GREMLIN Database
YFIR - Uncharacterized HTH-type transcriptional regulator YfiR
UniProt: O31560 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 205 (183)
Sequences: 44877 (35677)
Seq/√Len: 2637.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_K46_R3.9871.00
28_K37_D3.9401.00
23_T41_E3.5301.00
54_S58_E2.7751.00
25_F33_T2.4501.00
55_S58_E2.3561.00
39_V49_V2.1281.00
24_V41_E2.1171.00
14_Q62_R2.0291.00
27_R41_E1.9831.00
24_V37_D1.9771.00
139_S158_A1.9741.00
24_V28_K1.9421.00
24_V33_T1.9381.00
139_S143_Q1.9261.00
20_A41_E1.9241.00
13_R16_E1.8901.00
16_E20_A1.8901.00
15_A66_T1.8421.00
20_A23_T1.8241.00
83_S86_A1.8071.00
36_K40_E1.8031.00
87_S144_K1.7761.00
22_K66_T1.6581.00
45_S48_G1.6441.00
143_Q157_L1.6251.00
15_A19_E1.5651.00
18_L62_R1.5631.00
35_M46_R1.5521.00
143_Q146_I1.5511.00
23_T27_R1.5381.00
35_M50_Y1.5251.00
14_Q52_Y1.5141.00
37_D41_E1.5091.00
34_T37_D1.5051.00
143_Q147_D1.4931.00
62_R65_E1.4921.00
22_K67_G1.4901.00
159_T191_S1.4631.00
37_D40_E1.4631.00
21_A25_F1.4491.00
163_F167_M1.4011.00
53_F62_R1.3811.00
33_T38_V1.3791.00
61_R65_E1.3631.00
146_I153_P1.3521.00
145_G150_E1.3351.00
76_D137_R1.3221.00
48_G51_L1.3181.00
61_R126_Y1.3181.00
93_D189_A1.3071.00
66_T70_E1.3051.00
12_K16_E1.3011.00
89_S193_K1.2981.00
22_K63_I1.2921.00
21_A59_M1.2881.00
29_G32_L1.2801.00
29_G33_T1.2621.00
89_S190_E1.2621.00
20_A24_V1.2611.00
35_M49_V1.2511.00
145_G151_F1.2471.00
144_K148_Q1.2451.00
44_F48_G1.2431.00
74_K94_E1.2341.00
65_E126_Y1.2281.00
19_E66_T1.2071.00
28_K32_L1.1801.00
46_R50_Y1.1551.00
112_E116_T1.1481.00
146_I154_V1.1411.00
135_V162_K1.1351.00
86_A90_S1.1341.00
85_W89_S1.1331.00
89_S93_D1.1311.00
49_V59_M1.1151.00
45_S51_L1.1121.00
93_D186_S1.1121.00
57_E61_R1.0971.00
112_E115_V1.0971.00
108_P112_E1.0941.00
47_G51_L1.0921.00
184_D187_G1.0911.00
25_F30_F1.0781.00
156_P159_T1.0771.00
90_S93_D1.0751.00
135_V139_S1.0721.00
93_D190_E1.0621.00
57_E120_N1.0521.00
58_E62_R1.0501.00
20_A42_S1.0501.00
18_L53_F1.0491.00
87_S141_L1.0481.00
137_R140_R1.0421.00
13_R52_Y1.0351.00
30_F60_F1.0331.00
12_K15_A1.0261.00
22_K26_K1.0241.00
58_E61_R1.0231.00
141_L145_G1.0221.00
48_G52_Y1.0181.00
82_Q90_S1.0131.00
81_H87_S1.0111.00
93_D193_K1.0081.00
19_E23_T0.9961.00
57_E122_E0.9951.00
72_L133_L0.9801.00
139_S157_L0.9771.00
18_L63_I0.9771.00
18_L66_T0.9711.00
65_E69_D0.9711.00
10_K51_L0.9601.00
28_K41_E0.9561.00
50_Y55_S0.9561.00
38_V59_M0.9421.00
21_A63_I0.9331.00
146_I149_G0.9261.00
126_Y129_K0.9261.00
39_V46_R0.9201.00
86_A89_S0.9181.00
74_K77_K0.9131.00
107_A110_Q0.9131.00
146_I157_L0.9131.00
78_S94_E0.9051.00
140_R144_K0.9001.00
65_E130_R0.8971.00
190_E194_L0.8801.00
141_L144_K0.8801.00
90_S94_E0.8781.00
94_E97_E0.8741.00
159_T187_G0.8741.00
83_S150_E0.8711.00
13_R44_F0.8681.00
62_R66_T0.8661.00
78_S90_S0.8661.00
107_A111_F0.8651.00
166_N170_G0.8641.00
66_T69_D0.8581.00
40_E46_R0.8581.00
72_L76_D0.8571.00
93_D97_E0.8531.00
140_R143_Q0.8491.00
24_V27_R0.8481.00
46_R51_L0.8481.00
132_D136_E0.8411.00
187_G191_S0.8361.00
191_S194_L0.8311.00
139_S161_A0.8301.00
16_E42_S0.8231.00
135_V158_A0.8221.00
136_E140_R0.8171.00
73_R77_K0.8131.00
189_A192_A0.8121.00
98_G102_V0.8091.00
67_G70_E0.8081.00
186_S190_E0.8011.00
125_Q129_K0.8001.00
158_A162_K0.7971.00
175_A178_F0.7971.00
129_K133_L0.7951.00
16_E19_E0.7931.00
174_N177_Y0.7871.00
30_F56_T0.7821.00
11_D15_A0.7791.00
146_I151_F0.7781.00
126_Y130_R0.7751.00
9_H12_K0.7741.00
72_L137_R0.7741.00
84_V148_Q0.7711.00
189_A193_K0.7681.00
10_K13_R0.7581.00
102_V105_T0.7541.00
108_P116_T0.7451.00
23_T104_D0.7441.00
17_I49_V0.7431.00
28_K33_T0.7401.00
89_S194_L0.7391.00
17_I42_S0.7381.00
124_R128_E0.7321.00
70_E73_R0.7291.00
121_E125_Q0.7261.00
82_Q86_A0.7221.00
173_Q177_Y0.7211.00
166_N169_D0.7171.00
121_E124_R0.7151.00
69_D73_R0.7141.00
191_S195_Y0.7111.00
84_V145_G0.7061.00
144_K147_D0.7051.00
190_E193_K0.6981.00
111_F115_V0.6941.00
133_L137_R0.6901.00
100_R185_V0.6891.00
92_L164_F0.6861.00
27_R37_D0.6831.00
185_V188_L0.6811.00
18_L22_K0.6801.00
136_E139_S0.6741.00
13_R48_G0.6701.00
9_H13_R0.6681.00
159_T162_K0.6681.00
35_M39_V0.6671.00
133_L136_E0.6651.00
36_K50_Y0.6651.00
97_E189_A0.6651.00
31_E116_T0.6531.00
19_E22_K0.6511.00
42_S45_S0.6501.00
73_R76_D0.6491.00
81_H86_A0.6461.00
122_E125_Q0.6321.00
159_T163_F0.6281.00
97_E186_S0.6281.00
131_Y135_V0.6261.00
188_L192_A0.6241.00
77_K94_E0.6241.00
142_L157_L0.6221.00
35_M56_T0.6211.00
81_H90_S0.6191.00
30_F33_T0.6171.00
107_A112_E0.6141.00
111_F114_L0.6111.00
108_P111_F0.6071.00
113_Y116_T0.6011.00
89_S92_L0.6011.00
10_K52_Y0.5941.00
174_N178_F0.5941.00
157_L161_A0.5921.00
151_F156_P0.5861.00
142_L164_F0.5831.00
69_D130_R0.5791.00
83_S87_S0.5791.00
146_I152_Q0.5781.00
74_K98_G0.5741.00
84_V150_E0.5741.00
163_F166_N0.5691.00
97_E101_D0.5661.00
98_G101_D0.5661.00
188_L191_S0.5641.00
106_L109_V0.5631.00
128_E132_D0.5601.00
128_E131_Y0.5571.00
30_F57_E0.5561.00
142_L146_I0.5521.00
167_M192_A0.5511.00
25_F60_F0.5511.00
186_S189_A0.5491.00
97_E185_V0.5461.00
166_N174_N0.5461.00
183_A187_G0.5461.00
185_V189_A0.5451.00
116_T120_N0.5451.00
22_K70_E0.5431.00
65_E129_K0.5391.00
42_S46_R0.5361.00
46_R49_V0.5351.00
130_R133_L0.5341.00
120_N123_R0.5331.00
156_P160_I0.5321.00
14_Q53_F0.5301.00
156_P191_S0.5301.00
17_I52_Y0.5251.00
160_I163_F0.5231.00
182_K186_S0.5211.00
95_L99_L0.5211.00
187_G190_E0.5141.00
192_A196_L0.5131.00
125_Q128_E0.5111.00
68_L130_R0.5111.00
36_K45_S0.5071.00
183_A186_S0.5071.00
24_V34_T0.5041.00
162_K165_L0.5001.00
153_P156_P0.5001.00
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 0.9171 100 0.184 Contact Map
1rktA 2 0.9951 100 0.189 Contact Map
4jykA 2 0.9463 100 0.218 Contact Map
2ibdA 2 0.9317 100 0.22 Contact Map
3on2A 1 0.9415 100 0.223 Contact Map
3nrgA 2 0.9756 100 0.223 Contact Map
2xdnA 2 0.9659 100 0.224 Contact Map
3g1oA 2 0.9317 100 0.227 Contact Map
3kz9A 2 0.9756 100 0.235 Contact Map
3npiA 2 0.9415 100 0.236 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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