GREMLIN Database
YRBC - Probable transcriptional regulatory protein YrbC
UniProt: P94447 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 240 (230)
Sequences: 3293 (1727)
Seq/√Len: 113.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
135_E205_N4.3141.00
67_D71_K3.6161.00
112_N228_D3.5511.00
13_R17_Q3.3241.00
43_P53_I2.8801.00
99_V117_F2.8451.00
150_E153_E2.7861.00
211_D214_A2.7171.00
41_A74_A2.6291.00
187_T191_S2.3871.00
125_G129_C2.3251.00
16_A20_K2.2941.00
209_E239_R2.2891.00
210_A218_L2.1181.00
181_H184_E2.0941.00
8_K11_Q2.0861.00
138_G177_T2.0711.00
116_A228_D2.0581.00
153_E156_L2.0531.00
89_G117_F1.9631.00
143_D196_S1.9351.00
182_F198_A1.8791.00
156_L160_E1.8211.00
158_V163_G1.8071.00
11_Q15_N1.7781.00
207_Y239_R1.7751.00
28_L59_A1.7711.00
139_F201_T1.7611.00
83_E106_K1.7161.00
31_E48_A1.7011.00
101_C109_T1.6981.00
177_T185_V1.6931.00
120_N224_V1.6881.00
164_E181_H1.6801.00
86_T100_E1.6411.00
178_E181_H1.6371.00
65_N68_R1.6141.00
9_N13_R1.5671.00
157_D192_K1.5621.00
210_A214_A1.5551.00
97_V221_L1.5511.00
221_L225_L1.5491.00
62_P65_N1.5251.00
183_E187_T1.4981.00
9_N17_Q1.4921.00
161_A188_A1.4481.00
36_A74_A1.4421.00
222_I226_E1.4351.00
7_W11_Q1.4261.00
116_A224_V1.4111.00
140_I182_F1.4111.00
69_A73_A1.4081.00
140_I177_T1.4001.00
115_T118_N1.3941.00
86_T98_M1.3921.00
186_K190_E1.3891.00
151_E168_I1.3871.00
149_I154_L1.3861.00
204_P207_Y1.3801.00
100_E233_E1.3781.00
179_P200_V1.3751.00
158_V166_L1.3631.00
63_N67_D1.3611.00
167_R176_F1.3601.00
157_D193_Y1.3401.00
214_A217_K1.3391.00
120_N220_T1.3301.00
89_G99_V1.3261.00
213_Q217_K1.3231.00
51_L55_K1.3191.00
53_I66_I1.3171.00
161_A185_V1.3071.00
93_S214_A1.3051.00
144_R168_I1.3041.00
164_E178_E1.2900.99
34_V102_V1.2790.99
8_K12_K1.2730.99
151_E155_M1.2700.99
86_T202_M1.2700.99
97_V117_F1.2660.99
25_F61_M1.2640.99
213_Q216_E1.2610.99
142_I175_V1.2490.99
137_K164_E1.2470.99
141_T174_E1.2350.99
85_I101_C1.2210.99
139_F174_E1.2120.99
218_L238_Y1.2110.99
168_I173_Y1.2010.99
97_V218_L1.1980.99
53_I70_I1.1950.99
42_D45_A1.1920.99
90_Y96_A1.1910.99
91_G218_L1.1780.99
137_K203_L1.1730.99
222_I236_T1.1700.99
85_I106_K1.1630.99
155_M159_L1.1430.99
190_E195_I1.1270.99
9_N12_K1.1160.98
70_I73_A1.1130.98
144_R171_D1.1070.98
124_L127_S1.1000.98
113_V228_D1.0790.98
53_I57_K1.0770.98
187_T190_E1.0760.98
188_A192_K1.0740.98
12_K16_A1.0720.98
188_A191_S1.0710.98
142_I195_I1.0670.98
77_Q80_S1.0560.98
24_I59_A1.0540.98
57_K63_N1.0450.98
132_F206_T1.0410.98
153_E157_D1.0350.97
57_K62_P1.0240.97
14_K18_D1.0160.97
167_R174_E1.0140.97
93_S218_L1.0060.97
212_D216_E1.0050.97
33_Y73_A1.0030.97
111_S115_T0.9760.96
64_E68_R0.9750.96
141_T172_L0.9740.96
139_F203_L0.9700.96
6_K11_Q0.9680.96
91_G97_V0.9670.96
220_T223_D0.9550.96
115_T120_N0.9540.96
154_L173_Y0.9500.96
9_N21_R0.9490.96
212_D215_V0.9480.96
74_A77_Q0.9440.96
140_I186_K0.9420.96
172_L196_S0.9390.96
100_E136_R0.9370.95
133_L205_N0.9220.95
27_K227_D0.9170.95
115_T119_K0.9170.95
21_R25_F0.9150.95
151_E173_Y0.9080.95
215_V238_Y0.9050.95
10_I18_D0.9050.95
87_Y106_K0.9040.95
95_I238_Y0.9020.94
163_G175_V0.9010.94
226_E234_V0.8960.94
183_E186_K0.8890.94
10_I13_R0.8800.94
55_K199_E0.8770.94
24_I28_L0.8720.93
33_Y72_K0.8680.93
15_N21_R0.8630.93
89_G125_G0.8610.93
71_K77_Q0.8570.93
41_A70_I0.8550.93
61_M65_N0.8550.93
126_E132_F0.8520.93
137_K178_E0.8520.93
93_S210_A0.8510.93
166_L175_V0.8490.92
95_I218_L0.8480.92
12_K15_N0.8460.92
6_K9_N0.8410.92
169_E174_E0.8400.92
95_I210_A0.8330.92
139_F176_F0.8320.92
136_R202_M0.8310.92
182_F200_V0.8300.92
11_Q17_Q0.8300.92
132_F205_N0.8260.91
219_E238_Y0.8250.91
68_R71_K0.8250.91
74_A78_D0.8220.91
38_E48_A0.8190.91
208_A237_N0.8190.91
190_E194_L0.8190.91
54_E186_K0.8170.91
157_D161_A0.8090.91
10_I14_K0.8040.90
98_M131_A0.8040.90
10_I15_N0.8010.90
116_A120_N0.7990.90
156_L159_L0.7960.90
7_W18_D0.7950.90
184_E187_T0.7930.90
116_A225_L0.7910.90
99_V231_V0.7910.90
51_L54_E0.7900.89
176_F203_L0.7880.89
210_A215_V0.7880.89
124_L225_L0.7860.89
144_R173_Y0.7840.89
132_F208_A0.7830.89
169_E172_L0.7830.89
28_L66_I0.7750.89
48_A51_L0.7750.89
101_C126_E0.7740.89
23_K227_D0.7740.89
91_G95_I0.7730.88
141_T197_S0.7720.88
18_D21_R0.7700.88
15_N19_A0.7660.88
19_A22_G0.7640.88
32_I66_I0.7640.88
166_L173_Y0.7610.88
133_L206_T0.7590.88
17_Q20_K0.7530.87
140_I195_I0.7520.87
117_F124_L0.7510.87
62_P68_R0.7490.87
216_E219_E0.7480.87
85_I103_T0.7460.87
29_A33_Y0.7440.86
186_K198_A0.7430.86
218_L236_T0.7320.86
28_L31_E0.7310.86
97_V222_I0.7300.85
29_A65_N0.7300.85
216_E220_T0.7280.85
36_A73_A0.7220.85
220_T224_V0.7200.85
87_Y110_A0.7160.84
36_A41_A0.7150.84
110_A124_L0.7110.84
29_A61_M0.7080.84
142_I173_Y0.7060.84
15_N18_D0.7040.83
31_E50_R0.6970.83
215_V219_E0.6960.83
90_Y130_V0.6890.82
149_I153_E0.6870.82
47_S50_R0.6800.81
137_K176_F0.6800.81
82_Y102_V0.6790.81
40_G46_N0.6780.81
18_D22_G0.6770.81
142_I193_Y0.6760.81
140_I189_L0.6700.80
6_K18_D0.6690.80
12_K17_Q0.6650.80
46_N49_L0.6620.79
26_M33_Y0.6560.79
40_G45_A0.6530.78
89_G122_G0.6530.78
78_D81_S0.6530.78
30_K109_T0.6490.78
36_A69_A0.6480.78
119_K224_V0.6480.78
35_A52_V0.6410.77
20_K23_K0.6400.77
153_E193_Y0.6390.77
153_E160_E0.6390.77
28_L52_V0.6390.77
72_K82_Y0.6380.77
219_E223_D0.6360.77
210_A238_Y0.6350.77
27_K30_K0.6350.77
182_F195_I0.6340.76
48_A52_V0.6330.76
222_I238_Y0.6280.76
136_R200_V0.6280.76
54_E58_G0.6240.75
23_K47_S0.6180.75
15_N57_K0.6170.74
10_I21_R0.6140.74
54_E197_S0.6120.74
201_T235_Y0.6110.74
102_V232_Q0.6080.73
90_Y126_E0.6070.73
144_R154_L0.6060.73
142_I189_L0.6060.73
110_A114_R0.6030.73
151_E159_L0.6010.73
154_L166_L0.6010.73
109_T113_V0.6010.73
158_V162_G0.5970.72
113_V116_A0.5970.72
159_L163_G0.5960.72
98_M127_S0.5930.72
8_K13_R0.5920.71
75_G232_Q0.5920.71
112_N115_T0.5900.71
117_F221_L0.5880.71
84_E100_E0.5880.71
130_V133_L0.5870.71
86_T136_R0.5860.71
30_K38_E0.5860.71
107_N111_S0.5850.71
185_V188_A0.5840.70
115_T224_V0.5830.70
50_R61_M0.5820.70
141_T167_R0.5750.69
39_G46_N0.5710.69
111_S118_N0.5680.68
87_Y230_D0.5680.68
7_W10_I0.5670.68
20_K24_I0.5640.68
107_N110_A0.5640.68
13_R16_A0.5600.67
77_Q81_S0.5570.67
35_A39_G0.5560.67
73_A132_F0.5560.67
25_F50_R0.5550.67
15_N59_A0.5540.66
110_A127_S0.5540.66
17_Q21_R0.5530.66
109_T228_D0.5530.66
99_V113_V0.5520.66
135_E164_E0.5510.66
184_E188_A0.5490.66
95_I208_A0.5410.65
7_W14_K0.5400.64
96_A125_G0.5390.64
98_M202_M0.5370.64
77_Q84_E0.5340.64
155_M158_V0.5340.64
48_A84_E0.5340.64
209_E212_D0.5340.64
28_L61_M0.5330.63
106_K110_A0.5310.63
182_F199_E0.5300.63
84_E102_V0.5300.63
10_I17_Q0.5300.63
119_K237_N0.5290.63
97_V236_T0.5280.63
173_Y193_Y0.5200.62
47_S52_V0.5190.61
62_P82_Y0.5190.61
10_I16_A0.5190.61
150_E156_L0.5180.61
101_C110_A0.5180.61
61_M140_I0.5160.61
22_G28_L0.5150.61
106_K126_E0.5150.61
90_Y125_G0.5140.61
24_I60_N0.5110.60
55_K233_E0.5100.60
150_E184_E0.5060.59
9_N16_A0.5050.59
109_T124_L0.5040.59
51_L62_P0.5040.59
163_G166_L0.5030.59
29_A72_K0.5010.59
140_I185_V0.5000.59
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  
1lfpA 1 0.975 100 0.013 Contact Map
1konA 1 0.925 100 0.019 Contact Map
4f3qA 1 0.9458 100 0.025 Contact Map
1mw7A 1 0.8875 100 0.066 Contact Map
4pt7A 3 0.4583 57.8 0.954 Contact Map
2jsxA 1 0.3167 54.5 0.955 Contact Map
4ptaD 3 0.4208 47.7 0.957 Contact Map
2ra5A 2 0.3833 42.4 0.958 Contact Map
1pdnC 1 0.4833 38.5 0.959 Contact Map
4h0eA 2 0.3375 34.3 0.96 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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