GREMLIN Database
YFJR - Uncharacterized HTH-type transcriptional regulator YfjR
UniProt: P52133 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13204
Length: 233 (198)
Sequences: 5974 (4244)
Seq/√Len: 301.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
143_L153_L4.1831.00
131_L141_V4.0971.00
140_R154_A3.6621.00
142_T152_R3.2431.00
143_L183_I3.2191.00
140_R152_R3.2021.00
144_I150_C3.1341.00
153_L167_L3.1141.00
142_T187_Q2.9771.00
142_T150_C2.9481.00
133_Q137_G2.7471.00
14_R47_D2.7251.00
39_V44_L2.7001.00
31_R35_A2.6341.00
144_I185_L2.5181.00
140_R191_E2.3811.00
139_R188_P2.3071.00
146_E184_H2.2201.00
144_I148_R2.1441.00
138_R195_R2.0041.00
31_R41_V1.9831.00
139_R190_Q1.9651.00
153_L169_A1.9161.00
33_L44_L1.9111.00
59_Y62_G1.9021.00
142_T189_L1.8861.00
49_R52_L1.8831.00
30_V41_V1.8571.00
151_E178_F1.8341.00
29_S32_K1.8241.00
21_R28_L1.8071.00
196_N199_L1.8031.00
130_R186_I1.7851.00
144_I184_H1.7341.00
30_V45_R1.6591.00
200_C203_V1.6041.00
139_R192_T1.5901.00
152_R191_E1.5821.00
131_L180_L1.5651.00
98_R102_A1.5491.00
138_R193_F1.5471.00
32_K35_A1.5081.00
170_E173_G1.4881.00
133_Q188_P1.4651.00
27_T65_R1.4491.00
183_I186_I1.4451.00
156_C193_F1.4371.00
148_R184_H1.4321.00
130_R188_P1.4171.00
130_R133_Q1.4061.00
152_R189_L1.3961.00
78_D98_R1.3891.00
30_V64_C1.3531.00
151_E172_E1.3431.00
41_V45_R1.3161.00
203_V207_V1.2991.00
164_T179_T1.2891.00
143_L186_I1.2881.00
25_G28_L1.2721.00
169_A178_F1.2561.00
140_R189_L1.2451.00
43_T46_R1.2381.00
18_I44_L1.2321.00
152_R171_H1.2271.00
21_R36_E1.2181.00
21_R37_F1.2041.00
30_V44_L1.1731.00
199_L204_E1.1611.00
11_L50_E1.1571.00
143_L169_A1.1451.00
105_M109_S1.1211.00
48_F64_C1.1191.00
134_A188_P1.1171.00
156_C175_I1.1121.00
177_V208_F1.0971.00
154_A193_F1.0951.00
82_F86_S1.0931.00
154_A196_N1.0871.00
143_L185_L1.0771.00
58_E62_G1.0661.00
139_R189_L1.0601.00
34_A44_L1.0561.00
49_R53_M1.0501.00
171_H178_F1.0441.00
141_V153_L1.0381.00
201_R204_E1.0351.00
155_P167_L1.0311.00
112_V115_P1.0181.00
17_L37_F1.0071.00
172_E176_A1.0061.00
11_L15_L1.0061.00
131_L183_I1.0041.00
75_M94_G0.9971.00
127_S130_R0.9951.00
143_L178_F0.9901.00
157_R201_R0.9851.00
151_E176_A0.9801.00
106_C109_S0.9791.00
32_K36_E0.9741.00
27_T63_Y0.9641.00
95_L98_R0.9481.00
157_R168_V0.9461.00
19_I51_R0.9451.00
159_L168_V0.9371.00
158_L180_L0.9351.00
22_L66_L0.9271.00
127_S186_I0.9211.00
170_E174_H0.9211.00
118_P161_H0.9101.00
21_R33_L0.9081.00
166_Y177_V0.8981.00
143_L184_H0.8941.00
48_F52_L0.8781.00
156_C169_A0.8571.00
56_D70_G0.8531.00
141_V186_I0.8521.00
156_C199_L0.8481.00
19_I55_L0.8461.00
170_E196_N0.8451.00
177_V204_E0.8441.00
113_I116_A0.8421.00
172_E178_F0.8411.00
16_S20_S0.8401.00
107_D110_P0.8381.00
13_V50_E0.8381.00
135_I158_L0.8371.00
149_R171_H0.8261.00
63_Y66_L0.8241.00
201_R205_D0.8241.00
200_C204_E0.8211.00
56_D165_W0.8201.00
112_V116_A0.8201.00
161_H166_Y0.8191.00
149_R178_F0.8161.00
58_E61_S0.8161.00
156_C196_N0.8141.00
39_V43_T0.8111.00
94_G97_R0.8101.00
12_A50_E0.8091.00
12_A15_L0.8011.00
204_E208_F0.8001.00
168_V199_L0.7770.99
107_D111_C0.7720.99
168_V177_V0.7690.99
21_R25_G0.7620.99
145_A151_E0.7620.99
97_R100_V0.7610.99
179_T182_E0.7520.99
131_L186_I0.7490.99
175_I199_L0.7480.99
145_A182_E0.7450.99
20_S23_V0.7430.99
171_H174_H0.7400.99
55_L66_L0.7400.99
30_V34_A0.7370.99
128_F180_L0.7360.99
134_A141_V0.7360.99
37_F44_L0.7360.99
145_A178_F0.7270.99
52_L57_L0.7260.99
154_A170_E0.7190.99
168_V204_E0.7160.99
72_E79_V0.7140.99
78_D81_I0.7120.99
95_L102_A0.7120.99
28_L32_K0.7090.99
25_G32_K0.7070.99
87_G91_L0.6990.99
114_A118_P0.6980.99
13_V17_L0.6960.99
34_A41_V0.6940.99
144_I187_Q0.6930.99
188_P191_E0.6920.99
168_V201_R0.6910.99
104_L108_E0.6890.99
175_I196_N0.6890.99
55_L70_G0.6880.99
166_Y182_E0.6850.99
62_G66_L0.6820.99
50_E54_Y0.6780.98
185_L188_P0.6720.98
126_L130_R0.6710.98
51_R66_L0.6700.98
15_L51_R0.6690.98
106_C111_C0.6680.98
30_V48_F0.6640.98
39_V47_D0.6630.98
124_G127_S0.6610.98
64_C70_G0.6600.98
44_L47_D0.6600.98
98_R104_L0.6580.98
18_I28_L0.6550.98
159_L177_V0.6550.98
42_R63_Y0.6550.98
132_I158_L0.6530.98
52_L55_L0.6520.98
170_E178_F0.6500.98
28_L33_L0.6490.98
62_G166_Y0.6470.98
167_L183_I0.6470.98
104_L107_D0.6470.98
86_S96_D0.6460.98
153_L183_I0.6450.98
57_L63_Y0.6370.98
149_R172_E0.6330.98
83_A96_D0.6320.98
77_P91_L0.6310.98
11_L47_D0.6310.98
47_D51_R0.6300.98
168_V175_I0.6290.98
131_L167_L0.6280.97
202_L206_P0.6270.97
176_A182_E0.6270.97
17_L20_S0.6250.97
72_E78_D0.6240.97
150_C187_Q0.6230.97
89_A93_P0.6200.97
99_L103_L0.6180.97
155_P169_A0.6180.97
121_S124_G0.6170.97
11_L54_Y0.6130.97
114_A161_H0.6130.97
204_E207_V0.6130.97
137_G188_P0.6120.97
128_F165_W0.6110.97
150_C185_L0.6110.97
129_W133_Q0.6100.97
98_R103_L0.6090.97
92_F95_L0.6080.97
44_L48_F0.6050.97
100_V108_E0.6040.97
45_R64_C0.6040.97
90_G94_G0.6030.97
81_I95_L0.6030.97
167_L180_L0.6020.97
59_Y63_Y0.6000.97
105_M108_E0.6000.97
22_L57_L0.5950.97
116_A119_V0.5950.97
74_Q82_F0.5920.96
89_A92_F0.5890.96
62_G69_A0.5860.96
196_N200_C0.5850.96
15_L50_E0.5840.96
129_W132_I0.5840.96
96_D100_V0.5770.96
202_L207_V0.5750.96
200_C205_D0.5750.96
159_L164_T0.5740.96
77_P80_L0.5730.96
28_L55_L0.5720.96
19_I66_L0.5710.96
79_V95_L0.5710.96
24_A36_E0.5710.96
108_E111_C0.5700.96
87_G90_G0.5700.96
140_R144_I0.5690.96
92_F96_D0.5690.96
135_I155_P0.5680.95
18_I33_L0.5670.95
166_Y179_T0.5670.95
40_S43_T0.5610.95
23_V37_F0.5550.95
133_Q139_R0.5510.95
17_L21_R0.5480.95
129_W150_C0.5420.94
52_L67_R0.5410.94
185_L191_E0.5410.94
171_H176_A0.5360.94
80_L84_H0.5340.94
67_R70_G0.5340.94
62_G68_T0.5330.94
30_V40_S0.5330.94
135_I159_L0.5310.94
203_V206_P0.5300.94
87_G132_I0.5300.94
62_G165_W0.5300.94
174_H178_F0.5290.93
43_T48_F0.5250.93
88_L91_L0.5240.93
42_R46_R0.5220.93
30_V52_L0.5210.93
35_A38_G0.5210.93
46_R63_Y0.5190.93
119_V123_S0.5190.93
13_V38_G0.5180.93
105_M110_P0.5170.93
78_D94_G0.5160.93
19_I23_V0.5120.92
141_V188_P0.5110.92
184_H187_Q0.5080.92
66_L69_A0.5080.92
67_R71_S0.5040.92
34_A39_V0.5030.92
157_R195_R0.5030.92
197_D200_C0.5020.92
143_L152_R0.5000.91
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  
1j5yA 4 0.6609 98 0.835 Contact Map
2l0kA 1 0.3948 97.6 0.848 Contact Map
2p5kA 1 0.2489 97.6 0.849 Contact Map
3sqnA 2 0.8455 97.3 0.856 Contact Map
2heoA 1 0.2489 97.2 0.858 Contact Map
1oyiA 1 0.2532 97 0.863 Contact Map
1b4aA 5 0.6052 96.9 0.863 Contact Map
4a0zA 2 0.7425 96.8 0.866 Contact Map
2g7uA 6 0.8884 96.6 0.869 Contact Map
2ia2A 4 0.8755 96.5 0.871 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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