GREMLIN Database
LSRD - Autoinducer 2 import system permease protein LsrD
UniProt: P0AFS1 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13808
Length: 330 (270)
Sequences: 31300 (20001)
Seq/√Len: 1217.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
94_L220_L3.8641.00
98_A216_A3.6291.00
98_A220_L3.0691.00
75_A96_L2.9701.00
102_L216_A2.9191.00
197_P211_L2.8741.00
79_L92_L2.7631.00
53_T269_T2.5231.00
190_V214_L2.5121.00
206_P209_R2.5081.00
110_Y208_N2.4211.00
180_W186_A2.3591.00
46_G170_F2.3521.00
209_R213_A2.3411.00
97_G223_A2.2991.00
179_L183_K2.2791.00
101_G219_G2.2741.00
178_W182_H2.2721.00
102_L212_C2.2331.00
189_N210_T2.1661.00
104_N122_T2.1421.00
106_G110_Y2.1391.00
247_P280_Q2.1181.00
186_A213_A2.0821.00
176_V180_W2.0791.00
70_G130_A1.9511.00
76_L93_T1.9511.00
48_V248_A1.9501.00
87_P91_L1.9071.00
94_L224_V1.8991.00
85_P88_L1.8301.00
76_L227_V1.8191.00
175_L179_L1.7921.00
97_G219_G1.7871.00
193_I210_T1.7591.00
49_A269_T1.7501.00
42_F277_G1.7431.00
90_I227_V1.7231.00
55_V218_T1.6861.00
124_Y127_A1.6691.00
192_L200_A1.6651.00
54_M177_F1.6561.00
105_A212_C1.6371.00
154_D157_N1.5821.00
42_F274_L1.5791.00
185_H189_N1.5741.00
80_F89_A1.5431.00
46_G273_V1.5411.00
57_V191_F1.5351.00
247_P297_S1.5041.00
100_C126_F1.5001.00
71_L100_C1.4921.00
186_A190_V1.4781.00
67_S127_A1.4751.00
198_R201_L1.4751.00
94_L227_V1.4681.00
213_A216_A1.4621.00
110_Y212_C1.4601.00
122_T126_F1.4291.00
145_I148_F1.4291.00
78_V81_Q1.4261.00
197_P201_L1.4251.00
48_V69_I1.4171.00
69_I229_L1.4131.00
78_V133_L1.3901.00
189_N205_I1.3801.00
79_L82_S1.3741.00
265_S268_G1.3641.00
146_G149_P1.3641.00
47_I225_A1.3621.00
174_L270_A1.3521.00
143_E146_G1.3461.00
88_L91_L1.3401.00
255_G268_G1.3351.00
106_G212_C1.3321.00
200_A205_I1.3241.00
58_S214_L1.3211.00
189_N200_A1.3211.00
79_L84_V1.2781.00
51_P221_A1.2721.00
54_M214_L1.2651.00
193_I207_V1.2641.00
84_V88_L1.2611.00
34_M281_Q1.2501.00
84_V92_L1.2321.00
255_G272_A1.2311.00
212_C216_A1.2291.00
158_L161_L1.2281.00
109_I208_N1.2241.00
46_G270_A1.2221.00
47_I228_L1.2221.00
52_L252_V1.2181.00
89_A93_T1.2171.00
65_F222_S1.2171.00
91_L95_L1.2111.00
50_L177_F1.2031.00
60_G211_L1.1981.00
93_T97_G1.1931.00
205_I210_T1.1891.00
38_S278_Y1.1821.00
193_I200_A1.1731.00
38_S277_G1.1661.00
68_T100_C1.1561.00
182_H191_F1.1561.00
52_L248_A1.1511.00
75_A79_L1.1441.00
173_C221_A1.1321.00
95_L98_A1.1301.00
60_G115_P1.1301.00
216_A220_L1.1231.00
178_W183_K1.1141.00
60_G215_Y1.1111.00
42_F273_V1.1101.00
49_A251_A1.1031.00
156_A159_D1.0991.00
67_S126_F1.0881.00
201_L207_V1.0741.00
281_Q284_Q1.0741.00
201_L208_N1.0611.00
74_I130_A1.0581.00
244_F247_P1.0571.00
127_A131_L1.0521.00
213_A217_M1.0491.00
99_L102_L1.0471.00
210_T213_A1.0391.00
219_G223_A1.0381.00
51_P65_F1.0321.00
177_F217_M1.0271.00
280_Q297_S1.0221.00
174_L221_A1.0221.00
57_V264_G1.0211.00
107_L118_I1.0181.00
175_L178_W1.0121.00
159_D162_G1.0061.00
98_A223_A1.0051.00
36_L40_S1.0041.00
76_L231_S1.0031.00
172_I176_V1.0011.00
49_A252_V1.0011.00
93_T227_V1.0001.00
53_T252_V0.9921.00
78_V134_S0.9891.00
190_V210_T0.9891.00
144_G147_G0.9841.00
217_M221_A0.9841.00
251_A272_A0.9801.00
123_L127_A0.9801.00
91_L94_L0.9771.00
292_V295_A0.9741.00
74_I238_S0.9711.00
155_F158_L0.9671.00
104_N118_I0.9651.00
71_L75_A0.9601.00
106_G111_T0.9591.00
251_A273_V0.9581.00
79_L89_A0.9551.00
33_N36_L0.9521.00
186_A210_T0.9511.00
48_V225_A0.9471.00
164_P168_I0.9431.00
67_S123_L0.9431.00
226_A230_V0.9421.00
157_N161_L0.9421.00
109_I119_T0.9241.00
209_R212_C0.9231.00
267_I271_I0.9221.00
49_A273_V0.9091.00
276_V297_S0.9071.00
95_L99_L0.9041.00
56_I252_V0.9031.00
72_C97_G0.8981.00
178_W267_I0.8951.00
46_G174_L0.8941.00
76_L80_F0.8891.00
218_T222_S0.8891.00
282_G286_A0.8871.00
239_D242_A0.8871.00
53_T264_G0.8871.00
112_K197_P0.8861.00
66_G245_L0.8841.00
148_F151_A0.8841.00
107_L111_T0.8831.00
44_C225_A0.8811.00
161_L168_I0.8771.00
52_L65_F0.8761.00
188_R191_F0.8761.00
41_D45_I0.8751.00
74_I134_S0.8721.00
108_I118_I0.8721.00
157_N160_V0.8711.00
78_V82_S0.8691.00
133_L136_M0.8681.00
57_V182_H0.8641.00
171_L175_L0.8631.00
165_V168_I0.8631.00
147_G150_M0.8621.00
165_V169_I0.8581.00
77_G236_A0.8551.00
68_T222_S0.8541.00
73_A230_V0.8531.00
69_I244_F0.8511.00
50_L173_C0.8491.00
294_S297_S0.8481.00
144_G148_F0.8451.00
181_L190_V0.8441.00
193_I214_L0.8441.00
35_L282_G0.8431.00
105_A109_I0.8391.00
222_S226_A0.8361.00
196_S199_V0.8351.00
199_V203_S0.8341.00
54_M217_M0.8331.00
72_C93_T0.8281.00
88_L92_L0.8281.00
69_I241_G0.8251.00
208_N211_L0.8241.00
55_V62_D0.8201.00
283_L296_L0.8171.00
62_D65_F0.8141.00
72_C226_A0.8081.00
150_M153_T0.8041.00
58_S190_V0.8021.00
103_I107_L0.8001.00
134_S137_A0.7981.00
151_A154_D0.7971.00
164_P167_L0.7971.00
263_S267_I0.7931.00
75_A78_V0.7911.00
156_A161_L0.7901.00
303_V307_G0.7881.00
132_L292_V0.7871.00
207_V211_L0.7861.00
50_L269_T0.7861.00
68_T97_G0.7841.00
73_A236_A0.7831.00
265_S269_T0.7831.00
299_A303_V0.7831.00
54_M181_L0.7821.00
180_W183_K0.7781.00
168_I172_I0.7771.00
281_Q285_M0.7771.00
208_N212_C0.7761.00
250_T301_L0.7721.00
193_I211_L0.7721.00
220_L223_A0.7691.00
66_G243_S0.7691.00
166_P228_L0.7671.00
163_L168_I0.7651.00
99_L103_I0.7591.00
197_P207_V0.7581.00
150_M154_D0.7541.00
129_S133_L0.7511.00
102_L106_G0.7491.00
48_V65_F0.7481.00
128_G131_L0.7471.00
94_L223_A0.7431.00
73_A240_L0.7431.00
220_L224_V0.7421.00
269_T273_V0.7401.00
51_P222_S0.7331.00
143_E147_G0.7261.00
94_L98_A0.7221.00
48_V51_P0.7201.00
63_I249_I0.7191.00
37_F41_D0.7171.00
115_P215_Y0.7141.00
71_L97_G0.7091.00
43_I167_L0.7071.00
273_V277_G0.7031.00
243_S247_P0.6941.00
274_L278_Y0.6941.00
176_V179_L0.6911.00
47_I173_C0.6911.00
125_L129_S0.6901.00
76_L89_A0.6871.00
229_L233_F0.6871.00
55_V215_Y0.6871.00
69_I225_A0.6861.00
72_C96_L0.6791.00
60_G197_P0.6791.00
237_R240_L0.6781.00
105_A110_Y0.6781.00
291_Q294_S0.6761.00
42_F46_G0.6751.00
109_I212_C0.6701.00
34_M285_M0.6701.00
167_L171_L0.6701.00
71_L126_F0.6691.00
189_N206_P0.6651.00
280_Q293_S0.6631.00
127_A242_A0.6631.00
68_T72_C0.6631.00
45_I247_P0.6631.00
68_T104_N0.6621.00
38_S281_Q0.6621.00
90_I94_L0.6601.00
145_I149_P0.6581.00
40_S232_Y0.6581.00
47_I170_F0.6551.00
156_A160_V0.6541.00
80_F231_S0.6511.00
217_M220_L0.6461.00
56_I249_I0.6431.00
170_F174_L0.6421.00
37_F281_Q0.6421.00
101_G216_A0.6381.00
177_F221_A0.6331.00
68_T219_G0.6321.00
53_T57_V0.6311.00
45_I251_A0.6311.00
70_G241_G0.6301.00
174_L178_W0.6291.00
207_V210_T0.6291.00
186_A217_M0.6251.00
179_L182_H0.6251.00
132_L136_M0.6251.00
254_L272_A0.6231.00
68_T126_F0.6231.00
304_V308_R0.6181.00
38_S42_F0.6171.00
72_C222_S0.6171.00
53_T266_I0.6161.00
149_P153_T0.6141.00
236_A240_L0.6141.00
39_T43_I0.6131.00
32_L35_L0.6121.00
79_L96_L0.6101.00
223_A227_V0.6101.00
58_S193_I0.6091.00
45_I273_V0.6031.00
138_G237_R0.6021.00
143_E149_P0.5991.00
68_T101_G0.5981.00
84_V89_A0.5971.00
229_L244_F0.5971.00
177_F181_L0.5961.00
172_I175_L0.5951.00
180_W213_A0.5931.00
127_A245_L0.5921.00
173_C224_V0.5901.00
98_A101_G0.5891.00
51_P55_V0.5881.00
108_I115_P0.5871.00
108_I215_Y0.5841.00
97_G101_G0.5811.00
112_K208_N0.5771.00
45_I244_F0.5771.00
58_S211_L0.5771.00
75_A92_L0.5731.00
295_A299_A0.5701.00
76_L226_A0.5651.00
50_L174_L0.5651.00
306_V310_V0.5631.00
160_V168_I0.5621.00
64_S104_N0.5621.00
180_W184_T0.5611.00
247_P294_S0.5601.00
268_G272_A0.5581.00
283_L288_V0.5571.00
290_N293_S0.5561.00
143_E148_F0.5561.00
154_D159_D0.5551.00
44_C229_L0.5531.00
144_G149_P0.5521.00
219_G222_S0.5511.00
50_L178_W0.5481.00
211_L214_L0.5481.00
120_L124_Y0.5481.00
124_Y128_G0.5471.00
130_A134_S0.5461.00
200_A207_V0.5451.00
252_V269_T0.5431.00
135_G138_G0.5431.00
178_W265_S0.5431.00
198_R202_Y0.5421.00
41_D281_Q0.5421.00
54_M180_W0.5411.00
251_A269_T0.5401.00
236_A241_G0.5371.00
123_L245_L0.5321.00
35_L39_T0.5321.00
33_N37_F0.5301.00
216_A219_G0.5281.00
75_A97_G0.5261.00
158_L165_V0.5261.00
94_L97_G0.5251.00
149_P152_F0.5241.00
297_S301_L0.5241.00
254_L304_V0.5221.00
71_L96_L0.5221.00
92_L95_L0.5201.00
251_A276_V0.5191.00
134_S138_G0.5181.00
39_T42_F0.5171.00
255_G269_T0.5141.00
160_V165_V0.5111.00
98_A219_G0.5081.00
120_L123_L0.5081.00
153_T157_N0.5081.00
132_L137_A0.5071.00
55_V60_G0.5061.00
75_A93_T0.5061.00
32_L36_L0.5041.00
34_M37_F0.5021.00
79_L93_T0.5001.00
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  
2nq2A 2 0.8394 97.5 0.872 Contact Map
2qi9A 2 0.8667 97.5 0.873 Contact Map
4g1uA 2 0.8061 97.3 0.877 Contact Map
2cfqA 1 0.5879 60.2 0.937 Contact Map
2gfpA 2 0.5758 40.7 0.944 Contact Map
2kluA 1 0.1545 39.2 0.945 Contact Map
4m64A 1 0.6303 32.3 0.947 Contact Map
3wdoA 1 0.9182 31.6 0.947 Contact Map
1u7gA 3 0.5636 29.7 0.948 Contact Map
3d31C 2 0.7182 26 0.95 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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