GREMLIN Database
YKFD - Putative oligopeptide transport ATP-binding protein YkfD
UniProt: C0SP98 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 329 (270)
Sequences: 53548 (33916)
Seq/√Len: 2064.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_E221_R4.3691.00
89_K171_E3.6811.00
11_Q29_G3.6041.00
8_E33_Q3.4151.00
10_S67_S3.3571.00
25_K28_D3.0331.00
14_M56_V2.9981.00
40_F223_G2.8941.00
67_S74_N2.6971.00
235_E238_T2.6301.00
137_A201_K2.6211.00
41_G219_S2.6211.00
35_R38_E2.5741.00
28_D229_H2.5391.00
221_R233_I2.4721.00
223_G230_M2.4381.00
9_V12_L2.4281.00
71_R171_E2.4251.00
8_E69_T2.3571.00
15_H25_K2.3541.00
144_F147_R2.3431.00
13_K29_G2.2671.00
216_K237_G2.2011.00
54_G208_I2.1931.00
36_E171_E2.1921.00
13_K65_E2.1821.00
74_N77_A2.1521.00
134_L167_S2.1391.00
234_T239_L2.0891.00
209_A215_V1.9531.00
10_S69_T1.9391.00
16_F52_T1.9271.00
41_G215_V1.8581.00
130_V133_E1.8581.00
105_M109_E1.8191.00
130_V169_N1.7891.00
54_G174_V1.7871.00
132_D145_G1.7451.00
13_K25_K1.7201.00
14_M61_Y1.7031.00
112_L131_V1.6591.00
16_F26_A1.6591.00
197_L203_L1.6311.00
147_R151_E1.6301.00
223_G233_I1.6271.00
5_P35_R1.6241.00
11_Q31_T1.6231.00
112_L127_R1.6181.00
15_H64_T1.6171.00
144_F152_F1.6161.00
14_M64_T1.6081.00
9_V32_F1.5851.00
195_K217_H1.5741.00
5_P8_E1.5651.00
108_R146_S1.5321.00
12_L63_P1.5211.00
238_T242_E1.5151.00
133_E137_A1.5121.00
169_N201_K1.4961.00
234_T238_T1.4951.00
108_R145_G1.4851.00
71_R89_K1.4451.00
106_T109_E1.4271.00
13_K28_D1.4241.00
175_A205_F1.4181.00
9_V57_L1.4141.00
191_V214_M1.4071.00
122_N126_A1.3661.00
116_E127_R1.3641.00
38_E220_D1.3621.00
93_I175_A1.3561.00
152_F160_I1.3551.00
10_S33_Q1.3281.00
34_I40_F1.3251.00
108_R112_L1.3121.00
128_L132_D1.3001.00
39_T198_Q1.2991.00
111_I135_L1.2811.00
98_Y157_R1.2781.00
32_F223_G1.2751.00
59_R62_Q1.2701.00
58_M92_M1.2621.00
39_T205_F1.2501.00
125_K129_L1.2481.00
10_S31_T1.2431.00
109_E112_L1.2381.00
42_L206_L1.2201.00
32_F53_L1.2101.00
195_K198_Q1.1951.00
40_F221_R1.1921.00
73_T78_L1.1831.00
194_L205_F1.1741.00
249_K253_S1.1711.00
104_R150_H1.1701.00
127_R131_V1.1661.00
136_E142_P1.1591.00
246_P249_K1.1531.00
128_L145_G1.1511.00
236_S240_Y1.1501.00
69_T74_N1.1491.00
182_L190_V1.1441.00
237_G241_R1.1381.00
135_L145_G1.1341.00
126_A129_L1.1261.00
143_D147_R1.1221.00
110_I164_R1.1161.00
39_T219_S1.1131.00
30_V53_L1.1121.00
106_T146_S1.1111.00
40_F233_I1.1051.00
173_I203_L1.1001.00
11_Q65_E1.0921.00
86_F90_L1.0911.00
108_R131_V1.0881.00
36_E71_R1.0791.00
56_V63_P1.0781.00
5_P33_Q1.0741.00
27_V56_V1.0671.00
111_I167_S1.0661.00
141_H144_F1.0521.00
53_L225_M1.0351.00
132_D142_P1.0301.00
108_R128_L1.0291.00
35_R221_R1.0241.00
222_I236_S1.0201.00
34_I172_F1.0161.00
169_N203_L1.0151.00
238_T241_R1.0051.00
124_H127_R1.0031.00
14_M52_T1.0011.00
15_H28_D1.0001.00
105_M113_E0.9931.00
91_Q165_A0.9901.00
91_Q170_P0.9891.00
240_Y243_P0.9821.00
58_M174_V0.9801.00
133_E136_E0.9791.00
207_F218_I0.9781.00
173_I205_F0.9761.00
129_L133_E0.9741.00
132_D136_E0.9731.00
137_A196_R0.9561.00
57_L206_L0.9541.00
115_M167_S0.9541.00
119_N122_N0.9531.00
55_R60_L0.9491.00
112_L116_E0.9491.00
56_V68_V0.9481.00
9_V68_V0.9381.00
90_L172_F0.9351.00
35_R204_T0.9321.00
139_G196_R0.9301.00
42_L53_L0.9241.00
132_D140_L0.9221.00
18_A24_V0.9211.00
275_L278_P0.9181.00
48_C225_M0.9161.00
121_Y127_R0.9051.00
246_P250_A0.9021.00
230_M233_I0.8971.00
134_L137_A0.8941.00
281_P284_G0.8911.00
6_L71_R0.8891.00
198_Q205_F0.8851.00
12_L56_V0.8841.00
55_R61_Y0.8841.00
42_L223_G0.8841.00
248_T252_L0.8801.00
124_H128_L0.8791.00
257_I260_P0.8771.00
187_Q214_M0.8771.00
36_E202_G0.8731.00
187_Q211_D0.8691.00
27_V30_V0.8631.00
5_P36_E0.8581.00
106_T148_Y0.8561.00
128_L146_S0.8511.00
101_L157_R0.8511.00
237_G240_Y0.8431.00
119_N130_V0.8411.00
70_Y89_K0.8391.00
56_V61_Y0.8371.00
121_Y124_H0.8371.00
236_S239_L0.8351.00
115_M119_N0.8311.00
198_Q220_D0.8301.00
105_M110_I0.8241.00
195_K218_I0.8171.00
177_E210_H0.8171.00
81_K85_A0.8161.00
139_G189_Q0.8131.00
175_A194_L0.8131.00
107_V152_F0.8121.00
280_N283_S0.8121.00
29_G229_H0.8091.00
6_L70_Y0.8051.00
93_I162_I0.8051.00
34_I204_T0.8051.00
192_N217_H0.8011.00
214_M218_I0.7971.00
121_Y126_A0.7961.00
39_T195_K0.7951.00
219_S222_I0.7901.00
7_L57_L0.7891.00
126_A130_V0.7871.00
130_V134_L0.7861.00
74_N78_L0.7841.00
239_L243_P0.7821.00
26_A52_T0.7811.00
276_P280_N0.7791.00
278_P281_P0.7781.00
236_S247_Y0.7741.00
102_N105_M0.7741.00
131_V145_G0.7741.00
207_F219_S0.7731.00
268_R271_L0.7721.00
239_L248_T0.7721.00
107_V160_I0.7721.00
148_Y151_E0.7701.00
14_M27_V0.7681.00
134_L163_A0.7671.00
174_V206_L0.7661.00
11_Q14_M0.7631.00
30_V230_M0.7621.00
73_T89_K0.7601.00
188_A192_N0.7591.00
172_F206_L0.7571.00
93_I165_A0.7561.00
272_K275_L0.7531.00
138_V163_A0.7531.00
273_G278_P0.7531.00
226_Y231_M0.7521.00
277_S281_P0.7451.00
193_L196_R0.7441.00
136_E141_H0.7431.00
266_R270_L0.7411.00
276_P282_P0.7411.00
43_V215_V0.7411.00
39_T218_I0.7351.00
75_L86_F0.7311.00
191_V217_H0.7291.00
224_V243_P0.7271.00
118_H168_L0.7261.00
80_E85_A0.7261.00
277_S280_N0.7261.00
280_N284_G0.7251.00
152_F156_Q0.7201.00
245_H248_T0.7191.00
149_P160_I0.7171.00
172_F204_T0.7161.00
40_F206_L0.7131.00
112_L128_L0.7101.00
144_F156_Q0.7101.00
114_P117_I0.7091.00
59_R87_N0.7091.00
34_I206_L0.7061.00
279_V282_P0.7061.00
259_D262_L0.7031.00
39_T220_D0.7001.00
219_S236_S0.6981.00
114_P168_L0.6981.00
273_G277_S0.6971.00
250_A254_S0.6951.00
114_P164_R0.6941.00
275_L281_P0.6911.00
15_H65_E0.6901.00
276_P284_G0.6821.00
125_K128_L0.6821.00
37_G204_T0.6821.00
221_R232_E0.6811.00
140_L144_F0.6781.00
179_I214_M0.6771.00
43_V224_V0.6761.00
70_Y172_F0.6761.00
255_I258_P0.6751.00
134_L166_L0.6751.00
70_Y75_L0.6751.00
55_R92_M0.6741.00
253_S269_I0.6741.00
57_L68_V0.6721.00
101_L160_I0.6711.00
192_N195_K0.6711.00
212_L240_Y0.6681.00
78_L86_F0.6651.00
115_M121_Y0.6651.00
273_G276_P0.6641.00
60_L94_F0.6631.00
250_A253_S0.6571.00
56_V64_T0.6531.00
6_L172_F0.6521.00
118_H121_Y0.6521.00
19_G24_V0.6511.00
226_Y229_H0.6511.00
27_V53_L0.6511.00
278_P282_P0.6491.00
255_I259_D0.6481.00
58_M90_L0.6481.00
192_N196_R0.6471.00
270_L274_E0.6451.00
120_L127_R0.6401.00
274_E278_P0.6381.00
154_G159_R0.6381.00
106_T110_I0.6371.00
7_L70_Y0.6361.00
29_G65_E0.6351.00
278_P284_G0.6351.00
117_I121_Y0.6341.00
16_F61_Y0.6331.00
70_Y86_F0.6311.00
67_S76_H0.6301.00
7_L172_F0.6271.00
51_S55_R0.6271.00
99_A157_R0.6241.00
276_P281_P0.6221.00
268_R272_K0.6221.00
231_M245_H0.6211.00
247_Y251_L0.6091.00
75_L90_L0.6081.00
277_S282_P0.6081.00
226_Y250_A0.6071.00
131_V134_L0.6041.00
111_I131_V0.6031.00
247_Y250_A0.6031.00
85_A88_R0.6001.00
67_S77_A0.5991.00
234_T240_Y0.5871.00
234_T243_P0.5871.00
45_E48_C0.5841.00
129_L136_E0.5791.00
108_R111_I0.5791.00
100_S161_G0.5781.00
224_V239_L0.5771.00
115_M122_N0.5731.00
36_E204_T0.5731.00
96_D99_A0.5731.00
15_H26_A0.5681.00
179_I190_V0.5661.00
6_L204_T0.5661.00
110_I149_P0.5661.00
38_E233_I0.5651.00
215_V222_I0.5651.00
88_R119_N0.5651.00
101_L110_I0.5631.00
261_E265_K0.5611.00
147_R152_F0.5591.00
276_P279_V0.5591.00
122_N127_R0.5571.00
238_T244_L0.5551.00
268_R273_G0.5541.00
275_L280_N0.5541.00
15_H18_A0.5531.00
235_E239_L0.5511.00
271_L275_L0.5511.00
162_I190_V0.5501.00
140_L156_Q0.5501.00
276_P283_S0.5491.00
271_L276_P0.5481.00
128_L131_V0.5461.00
116_E124_H0.5451.00
118_H122_N0.5441.00
272_K278_P0.5421.00
166_L203_L0.5411.00
46_S177_E0.5391.00
5_P71_R0.5371.00
111_I114_P0.5371.00
158_Q181_A0.5371.00
267_E271_L0.5351.00
68_V76_H0.5341.00
236_S243_P0.5341.00
115_M120_L0.5321.00
69_T72_G0.5321.00
116_E122_N0.5311.00
25_K29_G0.5301.00
268_R275_L0.5291.00
6_L35_R0.5281.00
275_L279_V0.5281.00
135_L144_F0.5241.00
95_Q154_G0.5221.00
243_P248_T0.5211.00
277_S284_G0.5201.00
278_P283_S0.5201.00
215_V219_S0.5191.00
119_N169_N0.5181.00
279_V283_S0.5181.00
267_E270_L0.5181.00
107_V111_I0.5171.00
252_L256_P0.5161.00
268_R276_P0.5151.00
33_Q233_I0.5131.00
260_P263_E0.5121.00
115_M118_H0.5121.00
271_L274_E0.5101.00
9_V53_L0.5101.00
274_E279_V0.5081.00
45_E247_Y0.5081.00
59_R76_H0.5061.00
198_Q201_K0.5051.00
45_E226_Y0.5051.00
275_L284_G0.5031.00
113_E117_I0.5031.00
244_L249_K0.5021.00
115_M168_L0.5021.00
75_L78_L0.5011.00
131_V167_S0.5011.00
191_V209_A0.5001.00
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  
3tuiC 2 0.9696 100 0.218 Contact Map
4ry2A 2 0.7234 100 0.234 Contact Map
4mkiB 2 0.8693 100 0.236 Contact Map
1b0uA 2 0.7477 100 0.237 Contact Map
4u00A 1 0.7295 100 0.238 Contact Map
2oljA 2 0.7356 100 0.239 Contact Map
4fwiB 1 0.924 100 0.24 Contact Map
4f4cA 1 0.7021 100 0.24 Contact Map
4ymuJ 2 0.7295 100 0.241 Contact Map
4yerA 2 0.845 100 0.245 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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