GREMLIN Database
YDFF - Uncharacterized HTH-type transcriptional regulator YdfF
UniProt: P96683 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 226 (217)
Sequences: 937 (628)
Seq/√Len: 42.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
192_R196_E5.4201.00
20_I46_A4.5051.00
62_E71_R3.9221.00
113_D165_R3.7361.00
125_H178_Q3.7031.00
113_D187_N3.4001.00
115_L208_I3.2981.00
143_T146_G3.1171.00
199_I208_I3.0961.00
11_L56_A2.9491.00
80_V83_Q2.8101.00
132_M149_F2.6541.00
25_M85_L2.6411.00
200_V209_R2.6221.00
16_S41_I2.6061.00
124_A140_F2.3831.00
54_L59_I2.3801.00
165_R187_N2.3751.00
41_I45_T2.2661.00
166_A169_R2.2361.00
77_A87_I2.1300.99
194_L208_I2.0950.99
105_L174_W2.0700.99
47_S51_N2.0020.99
115_L120_G1.9890.99
198_W217_A1.9770.99
62_E179_H1.9410.99
165_R184_A1.9290.99
34_E177_R1.9070.99
32_A50_L1.8760.99
196_E217_A1.8010.98
54_L61_V1.7960.98
31_P64_H1.7860.98
80_V87_I1.7650.98
26_D30_H1.7270.98
127_L132_M1.7100.97
60_S71_R1.6820.97
106_H175_S1.6350.97
123_M222_L1.5790.96
172_L177_R1.5730.96
199_I210_I1.5720.96
213_S217_A1.5590.96
184_A187_N1.5450.95
197_E200_V1.5220.95
110_T190_L1.5070.95
12_L21_L1.4990.95
110_T208_I1.4940.94
28_R176_E1.4890.94
115_L199_I1.4760.94
191_V195_E1.4280.93
64_H67_H1.4270.93
34_E64_H1.4230.93
193_M218_F1.4160.93
81_I121_V1.4010.92
140_F168_A1.4000.92
190_L194_L1.3960.92
108_A208_I1.3490.91
126_S222_L1.3310.90
29_I64_H1.3210.90
58_L77_A1.3180.90
11_L59_I1.3090.89
16_S30_H1.3070.89
155_I192_R1.2810.88
85_L175_S1.2780.88
113_D184_A1.2730.88
124_A181_I1.2080.85
32_A43_P1.2040.85
193_M217_A1.2030.85
211_T214_G1.1910.84
110_T199_I1.1820.84
217_A220_K1.1650.83
19_S40_N1.1590.83
39_A46_A1.1530.82
130_Q145_E1.1460.82
31_P172_L1.1390.82
25_M34_E1.1370.81
69_Y177_R1.1280.81
132_M145_E1.1210.80
41_I46_A1.1120.80
102_K106_H1.1080.80
11_L68_R1.0990.79
47_S70_Y1.0960.79
42_K48_F1.0760.78
71_R85_L1.0680.77
26_D68_R1.0660.77
147_A167_F1.0480.76
29_I69_Y1.0470.76
31_P34_E1.0470.76
120_G123_M1.0440.75
23_S30_H1.0410.75
132_M146_G1.0340.75
67_H172_L1.0320.75
126_S129_E1.0310.75
33_G37_Y1.0210.74
21_L70_Y1.0190.74
135_K170_C1.0180.74
102_K168_A0.9990.72
80_V84_L0.9920.72
153_L192_R0.9800.71
151_S158_E0.9640.69
107_F119_V0.9640.69
194_L201_R0.9640.69
149_F222_L0.9610.69
108_A185_L0.9610.69
25_M78_A0.9560.69
150_F185_L0.9390.67
107_F215_K0.9330.67
11_L22_L0.9300.67
56_A59_I0.9280.66
45_T72_L0.9260.66
107_F210_I0.9250.66
13_S30_H0.9240.66
16_S99_S0.9200.66
10_S106_H0.9190.66
31_P170_C0.9180.66
127_L189_L0.9100.65
92_K95_S0.9080.65
79_N83_Q0.9040.64
25_M172_L0.9020.64
95_S98_E0.9010.64
153_L196_E0.8900.63
16_S45_T0.8880.63
99_S102_K0.8840.63
216_I220_K0.8770.62
181_I218_F0.8720.62
28_R98_E0.8720.62
50_L70_Y0.8710.62
63_K70_Y0.8650.61
148_L152_K0.8640.61
45_T49_H0.8600.61
78_A82_E0.8490.60
30_H44_Q0.8490.60
28_R68_R0.8460.59
11_L18_S0.8400.59
31_P69_Y0.8370.58
120_G190_L0.8360.58
5_I72_L0.8320.58
61_V68_R0.8310.58
14_D18_S0.8310.58
156_N159_Q0.8310.58
192_R195_E0.8260.57
108_A210_I0.8250.57
21_L106_H0.8240.57
30_H99_S0.8240.57
149_F152_K0.8150.56
85_L222_L0.8100.56
213_S216_I0.8090.56
4_N7_K0.8060.56
71_R154_G0.7960.55
42_K45_T0.7960.55
127_L150_F0.7920.54
50_L59_I0.7900.54
15_P185_L0.7890.54
70_Y185_L0.7890.54
112_Y173_D0.7860.54
16_S39_A0.7860.54
128_V135_K0.7850.54
61_V70_Y0.7830.53
138_L168_A0.7820.53
78_A172_L0.7810.53
12_L81_I0.7780.53
147_A158_E0.7740.53
146_G149_F0.7740.53
101_E168_A0.7730.52
116_A177_R0.7720.52
113_D164_R0.7710.52
158_E197_E0.7660.52
112_Y116_A0.7630.51
190_L208_I0.7610.51
159_Q195_E0.7570.51
12_L80_V0.7540.51
69_Y172_L0.7530.51
115_L181_I0.7530.51
155_I188_A0.7510.50
110_T207_A0.7470.50
200_V203_P0.7360.49
10_S86_H0.7360.49
26_D59_I0.7310.48
31_P59_I0.7300.48
55_E178_Q0.7280.48
190_L199_I0.7270.48
126_S130_Q0.7270.48
194_L199_I0.7270.48
63_K89_P0.7250.48
152_K191_V0.7230.48
24_L121_V0.7180.47
5_I108_A0.7180.47
120_G220_K0.7160.47
80_V169_R0.7150.47
189_L193_M0.7110.47
144_S151_S0.6980.45
217_A221_H0.6920.45
112_Y206_R0.6900.45
13_S26_D0.6890.45
127_L218_F0.6880.44
118_Y122_Q0.6850.44
29_I67_H0.6810.44
57_K130_Q0.6790.44
26_D110_T0.6780.43
97_K106_H0.6720.43
151_S162_N0.6710.43
20_I27_G0.6700.43
133_L140_F0.6650.42
150_F165_R0.6640.42
13_S19_S0.6620.42
67_H198_W0.6620.42
75_S79_N0.6620.42
10_S52_K0.6620.42
124_A133_L0.6610.42
144_S216_I0.6590.42
156_N167_F0.6570.42
98_E102_K0.6520.41
67_H177_R0.6500.41
51_N91_A0.6450.40
123_M193_M0.6440.40
131_G144_S0.6440.40
142_V147_A0.6410.40
48_F108_A0.6390.40
134_K141_E0.6370.40
45_T198_W0.6350.40
44_Q52_K0.6330.39
8_I175_S0.6290.39
148_L201_R0.6280.39
36_A46_A0.6260.39
75_S133_L0.6260.39
13_S56_A0.6250.39
21_L175_S0.6240.39
38_L83_Q0.6200.38
76_D131_G0.6200.38
45_T48_F0.6180.38
113_D124_A0.6170.38
169_R175_S0.6160.38
192_R217_A0.6150.38
120_G126_S0.6150.38
62_E85_L0.6120.37
22_L85_L0.6110.37
67_H208_I0.6100.37
108_A203_P0.6090.37
46_A82_E0.6090.37
78_A150_F0.6080.37
43_P208_I0.6080.37
29_I34_E0.6050.37
5_I18_S0.6050.37
55_E148_L0.6040.37
197_E201_R0.6030.37
124_A211_T0.6020.37
79_N189_L0.6000.36
22_L120_G0.5990.36
30_H61_V0.5990.36
21_L30_H0.5970.36
140_F170_C0.5950.36
211_T217_A0.5940.36
131_G134_K0.5940.36
42_K118_Y0.5900.36
34_E172_L0.5870.35
20_I101_E0.5870.35
188_A192_R0.5790.35
25_M31_P0.5790.35
28_R96_L0.5790.35
122_Q125_H0.5760.34
8_I88_A0.5730.34
202_M209_R0.5700.34
72_L78_A0.5700.34
45_T81_I0.5680.34
30_H70_Y0.5670.34
68_R106_H0.5660.33
12_L87_I0.5660.33
112_Y121_V0.5620.33
115_L193_M0.5600.33
4_N88_A0.5580.33
42_K52_K0.5570.33
75_S125_H0.5570.33
156_N168_A0.5560.33
126_S223_N0.5550.33
132_M218_F0.5540.32
23_S38_L0.5530.32
59_I164_R0.5520.32
122_Q223_N0.5510.32
145_E148_L0.5500.32
181_I185_L0.5500.32
31_P70_Y0.5470.32
129_E219_E0.5470.32
5_I13_S0.5450.32
81_I85_L0.5450.32
30_H38_L0.5450.32
6_A192_R0.5450.32
134_K152_K0.5440.32
184_A188_A0.5430.32
131_G141_E0.5430.32
202_M205_T0.5420.31
75_S216_I0.5410.31
83_Q190_L0.5400.31
64_H69_Y0.5390.31
81_I122_Q0.5380.31
44_Q48_F0.5380.31
30_H69_Y0.5350.31
28_R110_T0.5340.31
12_L216_I0.5320.31
154_G197_E0.5310.31
80_V147_A0.5300.31
7_K88_A0.5280.30
187_N198_W0.5260.30
132_M143_T0.5260.30
4_N83_Q0.5230.30
96_L194_L0.5190.30
5_I79_N0.5180.30
48_F120_G0.5180.30
26_D82_E0.5180.30
188_A222_L0.5170.29
157_E200_V0.5170.29
84_L123_M0.5130.29
109_R206_R0.5110.29
119_V210_I0.5100.29
95_S100_K0.5100.29
150_F193_M0.5060.29
193_M199_I0.5060.29
15_P223_N0.5060.29
171_C186_G0.5060.29
67_H165_R0.5050.29
12_L26_D0.5040.28
23_S168_A0.5040.28
22_L182_A0.5030.28
121_V154_G0.5030.28
34_E170_C0.5010.28
10_S43_P0.5000.28
76_D90_K0.5000.28
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  
2kkoA 2 0.4336 99.4 0.828 Contact Map
1r1tA 2 0.3982 99.4 0.83 Contact Map
1u2wA 2 0.4071 99.4 0.831 Contact Map
1q1hA 1 0.3451 99.3 0.835 Contact Map
1r1uA 2 0.4071 99.3 0.837 Contact Map
2zkzA 2 0.3805 99.3 0.838 Contact Map
3pqkA 2 0.4115 99.3 0.838 Contact Map
3cuoA 2 0.3938 99.3 0.841 Contact Map
4k2eA 2 0.3938 99.2 0.841 Contact Map
3f6vA 2 0.4248 99.2 0.846 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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