GREMLIN Database
YDCH - Uncharacterized HTH-type transcriptional regulator YdcH
UniProt: P96625 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 147 (129)
Sequences: 19159 (14106)
Seq/√Len: 1242.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
58_T103_S3.1221.00
91_S103_S3.0581.00
133_K142_E2.7111.00
93_N101_L2.6871.00
60_T99_E2.5351.00
89_E103_S2.5131.00
135_N139_G2.4201.00
135_N138_S2.3241.00
50_K112_V2.0661.00
58_T101_L2.0191.00
92_K100_V2.0121.00
42_Q85_K1.9691.00
60_T63_K1.9621.00
50_K104_L1.7761.00
93_N99_E1.7441.00
130_A139_G1.7381.00
86_G107_I1.6061.00
32_A118_I1.6061.00
111_K114_A1.5891.00
36_F118_I1.5861.00
42_Q81_T1.5801.00
58_T91_S1.5621.00
107_I111_K1.5571.00
107_I110_E1.5141.00
39_T42_Q1.4921.00
136_F139_G1.4631.00
48_S67_F1.4621.00
61_Q79_V1.4591.00
17_L141_Q1.4291.00
79_V102_L1.4231.00
83_E90_R1.4141.00
36_F114_A1.4101.00
80_R84_K1.3821.00
50_K109_G1.3101.00
45_L78_V1.3001.00
133_K138_S1.2911.00
57_E109_G1.2891.00
139_G142_E1.2861.00
62_K72_I1.2551.00
63_K66_S1.2541.00
70_T74_M1.2541.00
61_Q100_V1.2521.00
56_G67_F1.2181.00
110_E114_A1.2181.00
17_L137_L1.1921.00
138_S142_E1.1731.00
80_R97_K1.1531.00
137_L141_Q1.1461.00
133_K139_G1.1391.00
87_F111_K1.1391.00
30_G34_A1.1301.00
20_Q144_L1.1291.00
36_F115_A1.1211.00
61_Q102_L1.1141.00
62_K66_S1.0731.00
32_A121_K1.0661.00
19_W22_T1.0541.00
132_K135_N1.0461.00
21_A144_L1.0361.00
17_L144_L1.0351.00
32_A125_A1.0351.00
35_E118_I1.0261.00
85_K111_K1.0241.00
45_L75_V1.0221.00
76_S80_R1.0201.00
22_T26_Q1.0201.00
123_D126_F1.0041.00
28_K122_I1.0001.00
90_R100_V0.9991.00
71_N74_M0.9981.00
118_I121_K0.9961.00
85_K107_I0.9951.00
21_A140_L0.9821.00
41_V78_V0.9811.00
14_P137_L0.9711.00
74_M77_E0.9591.00
109_G113_T0.9581.00
61_Q75_V0.9571.00
37_D85_K0.9541.00
87_F107_I0.9301.00
92_K97_K0.9271.00
80_R83_E0.9241.00
59_V67_F0.9161.00
104_L108_G0.9151.00
46_L112_V0.9101.00
106_E109_G0.9091.00
18_L22_T0.9051.00
57_E103_S0.8981.00
59_V63_K0.8921.00
24_S144_L0.8891.00
106_E110_E0.8891.00
30_G40_H0.8771.00
73_M76_S0.8751.00
119_V123_D0.8741.00
50_K113_T0.8711.00
117_P121_K0.8631.00
114_A118_I0.8591.00
79_V88_I0.8591.00
77_E81_T0.8581.00
89_E105_T0.8571.00
70_T75_V0.8531.00
121_K124_Q0.8451.00
91_S101_L0.8431.00
130_A143_L0.8411.00
63_K67_F0.8341.00
49_C88_I0.8301.00
44_V68_S0.8261.00
79_V83_E0.8251.00
94_P101_L0.8161.00
77_E80_R0.8111.00
135_N142_E0.8081.00
32_A122_I0.8051.00
104_L109_G0.7961.00
45_L64_L0.7881.00
121_K125_A0.7771.00
117_P120_E0.7761.00
71_N77_E0.7751.00
82_L87_F0.7741.00
61_Q72_I0.7611.00
134_E138_S0.7571.00
18_L21_A0.7561.00
26_Q30_G0.7511.00
19_W23_Q0.7471.00
43_F115_A0.7451.00
41_V74_M0.7421.00
47_T51_Y0.7421.00
50_K116_L0.7311.00
28_K125_A0.7271.00
49_C104_L0.7221.00
23_Q27_R0.7171.00
134_E137_L0.7171.00
96_D99_E0.7091.00
120_E124_Q0.6981.00
48_S59_V0.6971.00
65_A75_V0.6881.00
65_A72_I0.6881.00
43_F119_V0.6861.00
32_A35_E0.6851.00
83_E89_E0.6821.00
56_G59_V0.6811.00
48_S68_S0.6701.00
64_L102_L0.6691.00
125_A128_A0.6681.00
21_A143_L0.6661.00
122_I125_A0.6661.00
49_C59_V0.6631.00
81_T84_K0.6591.00
116_L120_E0.6581.00
110_E113_T0.6581.00
93_N96_D0.6521.00
75_V79_V0.6481.00
17_L20_Q0.6461.00
114_A117_P0.6361.00
29_V32_A0.6351.00
62_K65_A0.6291.00
47_T112_V0.6281.00
28_K31_K0.6271.00
56_G63_K0.6271.00
45_L68_S0.6271.00
130_A142_E0.6151.00
139_G143_L0.6141.00
127_F131_M0.6111.00
113_T116_L0.6111.00
43_F112_V0.6091.00
38_L111_K0.6071.00
48_S64_L0.6011.00
61_Q76_S0.6001.00
91_S94_P0.5961.00
80_R90_R0.5961.00
44_V48_S0.5941.00
131_M142_E0.5931.00
18_L25_W0.5931.00
20_Q24_S0.5861.00
86_G89_E0.5851.00
47_T116_L0.5841.00
24_S28_K0.5751.00
27_R31_K0.5701.00
113_T117_P0.5691.00
49_C102_L0.5601.00
42_Q78_V0.5571.00
17_L140_L0.5541.00
33_L43_F0.5481.00
61_Q99_E0.5381.00
29_V119_V0.5351.00
83_E88_I0.5331.00
130_A133_K0.5311.00
40_H44_V0.5271.00
112_V116_L0.5181.00
46_L50_K0.5161.00
62_K99_E0.5121.00
129_A142_E0.5101.00
81_T85_K0.5051.00
18_L140_L0.5001.00
31_K34_A0.5001.00
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  
2fbkA 2 0.898 99.9 0.296 Contact Map
3broA 2 0.9388 99.9 0.297 Contact Map
3cdhA 4 0.9048 99.9 0.303 Contact Map
3cjnA 2 0.9456 99.9 0.305 Contact Map
3u2rA 4 0.898 99.9 0.307 Contact Map
4yifA 2 0.9184 99.9 0.308 Contact Map
3e6mA 2 0.9728 99.9 0.31 Contact Map
3deuA 2 0.8639 99.9 0.312 Contact Map
3fm5A 4 0.9592 99.9 0.312 Contact Map
4rguA 4 0.9252 99.9 0.313 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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