GREMLIN Database
YVMB - Uncharacterized HTH-type transcriptional regulator YvmB
UniProt: P40762 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 169 (131)
Sequences: 1843 (1499)
Seq/√Len: 131.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
92_N106_K2.8471.00
56_I62_I2.6891.00
140_E150_Q2.4841.00
137_S140_E2.4501.00
144_V147_F2.4291.00
89_E110_K2.3711.00
110_K113_R2.3701.00
94_Y106_K2.3411.00
99_N102_E2.3001.00
57_G115_F2.2911.00
63_N66_G2.2681.00
56_I91_I2.2331.00
49_S88_E2.2101.00
136_F147_F2.2071.00
143_A146_K2.1841.00
109_R112_R2.1821.00
82_S91_I2.1661.00
63_N102_E2.0721.00
96_L99_N2.0541.00
93_S100_K2.0411.00
61_P106_K2.0301.00
51_H118_H1.8971.00
136_F150_Q1.8801.00
140_E146_K1.8221.00
73_L78_V1.7941.00
46_N49_S1.7671.00
82_S86_I1.6961.00
59_H62_I1.6811.00
62_I70_K1.6291.00
77_N80_K1.6091.00
140_E143_A1.5681.00
64_N105_F1.5341.00
67_I105_F1.4681.00
118_H122_H1.4591.00
95_Q103_V1.4111.00
93_S103_V1.3961.00
57_G107_L1.3741.00
96_L101_K1.3671.00
53_I107_L1.3521.00
53_I115_F1.3501.00
86_I105_F1.3491.00
135_S154_T1.3181.00
54_D76_A1.3121.00
86_I93_S1.3121.00
52_V81_I1.3091.00
74_S77_N1.2971.00
96_L102_E1.2941.00
64_N82_S1.2421.00
120_K124_K1.2271.00
80_K84_K1.2251.00
112_R116_D1.2131.00
53_I57_G1.1990.99
83_T100_K1.1990.99
74_S80_K1.1980.99
46_N84_K1.1640.99
59_H70_K1.1550.99
134_D142_K1.1040.99
143_A147_F1.0990.99
52_V78_V1.0960.99
96_L104_Y1.0610.99
83_T93_S1.0600.99
138_Q142_K1.0440.99
130_Y134_D1.0400.98
142_K146_K1.0360.98
145_L149_E1.0250.98
52_V67_I1.0220.98
79_T83_T1.0070.98
55_C62_I1.0040.98
68_A74_S0.9970.98
62_I66_G0.9850.98
27_S31_F0.9850.98
44_P88_E0.9770.98
53_I85_L0.9580.97
60_E106_K0.9510.97
65_A75_K0.9440.97
100_K103_V0.9300.97
57_G112_R0.9220.97
82_S105_F0.9150.97
55_C71_M0.8970.96
76_A82_S0.8830.96
80_K99_N0.8770.96
46_N129_F0.8670.95
64_N79_T0.8620.95
66_G69_R0.8580.95
51_H122_H0.8570.95
36_A39_D0.8490.95
109_R113_R0.8370.94
50_I56_I0.8300.94
54_D58_Q0.8270.94
65_A102_E0.8220.94
113_R116_D0.8110.93
73_L80_K0.8110.93
52_V56_I0.8110.93
32_F35_A0.8040.93
45_K131_Q0.7870.92
65_A77_N0.7860.92
139_E142_K0.7830.92
137_S141_Q0.7790.92
31_F35_A0.7720.92
131_Q157_A0.7540.91
28_L36_A0.7510.90
51_H76_A0.7500.90
142_K153_S0.7180.88
81_I84_K0.7160.88
145_L152_T0.7160.88
63_N104_Y0.7110.88
46_N74_S0.7020.87
29_Q33_K0.7000.87
36_A40_V0.6930.87
45_K90_F0.6890.86
68_A77_N0.6870.86
107_L111_G0.6870.86
26_T35_A0.6860.86
87_K98_D0.6850.86
44_P110_K0.6850.86
139_E143_A0.6760.85
87_K114_I0.6710.85
64_N78_V0.6690.85
48_T77_N0.6660.84
73_L144_V0.6650.84
65_A69_R0.6620.84
146_K150_Q0.6480.83
78_V86_I0.6470.83
49_S64_N0.6410.82
50_I101_K0.6410.82
68_A78_V0.6400.82
116_D142_K0.6350.81
131_Q134_D0.6350.81
87_K137_S0.6350.81
85_L90_F0.6300.81
37_E40_V0.6300.81
79_T102_E0.6280.81
83_T87_K0.6230.80
58_Q115_F0.6210.80
49_S154_T0.6200.80
141_Q145_L0.6160.79
27_S34_E0.6120.79
46_N100_K0.6110.79
147_F150_Q0.6070.78
51_H55_C0.6030.78
79_T99_N0.6010.78
119_E123_K0.6000.78
59_H134_D0.6000.78
86_I97_T0.5980.77
25_N29_Q0.5940.77
95_Q100_K0.5920.77
64_N75_K0.5910.77
49_S101_K0.5870.76
60_E105_F0.5850.76
90_F107_L0.5840.76
135_S150_Q0.5780.75
39_D42_E0.5760.75
136_F155_L0.5740.75
68_A83_T0.5720.74
49_S74_S0.5720.74
43_I117_L0.5700.74
48_T81_I0.5690.74
150_Q153_S0.5660.74
66_G156_E0.5660.74
136_F140_E0.5640.73
46_N50_I0.5640.73
48_T52_V0.5630.73
77_N132_F0.5630.73
92_N109_R0.5620.73
49_S118_H0.5610.73
135_S143_A0.5600.73
95_Q102_E0.5600.73
68_A75_K0.5580.72
78_V83_T0.5490.71
149_E152_T0.5480.71
122_H125_K0.5460.71
80_K105_F0.5450.71
148_L156_E0.5450.71
49_S114_I0.5440.71
119_E146_K0.5430.70
82_S119_E0.5420.70
51_H68_A0.5420.70
48_T71_M0.5390.70
35_A40_V0.5340.69
62_I67_I0.5340.69
73_L77_N0.5320.69
44_P90_F0.5320.69
37_E41_A0.5320.69
130_Y151_L0.5290.68
50_I118_H0.5220.67
89_E108_T0.5170.67
86_I91_I0.5170.67
149_E157_A0.5160.67
43_I58_Q0.5120.66
55_C153_S0.5110.66
63_N75_K0.5090.66
93_S105_F0.5060.65
90_F110_K0.5030.65
80_K83_T0.5020.64
31_F72_N0.5010.64
56_I85_L0.5000.64
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  
2rdpA 2 0.8284 99.9 0.451 Contact Map
4mnuA 2 0.8876 99.9 0.46 Contact Map
1lj9A 2 0.8521 99.9 0.46 Contact Map
2fbkA 2 0.8107 99.8 0.462 Contact Map
4yifA 2 0.8343 99.8 0.462 Contact Map
3s2wA 3 0.8343 99.8 0.464 Contact Map
1s3jA 2 0.8521 99.8 0.464 Contact Map
3g3zA 2 0.8402 99.8 0.466 Contact Map
3tgnA 2 0.8639 99.8 0.466 Contact Map
3deuA 2 0.7751 99.8 0.467 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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