GREMLIN Database
YDFL - Uncharacterized HTH-type transcriptional regulator YdfL
UniProt: P96690 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 270 (228)
Sequences: 3777 (3199)
Seq/√Len: 211.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
88_Q106_S5.1021.00
95_K99_E4.9591.00
36_D39_T3.7811.00
92_D102_E3.2211.00
87_Q90_E3.1441.00
18_I22_R3.0461.00
45_S48_Q2.9201.00
25_D31_K2.8731.00
30_L55_I2.6431.00
23_Y27_I2.4591.00
51_R73_N2.4071.00
94_K97_E2.3701.00
85_K113_E2.3111.00
95_K98_L2.2441.00
7_I22_R2.2371.00
207_S211_L2.2211.00
36_D43_Y2.1661.00
59_R65_I2.1521.00
33_E48_Q2.1461.00
189_F192_L2.1191.00
215_F225_Y2.1151.00
88_Q102_E2.0721.00
8_G12_K2.0541.00
27_I65_I2.0281.00
64_P67_K1.9471.00
81_L109_I1.9241.00
62_G94_K1.9181.00
88_Q92_D1.9001.00
85_K109_I1.8091.00
211_L233_M1.7861.00
67_K70_D1.7671.00
94_K98_L1.7521.00
91_I98_L1.7121.00
69_L73_N1.6871.00
188_I192_L1.6631.00
10_V52_L1.5961.00
6_S9_E1.5871.00
91_I102_E1.5861.00
88_Q109_I1.5481.00
98_L102_E1.5271.00
95_K102_E1.5101.00
89_V93_R1.5061.00
33_E45_S1.4951.00
28_G31_K1.4871.00
7_I18_I1.4551.00
92_D106_S1.4481.00
81_L113_E1.4321.00
5_F46_T1.4301.00
34_Y43_Y1.4291.00
23_Y26_E1.4291.00
63_L71_F1.4191.00
84_L105_I1.4091.00
127_K209_E1.4081.00
23_Y65_I1.3981.00
187_S192_L1.3981.00
67_K86_S1.3921.00
16_V52_L1.3871.00
211_L232_Y1.3861.00
178_K181_Q1.3641.00
169_G189_F1.3441.00
188_I193_E1.3441.00
56_K59_R1.3401.00
52_L56_K1.3401.00
186_S189_F1.3341.00
174_A178_K1.3341.00
10_V49_F1.3291.00
20_A23_Y1.3271.00
19_S26_E1.3031.00
21_L25_D1.3011.00
114_D118_M1.2971.00
91_I101_I1.2681.00
149_S152_E1.2661.00
51_R72_Y1.2591.00
9_E12_K1.2561.00
169_G172_I1.2511.00
90_E94_K1.2391.00
33_E47_Q1.2251.00
88_Q105_I1.2181.00
175_A178_K1.2181.00
96_K99_E1.2171.00
146_I150_L1.2091.00
109_I113_E1.2061.00
187_S190_M1.2021.00
192_L196_N1.2021.00
174_A177_V1.1891.00
11_S17_K1.1781.00
76_N79_T1.1751.00
130_A204_I1.1731.00
91_I105_I1.1621.00
186_S192_L1.1581.00
35_K48_Q1.1361.00
24_Y52_L1.1261.00
32_P35_K1.1251.00
92_D95_K1.1191.00
39_T43_Y1.1191.00
6_S43_Y1.1141.00
180_K184_K1.1091.00
97_E101_I1.1051.00
127_K207_S1.1031.00
21_L27_I1.1001.00
189_F196_N1.0991.00
162_D166_G1.0941.00
4_F34_Y1.0911.00
31_K35_K1.0901.00
177_V180_K1.0811.00
213_I225_Y1.0671.00
14_F52_L1.0621.00
8_G18_I1.0541.00
90_E93_R1.0521.00
29_L55_I1.0461.00
153_L157_L1.0411.00
156_H160_N1.0411.00
63_L87_Q1.0401.00
89_V92_D1.0141.00
134_A138_H1.0131.00
10_V48_Q1.0111.00
168_I171_S1.0091.00
157_L160_N1.0041.00
35_K43_Y0.9971.00
193_E197_E0.9961.00
193_E196_N0.9821.00
120_L124_S0.9761.00
143_G147_E0.9751.00
150_L153_L0.9751.00
190_M193_E0.9671.00
10_V14_F0.9611.00
169_G173_S0.9601.00
147_E151_A0.9410.99
84_L109_I0.9360.99
25_D42_R0.9360.99
222_A226_Y0.9360.99
180_K183_D0.9300.99
11_S14_F0.9240.99
115_A118_M0.9230.99
106_S110_T0.9200.99
137_Q183_D0.9170.99
176_N181_Q0.9140.99
59_R62_G0.9090.99
130_A207_S0.9070.99
152_E156_H0.9050.99
148_H151_A0.8910.99
125_K209_E0.8840.99
153_L156_H0.8790.99
11_S18_I0.8730.99
81_L85_K0.8700.99
186_S190_M0.8680.99
17_K23_Y0.8590.99
93_R96_K0.8550.99
149_S157_L0.8520.99
213_I229_L0.8500.99
175_A179_A0.8490.99
168_I172_I0.8480.99
149_S156_H0.8470.99
110_T115_A0.8450.99
153_L161_E0.8430.99
121_H125_K0.8420.99
120_L125_K0.8350.99
55_I68_L0.8340.99
192_L197_E0.8330.99
60_A101_I0.8290.99
176_N180_K0.8280.99
177_V184_K0.8250.99
7_I42_R0.8250.99
86_S89_V0.8200.99
18_I39_T0.8110.98
227_K231_A0.8050.98
191_I196_N0.7980.98
189_F193_E0.7950.98
17_K20_A0.7900.98
177_V181_Q0.7900.98
63_L83_L0.7830.98
148_H152_E0.7820.98
178_K183_D0.7810.98
128_L131_M0.7780.98
145_D148_H0.7770.98
215_F221_E0.7760.98
82_H86_S0.7750.98
14_F30_L0.7750.98
179_A182_F0.7710.98
70_D74_S0.7650.98
179_A184_K0.7630.98
186_S191_I0.7540.98
96_K100_R0.7530.97
59_R68_L0.7520.97
198_K201_S0.7520.97
155_T159_V0.7450.97
176_N184_K0.7430.97
174_A180_K0.7420.97
183_D186_S0.7380.97
177_V182_F0.7370.97
78_N82_H0.7360.97
88_Q91_I0.7360.97
67_K87_Q0.7340.97
216_K228_K0.7320.97
7_I11_S0.7320.97
19_S22_R0.7300.97
174_A184_K0.7290.97
156_H161_E0.7280.97
228_K231_A0.7280.97
98_L101_I0.7270.97
43_Y48_Q0.7270.97
181_Q184_K0.7250.97
58_L71_F0.7240.97
184_K187_S0.7240.97
150_L156_H0.7210.97
27_I59_R0.7170.97
192_L198_K0.7160.97
21_L44_Y0.7150.97
209_E215_F0.7130.97
167_K171_S0.7100.96
178_K182_F0.7100.96
152_E157_L0.7090.96
25_D30_L0.7050.96
221_E224_P0.7010.96
127_K130_A0.7010.96
188_I191_I0.6940.96
179_A183_D0.6910.96
60_A97_E0.6890.96
175_A182_F0.6880.96
161_E165_I0.6870.96
133_V203_I0.6830.96
16_V20_A0.6800.95
62_G97_E0.6790.95
135_Y214_R0.6770.95
192_L195_E0.6770.95
133_V137_Q0.6740.95
166_G169_G0.6720.95
30_L52_L0.6690.95
154_R157_L0.6690.95
187_S191_I0.6660.95
165_I169_G0.6650.95
14_F19_S0.6640.95
143_G146_I0.6620.95
195_E198_K0.6620.95
143_G149_S0.6570.95
176_N182_F0.6560.94
145_D149_S0.6540.94
150_L154_R0.6520.94
110_T114_D0.6490.94
53_D57_Y0.6490.94
136_L140_Y0.6460.94
85_K89_V0.6440.94
224_P227_K0.6400.94
14_F49_F0.6380.94
53_D108_R0.6360.94
71_F83_L0.6350.93
70_D73_N0.6320.93
92_D96_K0.6300.93
7_I25_D0.6290.93
10_V30_L0.6250.93
157_L161_E0.6230.93
107_R111_H0.6190.93
184_K188_I0.6180.93
204_I208_R0.6180.93
5_F140_Y0.6160.92
165_I168_I0.6110.92
184_K189_F0.6110.92
21_L65_I0.6100.92
159_V162_D0.6090.92
34_Y45_S0.6090.92
149_S153_L0.6080.92
94_K101_I0.6050.92
63_L90_E0.6040.92
25_D59_R0.6030.92
87_Q105_I0.5980.91
22_R30_L0.5980.91
78_N116_V0.5970.91
166_G170_L0.5920.91
176_N183_D0.5910.91
127_K131_M0.5900.91
174_A182_F0.5880.91
136_L146_I0.5880.91
8_G11_S0.5870.91
220_P225_Y0.5870.91
132_R136_L0.5850.90
186_S193_E0.5830.90
216_K220_P0.5810.90
194_D197_E0.5800.90
38_Q43_Y0.5770.90
201_S204_I0.5770.90
191_I194_D0.5750.90
128_L133_V0.5750.90
48_Q51_R0.5680.89
112_I116_V0.5650.89
147_E150_L0.5650.89
44_Y68_L0.5650.89
208_R215_F0.5620.89
155_T161_E0.5600.88
175_A181_Q0.5590.88
59_R64_P0.5580.88
79_T82_H0.5580.88
87_Q91_I0.5550.88
16_V98_L0.5540.88
20_A52_L0.5540.88
173_S183_D0.5520.88
14_F25_D0.5520.88
44_Y65_I0.5500.88
135_Y141_V0.5500.88
82_H85_K0.5490.87
103_R106_S0.5480.87
29_L65_I0.5480.87
150_L157_L0.5470.87
13_L41_Y0.5460.87
213_I217_G0.5450.87
60_A94_K0.5430.87
19_S23_Y0.5420.87
14_F108_R0.5400.87
165_I172_I0.5400.87
205_F208_R0.5390.86
199_T202_E0.5380.86
184_K193_E0.5340.86
102_E106_S0.5330.86
204_I209_E0.5320.86
77_T83_L0.5300.86
74_S79_T0.5280.85
217_G221_E0.5260.85
85_K88_Q0.5240.85
20_A65_I0.5230.85
111_H118_M0.5220.85
25_D43_Y0.5210.85
71_F80_L0.5190.84
211_L221_E0.5190.84
136_L139_E0.5180.84
8_G22_R0.5180.84
186_S196_N0.5180.84
204_I207_S0.5170.84
87_Q101_I0.5130.84
153_L172_I0.5130.84
189_F197_E0.5130.84
93_R97_E0.5110.83
78_N206_P0.5110.83
180_K191_I0.5100.83
223_E227_K0.5060.83
23_Y59_R0.5050.83
24_Y207_S0.5040.83
154_R158_N0.5030.82
82_H231_A0.5020.82
216_K227_K0.5020.82
189_F198_K0.5010.82
191_I195_E0.5000.82
92_D99_E0.5000.82
112_I115_A0.5000.82
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  
1r8eA 2 0.9889 100 0.221 Contact Map
3qaoA 2 0.5111 99.9 0.509 Contact Map
3gpvA 2 0.4111 99.9 0.524 Contact Map
3hh0A 4 0.4889 99.9 0.524 Contact Map
3gp4A 4 0.4704 99.9 0.536 Contact Map
1r8dA 2 0.4037 99.9 0.543 Contact Map
2zhgA 2 0.4444 99.9 0.544 Contact Map
2vz4A 2 0.3704 99.9 0.547 Contact Map
1q06A 2 0.4519 99.9 0.555 Contact Map
4ua1A 2 0.4444 99.9 0.567 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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