GREMLIN Database
YBDJ - Uncharacterized transcriptional regulatory protein YbdJ
UniProt: O31432 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 223 (203)
Sequences: 75703 (54009)
Seq/√Len: 3790.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_G32_W3.7521.00
16_G34_T3.3281.00
20_Q32_W3.2181.00
9_V39_V2.7551.00
37_A57_G2.6461.00
40_L66_K2.6111.00
31_I46_V2.5821.00
44_Q70_L2.5071.00
36_G58_E2.4811.00
35_D57_G2.4771.00
58_E66_K2.3861.00
5_R31_I2.1801.00
5_R29_R2.1641.00
33_K42_V2.0691.00
22_I105_P2.0561.00
20_Q24_Q1.9831.00
88_K107_E1.9621.00
152_I155_K1.9311.00
34_T38_D1.9301.00
64_S76_V1.9111.00
51_M63_M1.8891.00
54_M82_R1.8871.00
186_N189_N1.8791.00
26_E109_L1.8451.00
78_F91_G1.8171.00
7_L33_K1.7671.00
35_D38_D1.7541.00
85_M104_D1.7341.00
66_K70_L1.6921.00
68_K96_E1.6821.00
59_D62_Q1.6681.00
158_F162_E1.6191.00
31_I42_V1.6121.00
58_E62_Q1.5781.00
36_G63_M1.5541.00
97_D111_R1.5321.00
23_L112_M1.5301.00
159_Y176_Y1.5271.00
71_G74_I1.5161.00
4_Y116_L1.5161.00
66_K69_K1.5101.00
128_H141_E1.5061.00
64_S78_F1.4931.00
170_K189_N1.4751.00
43_I67_I1.4581.00
42_V46_V1.4511.00
42_V45_K1.4311.00
82_R87_S1.4241.00
191_H194_K1.4221.00
40_L63_M1.4161.00
62_Q65_A1.4131.00
49_V74_I1.3991.00
153_E198_K1.3971.00
96_E118_H1.3951.00
53_V78_F1.3781.00
37_A58_E1.3761.00
48_L112_M1.3711.00
168_L176_Y1.3601.00
77_I115_M1.3531.00
169_T172_H1.3461.00
159_Y163_N1.3431.00
10_E16_G1.3281.00
65_A94_I1.3261.00
51_M64_S1.3111.00
53_V61_Y1.2831.00
194_K197_A1.2801.00
9_V55_L1.2571.00
41_S45_K1.2561.00
11_D52_D1.2491.00
40_L58_E1.2431.00
96_E115_M1.2401.00
7_L46_V1.2331.00
33_K39_V1.2171.00
125_Q130_Y1.2151.00
13_V34_T1.2151.00
38_D41_S1.2091.00
37_A41_S1.1971.00
28_Y113_R1.1901.00
38_D42_V1.1851.00
65_A90_Q1.1711.00
61_Y90_Q1.1611.00
84_D87_S1.1581.00
7_L39_V1.1511.00
6_I28_Y1.1361.00
27_G113_R1.1301.00
93_Q113_R1.1261.00
109_L113_R1.1191.00
172_H176_Y1.1091.00
132_D135_T1.1001.00
107_E110_L1.0981.00
7_L42_V1.0881.00
43_I71_G1.0781.00
26_E113_R1.0521.00
171_E185_P1.0391.00
154_R158_F1.0381.00
39_V63_M1.0331.00
7_L43_I1.0321.00
155_K158_F1.0321.00
61_Y91_G1.0311.00
90_Q94_I1.0281.00
159_Y168_L1.0261.00
130_Y139_F1.0191.00
40_L44_Q1.0161.00
85_M89_L1.0141.00
190_V193_K1.0091.00
129_L132_D1.0031.00
48_L116_L1.0001.00
110_L114_N0.9991.00
137_K146_E0.9961.00
39_V43_I0.9951.00
89_L93_Q0.9921.00
9_V49_V0.9881.00
86_D90_Q0.9821.00
201_D209_N0.9731.00
49_V67_I0.9721.00
17_D32_W0.9691.00
61_Y94_I0.9621.00
187_I191_H0.9511.00
186_N190_V0.9511.00
13_V17_D0.9501.00
49_V76_V0.9391.00
64_S94_I0.9381.00
19_L79_L0.9291.00
41_S44_Q0.9291.00
51_M76_V0.9271.00
88_K100_V0.9221.00
51_M78_F0.9221.00
85_M88_K0.9171.00
33_K38_D0.9161.00
50_I108_L0.9131.00
90_Q93_Q0.9131.00
53_V59_D0.9121.00
14_M18_L0.9041.00
77_I111_R0.9031.00
8_I19_L0.8931.00
62_Q66_K0.8861.00
9_V33_K0.8861.00
13_V16_G0.8801.00
159_Y173_F0.8801.00
151_A155_K0.8761.00
5_R46_V0.8741.00
8_I30_V0.8731.00
20_Q30_V0.8671.00
17_D20_Q0.8661.00
83_N100_V0.8581.00
168_L172_H0.8541.00
55_L63_M0.8511.00
133_A158_F0.8501.00
115_M118_H0.8501.00
131_I161_Y0.8491.00
75_P96_E0.8471.00
28_Y109_L0.8391.00
53_V87_S0.8351.00
4_Y28_Y0.8281.00
89_L106_R0.8251.00
65_A69_K0.8201.00
43_I46_V0.8101.00
107_E111_R0.8041.00
19_L108_L0.8011.00
114_N117_E0.7981.00
192_I196_R0.7961.00
186_N193_K0.7941.00
4_Y120_Y0.7931.00
5_R47_D0.7931.00
171_E175_E0.7911.00
21_K25_R0.7901.00
129_L138_V0.7881.00
139_F146_E0.7841.00
150_T198_K0.7841.00
63_M67_I0.7831.00
105_P109_L0.7771.00
204_G212_G0.7751.00
193_K197_A0.7731.00
54_M81_A0.7731.00
172_H175_E0.7631.00
58_E63_M0.7621.00
9_V63_M0.7581.00
190_V194_K0.7581.00
201_D205_E0.7571.00
136_K213_E0.7571.00
103_F108_L0.7551.00
50_I79_L0.7541.00
36_G40_L0.7541.00
138_V142_S0.7531.00
53_V82_R0.7521.00
92_L111_R0.7491.00
8_I20_Q0.7481.00
87_S90_Q0.7481.00
202_Q205_E0.7441.00
43_I74_I0.7411.00
129_L140_N0.7351.00
17_D21_K0.7291.00
67_I72_L0.7271.00
44_Q71_G0.7261.00
67_I76_V0.7231.00
162_E176_Y0.7221.00
97_D114_N0.7161.00
104_D107_E0.7151.00
86_D106_R0.7091.00
114_N119_H0.7081.00
200_N203_A0.7011.00
93_Q110_L0.6981.00
139_F142_S0.6921.00
75_P118_H0.6881.00
77_I97_D0.6881.00
44_Q66_K0.6851.00
10_E55_L0.6851.00
36_G57_G0.6851.00
119_H123_F0.6831.00
40_L43_I0.6831.00
116_L119_H0.6811.00
106_R110_L0.6761.00
79_L103_F0.6751.00
170_K185_P0.6741.00
204_G207_I0.6741.00
8_I32_W0.6691.00
50_I77_I0.6691.00
209_N213_E0.6671.00
86_D89_L0.6631.00
126_I129_L0.6621.00
15_I103_F0.6501.00
131_I154_R0.6491.00
85_M106_R0.6471.00
16_G20_Q0.6401.00
73_G122_T0.6401.00
128_H140_N0.6381.00
152_I191_H0.6361.00
80_S88_K0.6341.00
159_Y162_E0.6331.00
111_R115_M0.6321.00
18_L22_I0.6321.00
156_I160_L0.6281.00
43_I49_V0.6251.00
196_R201_D0.6251.00
128_H132_D0.6231.00
50_I112_M0.6211.00
130_Y142_S0.6191.00
61_Y87_S0.6101.00
185_P189_N0.6091.00
12_D15_I0.6051.00
182_D185_P0.6051.00
75_P116_L0.6021.00
68_K75_P0.5991.00
162_E168_L0.5981.00
12_D81_A0.5951.00
46_V71_G0.5951.00
51_M55_L0.5911.00
53_V91_G0.5911.00
68_K74_I0.5901.00
43_I63_M0.5871.00
23_L28_Y0.5831.00
75_P122_T0.5831.00
167_I213_E0.5821.00
81_A102_P0.5811.00
64_S68_K0.5811.00
22_I109_L0.5791.00
204_G208_E0.5771.00
36_G55_L0.5741.00
6_I23_L0.5701.00
24_Q29_R0.5691.00
4_Y47_D0.5681.00
136_K155_K0.5671.00
24_Q30_V0.5671.00
88_K104_D0.5661.00
73_G121_G0.5661.00
189_N192_I0.5641.00
129_L133_A0.5631.00
103_F107_E0.5621.00
89_L92_L0.5611.00
200_N205_E0.5611.00
160_L192_I0.5591.00
15_I18_L0.5531.00
6_I48_L0.5501.00
40_L70_L0.5481.00
110_L113_R0.5481.00
155_K159_Y0.5431.00
125_Q128_H0.5421.00
153_E156_I0.5401.00
205_E208_E0.5391.00
114_N118_H0.5371.00
11_D80_S0.5351.00
80_S98_Y0.5351.00
113_R117_E0.5341.00
67_I71_G0.5331.00
145_D148_L0.5331.00
127_K130_Y0.5301.00
8_I16_G0.5161.00
91_G98_Y0.5151.00
135_T139_F0.5151.00
67_I74_I0.5151.00
33_K36_G0.5141.00
9_V36_G0.5121.00
156_I177_L0.5111.00
35_D55_L0.5111.00
200_N204_G0.5101.00
135_T138_V0.5091.00
146_E209_N0.5091.00
6_I112_M0.5081.00
160_L163_N0.5081.00
9_V51_M0.5061.00
209_N212_G0.5061.00
75_P119_H0.5021.00
163_N176_Y0.5001.00
183_R188_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  
3r0jA 2 0.9552 100 0.275 Contact Map
1ys7A 2 0.9686 100 0.28 Contact Map
2gwrA 1 0.9641 100 0.288 Contact Map
1kgsA 1 0.9507 100 0.298 Contact Map
1p2fA 1 0.9596 100 0.301 Contact Map
4b09A 2 0.9238 100 0.301 Contact Map
3q9sA 1 0.9193 100 0.305 Contact Map
2oqrA 2 0.9552 100 0.311 Contact Map
4kfcA 2 0.9552 100 0.313 Contact Map
2hqrA 2 0.9596 100 0.316 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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