GREMLIN Database
YIDP - Uncharacterized HTH-type transcriptional regulator YidP
UniProt: P31453 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11711
Length: 238 (191)
Sequences: 24422 (18474)
Seq/√Len: 1336.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
13_R18_D3.7301.00
20_T23_S3.6891.00
7_A48_L3.1311.00
13_R34_E3.0981.00
11_R52_W3.0851.00
56_V66_V2.7851.00
112_R174_E2.6911.00
28_E39_R2.5841.00
177_T180_L2.5311.00
9_R13_R2.5131.00
97_I182_D2.4961.00
6_I37_V2.3911.00
57_R63_T2.3201.00
58_R61_S2.2051.00
24_L64_Y2.1221.00
7_A52_W2.0961.00
12_I16_S2.0271.00
104_P107_I2.0231.00
9_R35_F1.9131.00
90_T94_Q1.9071.00
6_I35_F1.9071.00
107_I129_E1.8891.00
7_A11_R1.8021.00
101_M178_P1.7901.00
50_V57_R1.7801.00
126_R134_M1.7771.00
61_S64_Y1.7631.00
83_V131_K1.7401.00
44_K47_D1.7291.00
11_R15_N1.7251.00
29_K33_E1.6701.00
27_G30_K1.5931.00
182_D185_L1.5921.00
13_R19_F1.5881.00
108_A174_E1.5501.00
11_R54_L1.5421.00
182_D186_A1.5151.00
30_K34_E1.4841.00
47_D57_R1.4841.00
31_L42_I1.4821.00
123_R126_R1.4811.00
92_T127_F1.4761.00
50_V55_V1.4601.00
121_F137_D1.4421.00
103_A108_A1.4301.00
122_S138_S1.4301.00
9_R12_I1.4181.00
46_I55_V1.4121.00
58_R64_Y1.3881.00
172_N180_L1.3511.00
14_L65_L1.3361.00
56_V64_Y1.3311.00
19_F65_L1.3271.00
55_V63_T1.3141.00
180_L184_L1.3121.00
48_L51_A1.2981.00
110_Q123_R1.2821.00
21_L67_R1.2791.00
89_K190_K1.2781.00
103_A107_I1.2751.00
37_V42_I1.2651.00
13_R17_A1.2621.00
30_K33_E1.2621.00
86_R98_F1.2471.00
180_L196_P1.2391.00
122_S126_R1.2371.00
158_F162_E1.2361.00
47_D51_A1.2341.00
5_S9_R1.2261.00
107_I139_Y1.2211.00
94_Q127_F1.2181.00
97_I178_P1.2101.00
135_L139_Y1.2071.00
58_R62_G1.2011.00
159_E163_Q1.1891.00
178_P182_D1.1801.00
28_E43_R1.1741.00
93_S186_A1.1731.00
13_R35_F1.1641.00
183_R187_R1.1591.00
89_K186_A1.1501.00
24_L62_G1.1361.00
116_N119_I1.1281.00
101_M121_F1.1241.00
165_C191_V1.1231.00
157_K161_I1.1021.00
48_L52_W1.0921.00
47_D50_V1.0901.00
167_I171_G1.0871.00
87_Q136_E1.0731.00
170_G174_E1.0691.00
15_N54_L1.0651.00
132_P143_K1.0531.00
135_L185_L1.0461.00
186_A190_K1.0451.00
123_R137_D1.0411.00
114_Q117_E1.0331.00
46_I63_T1.0281.00
19_F23_S1.0271.00
99_E121_F1.0181.00
112_R170_G1.0071.00
38_S41_T0.9871.00
100_I118_Q0.9821.00
103_A176_L0.9821.00
123_R127_F0.9801.00
119_I123_R0.9661.00
124_R173_Y0.9611.00
89_K93_S0.9571.00
97_I121_F0.9531.00
160_Y165_C0.9521.00
100_I142_V0.9491.00
134_M138_S0.9471.00
93_S182_D0.9301.00
125_V137_D0.9281.00
8_E11_R0.9221.00
105_P109_S0.9181.00
157_K160_Y0.8981.00
94_Q97_I0.8941.00
192_A195_T0.8941.00
108_A170_G0.8911.00
171_G175_S0.8881.00
103_A127_F0.8881.00
180_L183_R0.8871.00
110_Q113_I0.8861.00
92_T130_G0.8761.00
97_I179_V0.8761.00
22_N56_V0.8681.00
44_K48_L0.8681.00
168_L184_L0.8641.00
115_I119_I0.8611.00
96_L100_I0.8591.00
108_A112_R0.8581.00
181_A191_V0.8531.00
109_S113_I0.8301.00
10_L31_L0.8291.00
171_G174_E0.8271.00
118_Q142_V0.8241.00
24_L27_G0.8241.00
121_F166_G0.8211.00
31_L46_I0.8161.00
156_S159_E0.8151.00
83_V87_Q0.8131.00
95_V125_V0.8111.00
32_A42_I0.7971.00
110_Q126_R0.7941.00
108_A176_L0.7931.00
108_A113_I0.7781.00
60_G63_T0.7771.00
123_R184_L0.7761.00
96_L185_L0.7751.00
25_L55_V0.7701.00
128_V134_M0.7661.00
179_V185_L0.7651.00
175_S180_L0.7641.00
179_V182_D0.7621.00
106_A110_Q0.7541.00
136_E139_Y0.7501.00
22_N67_R0.7481.00
6_I42_I0.7431.00
107_I127_F0.7411.00
35_F42_I0.7411.00
102_P118_Q0.7381.00
120_Y170_G0.7371.00
111_L123_R0.7371.00
183_R186_A0.7371.00
28_E57_R0.7321.00
9_R34_E0.7311.00
89_K193_E0.7301.00
21_L66_V0.7261.00
107_I110_Q0.7211.00
88_G92_T0.7181.00
168_L171_G0.7171.00
86_R102_P0.7171.00
117_E143_K0.7151.00
10_L19_F0.7121.00
26_P34_E0.7111.00
94_Q98_F0.7051.00
118_Q145_F0.7031.00
97_I123_R0.7021.00
46_I50_V0.7001.00
105_P108_A0.6911.00
19_F25_L0.6911.00
141_P144_L0.6881.00
169_I185_L0.6861.00
83_V132_P0.6831.00
13_R16_S0.6821.00
172_N177_T0.6771.00
191_V195_T0.6761.00
84_L128_V0.6761.00
96_L181_A0.6731.00
41_T45_A0.6721.00
94_Q182_D0.6721.00
33_E36_A0.6681.00
122_S134_M0.6661.00
8_E12_I0.6621.00
6_I9_R0.6571.00
185_L188_Q0.6551.00
167_I170_G0.6521.00
122_S141_P0.6521.00
156_S161_I0.6521.00
179_V183_R0.6511.00
187_R191_V0.6511.00
112_R167_I0.6501.00
29_K32_A0.6431.00
18_D34_E0.6431.00
98_F102_P0.6421.00
85_K88_G0.6421.00
105_P176_L0.6411.00
184_L187_R0.6391.00
119_I122_S0.6371.00
87_Q132_P0.6351.00
93_S97_I0.6321.00
108_A111_L0.6271.00
128_V133_L0.6251.00
149_S152_H0.6221.00
143_K146_R0.6191.00
132_P135_L0.6191.00
97_I101_M0.6161.00
160_Y163_Q0.6151.00
83_V130_G0.6131.00
181_A186_A0.6131.00
50_V63_T0.6111.00
7_A45_A0.6091.00
113_I119_I0.6061.00
93_S96_L0.6001.00
41_T44_K0.5981.00
100_I120_Y0.5981.00
169_I184_L0.5931.00
100_I173_Y0.5881.00
29_K39_R0.5861.00
69_D73_Q0.5851.00
162_E168_L0.5841.00
184_L188_Q0.5841.00
115_I118_Q0.5821.00
42_I55_V0.5781.00
19_F26_P0.5761.00
31_L35_F0.5711.00
59_H62_G0.5701.00
32_A35_F0.5701.00
79_G82_E0.5671.00
96_L125_V0.5661.00
28_E63_T0.5651.00
103_A173_Y0.5641.00
107_I126_R0.5621.00
181_A195_T0.5611.00
85_K192_A0.5581.00
110_Q119_I0.5521.00
157_K165_C0.5501.00
159_E162_E0.5501.00
40_M44_K0.5501.00
168_L180_L0.5441.00
46_I57_R0.5421.00
74_T77_L0.5411.00
94_Q125_V0.5411.00
145_F149_S0.5381.00
118_Q141_P0.5371.00
127_F130_G0.5351.00
86_R130_G0.5331.00
165_C188_Q0.5311.00
142_V146_R0.5311.00
137_D185_L0.5261.00
109_S112_R0.5231.00
161_I165_C0.5231.00
64_Y67_R0.5211.00
100_I178_P0.5211.00
103_A119_I0.5201.00
181_A185_L0.5201.00
132_P136_E0.5191.00
85_K90_T0.5191.00
98_F101_M0.5171.00
83_V86_R0.5171.00
158_F161_I0.5161.00
100_I176_L0.5161.00
151_Q154_E0.5151.00
125_V141_P0.5151.00
82_E86_R0.5151.00
32_A39_R0.5141.00
117_E166_G0.5131.00
24_L61_S0.5121.00
111_L170_G0.5111.00
162_E167_I0.5071.00
49_L55_V0.5051.00
185_L189_M0.5021.00
82_E85_K0.5011.00
81_V85_K0.5011.00
138_S141_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  
4u0wA 2 0.979 100 0.142 Contact Map
3f8mA 2 0.9622 100 0.171 Contact Map
2ra5A 2 0.6218 100 0.173 Contact Map
3edpA 2 0.916 100 0.181 Contact Map
3eetA 2 0.958 100 0.192 Contact Map
3bwgA 2 0.9538 100 0.209 Contact Map
1hw1A 2 0.8445 100 0.425 Contact Map
4p96A 2 0.8824 100 0.437 Contact Map
3sxyA 2 0.7815 99.9 0.452 Contact Map
2di3A 2 0.8319 99.9 0.453 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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