GREMLIN Database
YVAF - Uncharacterized HTH-type transcriptional regulator YvaF
UniProt: O32228 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 190 (174)
Sequences: 36345 (28764)
Seq/√Len: 2180.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
16_K24_D3.9181.00
23_N33_K3.9071.00
11_R28_A3.7211.00
41_S45_Q2.8001.00
122_L140_D2.3101.00
13_I20_F2.3091.00
76_K127_E2.1711.00
26_A36_L2.1691.00
12_L20_F2.1391.00
15_Q28_A2.1141.00
42_S45_Q2.0921.00
32_S35_T2.0801.00
72_N75_E1.9111.00
3_K53_Q1.9021.00
94_G98_E1.9021.00
126_N130_Q1.8641.00
122_L126_N1.8631.00
4_R8_E1.7361.00
22_M33_K1.7291.00
23_N27_A1.7141.00
126_N139_P1.6961.00
12_L28_A1.6931.00
8_E28_A1.6901.00
129_K136_N1.6811.00
10_F53_Q1.6771.00
12_L24_D1.6531.00
126_N129_K1.6281.00
12_L16_K1.5791.00
9_T13_I1.5591.00
22_M37_Y1.5301.00
3_K7_A1.4961.00
49_A52_E1.4711.00
6_L49_A1.4701.00
78_K171_E1.4641.00
8_E11_R1.4561.00
17_G20_F1.4341.00
35_T38_A1.4211.00
128_C134_I1.4201.00
82_I167_G1.4041.00
128_C133_R1.3981.00
22_M36_L1.3901.00
40_Y49_A1.3881.00
48_E109_T1.3821.00
127_E131_Q1.3721.00
52_E109_T1.3691.00
72_N133_R1.3561.00
24_D27_A1.3531.00
10_F50_V1.3391.00
63_R120_I1.3371.00
20_F25_L1.3311.00
7_A53_Q1.3181.00
11_R15_Q1.3151.00
32_S38_A1.2931.00
141_L172_S1.2911.00
21_T24_D1.2861.00
129_K137_I1.2791.00
10_F54_F1.2621.00
138_N141_L1.2481.00
24_D28_A1.2381.00
82_I170_L1.2361.00
118_W144_H1.2361.00
145_M149_S1.2351.00
82_I171_E1.2341.00
53_Q57_E1.2161.00
44_D103_H1.2051.00
48_E52_E1.1971.00
9_T46_L1.1961.00
31_T35_T1.1901.00
18_F47_V1.1901.00
61_I83_S1.1871.00
74_L78_K1.1861.00
124_L128_C1.1751.00
45_Q49_A1.1721.00
78_K82_I1.1631.00
91_L98_E1.1601.00
34_R38_A1.1421.00
165_T168_E1.1221.00
75_E79_Q1.1201.00
8_E12_L1.1131.00
118_W122_L1.0921.00
13_I18_F1.0801.00
25_L46_L1.0791.00
8_E29_L1.0711.00
35_T39_Y1.0491.00
37_Y42_S1.0421.00
6_L50_V1.0391.00
52_E56_A1.0321.00
129_K139_P1.0321.00
148_G152_Q1.0121.00
74_L178_F1.0101.00
137_I142_F1.0011.00
44_D48_E0.9841.00
73_V131_Q0.9811.00
7_A11_R0.9791.00
33_K37_Y0.9781.00
45_Q48_E0.9731.00
6_L40_Y0.9661.00
61_I64_D0.9591.00
78_K174_V0.9561.00
83_S86_Q0.9491.00
141_L168_E0.9401.00
91_L94_G0.9401.00
123_A126_N0.9381.00
129_K132_K0.9351.00
75_E78_K0.9341.00
122_L139_P0.9331.00
44_D105_D0.9311.00
82_I86_Q0.9241.00
78_K175_D0.9241.00
73_V128_C0.9161.00
76_K124_L0.9141.00
92_N98_E0.9121.00
93_M98_E0.9091.00
123_A127_E0.9081.00
109_T112_A0.9061.00
120_I123_A0.9001.00
119_A123_A0.8981.00
127_E130_Q0.8831.00
92_N95_L0.8811.00
33_K38_A0.8801.00
167_G171_E0.8751.00
10_F14_K0.8721.00
63_R67_E0.8681.00
162_H165_T0.8651.00
79_Q82_I0.8641.00
112_A116_E0.8591.00
94_G97_N0.8551.00
5_I36_L0.8551.00
49_A53_Q0.8491.00
56_A60_Q0.8481.00
98_E101_K0.8471.00
118_W140_D0.8431.00
53_Q56_A0.8421.00
36_L46_L0.8421.00
16_K20_F0.8411.00
171_E175_D0.8381.00
18_F43_K0.8281.00
94_G101_K0.8271.00
52_E113_F0.8241.00
174_V178_F0.8231.00
104_Y107_W0.8101.00
139_P143_V0.8071.00
109_T113_F0.8061.00
170_L174_V0.7991.00
65_I83_S0.7941.00
125_L139_P0.7891.00
140_D144_H0.7891.00
146_Y177_L0.7861.00
65_I79_Q0.7831.00
59_K120_I0.7811.00
26_A33_K0.7791.00
95_L99_L0.7741.00
108_L112_A0.7741.00
16_K28_A0.7701.00
168_E172_S0.7691.00
122_L143_V0.7691.00
54_F57_E0.7681.00
73_V133_R0.7671.00
59_K116_E0.7591.00
68_N79_Q0.7571.00
172_S175_D0.7531.00
69_E72_N0.7531.00
86_Q167_G0.7521.00
104_Y108_L0.7461.00
82_I174_V0.7441.00
27_A33_K0.7431.00
157_E160_L0.7381.00
115_K119_A0.7381.00
22_M26_A0.7321.00
60_Q64_D0.7301.00
9_T50_V0.7291.00
81_L146_Y0.7281.00
97_N101_K0.7271.00
93_M96_L0.7241.00
18_F44_D0.7211.00
149_S173_I0.7201.00
96_L99_L0.7141.00
125_L129_K0.7121.00
119_A122_L0.7021.00
12_L15_Q0.7021.00
79_Q83_S0.7021.00
125_L146_Y0.7021.00
95_L98_E0.7011.00
126_N140_D0.7011.00
13_I47_V0.7011.00
86_Q90_L0.7001.00
19_S98_E0.6961.00
4_R29_L0.6951.00
93_M97_N0.6911.00
111_D115_K0.6851.00
72_N76_K0.6791.00
57_E60_Q0.6791.00
84_L88_M0.6731.00
23_N37_Y0.6651.00
69_E76_K0.6521.00
92_N97_N0.6521.00
31_T39_Y0.6471.00
60_Q63_R0.6461.00
6_L53_Q0.6411.00
86_Q166_T0.6381.00
5_I29_L0.6381.00
29_L32_S0.6371.00
148_G151_N0.6351.00
7_A10_F0.6271.00
86_Q170_L0.6231.00
166_T170_L0.6221.00
116_E119_A0.6191.00
59_K63_R0.6191.00
56_A113_F0.6161.00
111_D114_I0.6161.00
5_I39_Y0.6121.00
138_N172_S0.6111.00
107_W111_D0.6101.00
94_G99_L0.6071.00
108_L111_D0.6011.00
129_K134_I0.5981.00
124_L127_E0.5981.00
92_N99_L0.5911.00
69_E79_Q0.5881.00
64_D68_N0.5841.00
91_L95_L0.5821.00
78_K178_F0.5801.00
148_G156_P0.5801.00
83_S87_G0.5791.00
92_N96_L0.5771.00
125_L142_F0.5771.00
4_R7_A0.5751.00
138_N142_F0.5711.00
103_H106_A0.5701.00
66_Y120_I0.5671.00
156_P159_P0.5651.00
36_L41_S0.5631.00
73_V134_I0.5631.00
6_L10_F0.5631.00
78_K81_L0.5621.00
26_A29_L0.5591.00
89_E166_T0.5591.00
128_C132_K0.5571.00
169_V173_I0.5561.00
26_A31_T0.5551.00
65_I68_N0.5521.00
64_D83_S0.5511.00
168_E171_E0.5491.00
65_I69_E0.5471.00
19_S101_K0.5451.00
15_Q24_D0.5411.00
91_L97_N0.5381.00
141_L145_M0.5381.00
145_M148_G0.5361.00
73_V76_K0.5301.00
52_E112_A0.5261.00
76_K128_C0.5251.00
172_S176_V0.5241.00
170_L173_I0.5231.00
164_F168_E0.5191.00
66_Y123_A0.5161.00
84_L151_N0.5071.00
87_G90_L0.5041.00
113_F116_E0.5021.00
164_F167_G0.5001.00
167_G170_L0.5001.00
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  
4udsA 2 0.9421 100 0.262 Contact Map
2ibdA 2 0.9579 100 0.266 Contact Map
1vi0A 2 0.9632 100 0.27 Contact Map
2rasA 2 0.9947 100 0.272 Contact Map
2xdnA 2 0.9947 100 0.272 Contact Map
2hytA 2 0.9684 100 0.274 Contact Map
4kwaA 2 0.9579 100 0.274 Contact Map
2genA 2 0.9632 100 0.275 Contact Map
3bqzB 3 0.9474 100 0.276 Contact Map
3dcfA 2 0.9368 100 0.277 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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