
65_I83_C1.1171.00
38_A42_R1.1071.00
74_Y78_L1.1051.00
93_D96_K1.1021.00
49_G53_A1.1021.00
120_K124_V1.1001.00
79_H82_T1.0971.00
36_S42_R1.0921.00
67_E122_L1.0911.00
170_P173_K1.0821.00
21_Y51_V1.0771.00
48_Q52_E1.0711.00
16_L21_Y1.0641.00
49_G52_E1.0521.00
9_L44_F1.0521.00
93_D101_E1.0491.00
73_L133_K1.0471.00
9_L54_L1.0461.00
5_N43_N1.0451.00
126_Y130_M1.0431.00
39_T43_N1.0261.00
100_R104_M1.0241.00
70_E76_D1.0241.00
11_A33_A1.0241.00
111_H114_E1.0171.00
13_M17_V1.0041.00
71_G79_H0.9871.00
172_E176_E0.9771.00
10_D14_Q0.9741.00
159_R162_L0.9601.00
29_I50_L0.9571.00
124_V141_E0.9571.00
143_E173_K0.9561.00
14_Q93_D0.9511.00
76_D126_Y0.9501.00
131_G141_E0.9481.00
72_D135_V0.9461.00
114_E118_S0.9411.00
122_L125_D0.9401.00
93_D97_I0.9391.00
12_A54_L0.9371.00
109_I113_T0.9331.00
75_K78_L0.9311.00
101_E105_F0.9301.00
150_S154_G0.9271.00
87_E91_R0.9251.00
96_K100_R0.9201.00
125_D128_K0.9161.00
19_K32_K0.9151.00
30_A37_E0.9061.00
125_D129_T0.9061.00
129_T132_E0.9051.00
117_Q121_Q0.9031.00
169_M172_E0.8891.00
56_S60_S0.8861.00
40_I50_L0.8801.00
63_G118_S0.8771.00
97_I101_E0.8751.00
83_C86_E0.8711.00
82_T175_L0.8661.00
17_V93_D0.8641.00
57_Q60_S0.8631.00
58_H61_N0.8601.00
171_Q174_M0.8551.00
82_T86_E0.8441.00
65_I68_Q0.8391.00
53_A57_Q0.8341.00
131_G134_G0.8301.00
37_E42_R0.8261.00
7_R33_A0.8241.00
120_K142_A0.8231.00
22_R101_E0.8211.00
9_L57_Q0.8161.00
71_G75_K0.8121.00
8_I40_I0.8101.00
142_A146_D0.8081.00
4_T43_N0.8051.00
121_Q125_D0.8031.00
118_S122_L0.8021.00
124_V145_A0.8011.00
31_E37_E0.8001.00
169_M173_K0.7971.00
79_H83_C0.7971.00
95_I98_S0.7931.00
73_L130_M0.7921.00
173_K177_H0.7871.00
141_E145_A0.7741.00
126_Y129_T0.7681.00
131_G136_I0.7621.00
62_R66_L0.7621.00
175_L179_T0.7561.00
94_I97_I0.7551.00
27_K41_F0.7541.00
19_K24_T0.7401.00
121_Q124_V0.7371.00
10_D13_M0.7351.00
111_H115_Y0.7151.00
4_T35_V0.7141.00
86_E172_E0.7091.00
110_N113_T0.6991.00
7_R10_D0.6991.00
101_E104_M0.6951.00
48_Q107_D0.6951.00
172_E175_L0.6921.00
127_L148_F0.6911.00
15_L18_K0.6901.00
4_T36_S0.6891.00
81_G148_F0.6881.00
21_Y47_K0.6881.00
70_E75_K0.6771.00
22_R104_M0.6751.00
48_Q105_F0.6671.00
173_K176_E0.6671.00
97_I100_R0.6641.00
175_L178_S0.6611.00
56_S115_Y0.6591.00
96_K99_F0.6591.00
158_H161_H0.6571.00
127_L141_E0.6481.00
18_K28_E0.6481.00
110_N114_E0.6411.00
72_D76_D0.6381.00
56_S114_E0.6381.00
171_Q175_L0.6371.00
64_S68_Q0.6361.00
84_L88_L0.6351.00
143_E147_V0.6351.00
174_M177_H0.6331.00
8_I33_A0.6311.00
33_A36_S0.6271.00
60_S64_S0.6261.00
78_L81_G0.6241.00
21_Y48_Q0.6211.00
140_N144_H0.6201.00
118_S121_Q0.6191.00
170_P174_M0.6191.00
63_G122_L0.6181.00
26_T30_A0.6141.00
4_T39_T0.6141.00
127_L131_G0.6111.00
30_A35_V0.6051.00
9_L13_M0.6021.00
61_N64_S0.6011.00
150_S153_F0.5991.00
158_H162_L0.5981.00
108_V111_H0.5971.00
16_L51_V0.5961.00
70_E79_H0.5921.00
174_M178_S0.5901.00
21_Y24_T0.5891.00
64_S67_E0.5871.00
108_V112_V0.5851.00
95_I99_F0.5831.00
131_G137_Q0.5811.00
115_Y119_M0.5791.00
81_G84_L0.5741.00
69_T79_H0.5691.00
106_Q109_I0.5681.00
68_Q83_C0.5671.00
13_M61_N0.5671.00
151_I178_S0.5671.00
113_T116_P0.5661.00
107_D110_N0.5611.00
116_P120_K0.5601.00
128_K142_A0.5591.00
86_E171_Q0.5591.00
93_D102_P0.5581.00
35_V43_N0.5551.00
73_L76_D0.5541.00
143_E146_D0.5491.00
60_S115_Y0.5481.00
86_E90_H0.5481.00
26_T47_K0.5481.00
76_D130_M0.5351.00
100_R103_A0.5311.00
151_I154_G0.5281.00
94_I98_S0.5281.00
27_K36_S0.5261.00
33_A37_E0.5251.00
93_D100_R0.5211.00
59_S115_Y0.5161.00
113_T117_Q0.5121.00
83_C87_E0.5091.00
73_L135_V0.5081.00
37_E40_I0.5061.00
15_L25_T0.5061.00
29_I33_A0.5011.00
144_H147_V0.5001.00
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  
2id6A 2 0.9947 100 0.233 Contact Map
4udsA 2 0.9577 100 0.235 Contact Map
2xdnA 2 0.9841 100 0.238 Contact Map
3ppbA 2 0.9735 100 0.239 Contact Map
3cdlA 2 0.9735 100 0.241 Contact Map
3g1oA 2 0.9894 100 0.244 Contact Map
3c2bA 2 0.9947 100 0.246 Contact Map
4jykA 2 1 100 0.247 Contact Map
3npiA 2 1 100 0.247 Contact Map
2ibdA 2 0.9788 100 0.247 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.

Page generated in 0.0081 seconds.