GREMLIN Database
YRKP - Uncharacterized transcriptional regulatory protein YrkP
UniProt: P54443 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 231 (202)
Sequences: 73378 (52187)
Seq/√Len: 3671.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
15_G31_R3.7171.00
15_G33_K3.2561.00
19_E31_R3.1811.00
8_V38_A2.7431.00
39_L66_H2.6561.00
36_K57_G2.5861.00
30_L46_L2.5191.00
35_G58_I2.4621.00
58_I66_H2.3931.00
43_N70_S2.3921.00
34_D57_G2.3791.00
4_R30_L2.1621.00
21_S105_E2.0541.00
19_E23_T2.0321.00
32_A41_L2.0001.00
4_R28_E1.9901.00
25_A109_H1.9871.00
87_K107_E1.9201.00
33_K37_R1.8821.00
54_M81_R1.8751.00
51_L63_T1.8501.00
64_C75_I1.8111.00
195_N198_M1.8011.00
159_L162_R1.7811.00
77_F90_G1.7761.00
34_D37_R1.7611.00
84_T104_S1.7241.00
30_L41_L1.7081.00
77_F95_G1.7041.00
68_R96_D1.6981.00
6_L32_A1.6801.00
66_H70_S1.6671.00
137_K150_E1.6041.00
58_I62_E1.5961.00
177_A198_M1.5941.00
166_L183_S1.5871.00
59_S62_E1.5601.00
3_Y116_L1.5441.00
35_G63_T1.5321.00
165_K169_N1.5161.00
97_D111_R1.5161.00
81_R86_D1.5071.00
22_L112_V1.4801.00
66_H69_K1.4801.00
175_F183_S1.4491.00
42_V67_I1.4461.00
36_K58_I1.4211.00
64_C77_F1.4041.00
200_H203_K1.3931.00
41_L46_L1.3901.00
39_L63_T1.3861.00
65_Q93_A1.3841.00
48_L112_V1.3791.00
49_V73_V1.3631.00
176_S179_N1.3631.00
76_L115_Q1.3611.00
41_L44_D1.3541.00
62_E65_Q1.3411.00
134_I139_R1.3151.00
96_D118_R1.3131.00
53_I61_I1.2981.00
12_E33_K1.2951.00
139_R148_W1.2921.00
51_L64_C1.2741.00
9_E15_G1.2681.00
141_S144_F1.2611.00
166_L170_K1.2481.00
53_I77_F1.2451.00
8_V55_M1.2421.00
10_D52_D1.2351.00
39_L58_I1.2121.00
160_E207_K1.2111.00
37_R40_Q1.1891.00
32_A38_A1.1831.00
27_Y113_I1.1741.00
6_L46_L1.1701.00
37_R41_L1.1681.00
40_Q44_D1.1661.00
83_S86_D1.1651.00
146_E153_Q1.1651.00
36_K40_Q1.1621.00
96_D115_Q1.1611.00
84_T88_T1.1461.00
199_V202_R1.1461.00
109_H113_I1.1371.00
61_I89_E1.1131.00
179_N183_S1.1111.00
61_I90_G1.1071.00
6_L38_A1.0941.00
26_G113_I1.0831.00
25_A113_I1.0781.00
5_I27_Y1.0771.00
6_L41_L1.0761.00
3_Y27_Y1.0721.00
92_L113_I1.0711.00
89_E93_A1.0631.00
166_L175_F1.0581.00
107_E110_A1.0451.00
161_Y165_K1.0371.00
65_Q89_E1.0291.00
110_A114_A1.0291.00
162_R165_K1.0281.00
85_L89_E1.0271.00
38_A63_T1.0221.00
178_Q194_N1.0211.00
48_L116_L1.0161.00
140_V168_M1.0081.00
142_E165_K1.0051.00
38_A42_V1.0041.00
212_P215_P1.0011.00
196_T200_H1.0011.00
211_D215_P0.9991.00
201_I205_R0.9991.00
39_L43_N0.9911.00
16_D31_R0.9881.00
61_I93_A0.9851.00
32_A37_R0.9851.00
6_L42_V0.9751.00
87_K100_T0.9681.00
7_V18_L0.9681.00
88_T92_L0.9611.00
148_W153_Q0.9611.00
8_V49_V0.9611.00
159_L185_W0.9591.00
53_I59_S0.9561.00
19_E29_V0.9551.00
49_V67_I0.9551.00
195_N199_V0.9531.00
51_L75_I0.9381.00
145_N162_R0.9371.00
18_L78_L0.9331.00
13_D17_L0.9321.00
175_F179_N0.9301.00
12_E16_D0.9291.00
158_D162_R0.9161.00
8_V32_A0.9111.00
84_T87_K0.9031.00
132_F139_R0.9011.00
115_Q118_R0.9001.00
51_L77_F0.8901.00
64_C93_A0.8851.00
194_N198_M0.8851.00
62_E66_H0.8821.00
40_Q43_N0.8741.00
3_Y120_T0.8731.00
50_I108_L0.8671.00
64_C95_G0.8601.00
49_V75_I0.8581.00
82_S100_T0.8551.00
7_V29_V0.8551.00
20_E24_R0.8421.00
140_V161_Y0.8391.00
203_K206_S0.8391.00
27_Y109_H0.8381.00
55_M63_T0.8381.00
12_E15_G0.8361.00
74_P96_D0.8301.00
89_E92_L0.8251.00
88_T106_E0.8251.00
195_N202_R0.8221.00
53_I86_D0.8181.00
166_L180_I0.8111.00
105_E109_H0.8061.00
4_R46_L0.8051.00
16_D19_E0.8031.00
50_I78_L0.7971.00
63_T67_I0.7931.00
18_L108_L0.7931.00
65_Q69_K0.7861.00
42_V73_V0.7851.00
58_I63_T0.7841.00
202_R206_S0.7781.00
53_I81_R0.7661.00
67_I71_S0.7631.00
76_L111_R0.7591.00
4_R47_D0.7571.00
107_E111_R0.7551.00
209_E212_P0.7551.00
42_V46_L0.7551.00
210_D216_V0.7541.00
35_G39_L0.7531.00
54_M80_A0.7521.00
86_D89_E0.7481.00
85_L106_E0.7421.00
114_A119_Y0.7391.00
116_L119_Y0.7341.00
177_A194_N0.7321.00
178_Q182_E0.7271.00
114_A117_R0.7271.00
138_L149_K0.7251.00
104_S107_E0.7231.00
91_L111_R0.7201.00
157_S207_K0.7181.00
14_I103_F0.7131.00
39_L42_V0.7111.00
8_V63_T0.7091.00
103_F108_L0.7081.00
78_L103_F0.7021.00
90_G95_G0.7021.00
145_N161_Y0.7001.00
148_W151_E0.6991.00
7_V19_E0.6931.00
76_L97_D0.6931.00
179_N182_E0.6911.00
137_K149_K0.6901.00
84_T106_E0.6891.00
16_D20_E0.6821.00
35_G57_G0.6821.00
17_L21_S0.6761.00
169_N183_S0.6731.00
7_V31_R0.6721.00
92_L110_A0.6711.00
166_L169_N0.6681.00
192_C197_V0.6621.00
42_V49_V0.6611.00
163_I167_L0.6601.00
119_Y123_Q0.6571.00
205_R210_D0.6551.00
106_E110_A0.6541.00
209_E216_V0.6531.00
169_N175_F0.6521.00
43_N66_H0.6511.00
9_E55_M0.6511.00
199_V203_K0.6481.00
131_T143_E0.6481.00
3_Y47_D0.6471.00
87_K104_S0.6451.00
67_I75_I0.6451.00
97_D114_A0.6441.00
182_E185_W0.6391.00
206_S209_E0.6381.00
72_N122_Y0.6371.00
15_G19_E0.6331.00
21_S109_H0.6291.00
74_P116_L0.6281.00
53_I90_G0.6261.00
132_F141_S0.6251.00
68_R73_V0.6201.00
198_M201_I0.6191.00
193_S196_T0.6171.00
72_N121_I0.6161.00
111_R115_Q0.6151.00
61_I86_D0.6141.00
39_L70_S0.6131.00
52_D101_K0.6121.00
50_I112_V0.6101.00
210_D220_T0.6031.00
23_T29_V0.6001.00
11_D14_I0.5981.00
209_E215_P0.5971.00
50_I76_L0.5951.00
5_I22_L0.5941.00
181_Y185_W0.5931.00
35_G55_M0.5891.00
196_T201_I0.5851.00
215_P218_I0.5851.00
68_R74_P0.5821.00
79_T87_K0.5811.00
103_F107_E0.5801.00
11_D80_A0.5781.00
22_L27_Y0.5781.00
140_V147_V0.5781.00
64_C68_R0.5741.00
149_K211_D0.5701.00
142_E169_N0.5691.00
85_L88_T0.5651.00
74_P122_Y0.5571.00
10_D79_T0.5551.00
45_S71_S0.5541.00
5_I48_L0.5511.00
149_K209_E0.5501.00
74_P118_R0.5501.00
134_I137_K0.5481.00
162_R166_L0.5461.00
88_T91_L0.5431.00
23_T28_E0.5431.00
51_L55_M0.5421.00
110_A113_I0.5371.00
37_R57_G0.5351.00
82_S102_P0.5331.00
138_L147_V0.5291.00
167_L201_I0.5291.00
80_A102_P0.5281.00
170_K183_S0.5271.00
14_I17_L0.5271.00
139_R151_E0.5221.00
90_G98_Y0.5211.00
149_K152_K0.5211.00
74_P119_Y0.5191.00
42_V71_S0.5181.00
133_L142_E0.5161.00
7_V15_G0.5161.00
42_V63_T0.5151.00
42_V70_S0.5151.00
149_K210_D0.5141.00
159_L200_H0.5111.00
141_S146_E0.5111.00
140_V165_K0.5101.00
20_E23_T0.5071.00
5_I112_V0.5051.00
21_S25_A0.5051.00
164_L216_V0.5021.00
67_I73_V0.5001.00
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  
2gwrA 1 0.961 100 0.189 Contact Map
2oqrA 2 0.974 100 0.202 Contact Map
4b09A 2 0.9091 100 0.214 Contact Map
3r0jA 2 0.9481 100 0.22 Contact Map
1kgsA 1 0.9394 100 0.226 Contact Map
1ys7A 2 0.9697 100 0.226 Contact Map
1p2fA 1 0.9351 100 0.229 Contact Map
4kfcA 2 0.9654 100 0.23 Contact Map
3q9sA 1 0.9004 100 0.267 Contact Map
2hqrA 2 0.9264 100 0.271 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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