GREMLIN Database
APPD - Oligopeptide transport ATP-binding protein AppD
UniProt: P42064 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 328 (267)
Sequences: 55548 (34596)
Seq/√Len: 2117.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
35_E225_R4.1821.00
92_E175_K3.5041.00
9_N26_G3.3971.00
6_E30_H3.2021.00
8_N69_S3.1651.00
22_P25_D2.8971.00
12_T53_S2.8881.00
37_V227_I2.7881.00
69_S76_D2.5931.00
239_T242_D2.5761.00
38_A223_A2.5311.00
25_D233_Q2.4831.00
32_S35_E2.4471.00
225_R237_N2.4031.00
148_I151_E2.3861.00
227_I234_V2.3741.00
139_M205_F2.3691.00
73_E175_K2.2981.00
200_D204_K2.2821.00
7_V10_L2.2781.00
13_Y22_P2.2721.00
6_E71_K2.2511.00
51_S212_I2.2041.00
11_K26_G2.1981.00
33_K175_K2.1351.00
76_D79_S2.1051.00
238_A243_L2.0881.00
139_M204_K2.0841.00
132_R135_E2.0771.00
220_S241_D2.0431.00
136_L171_S2.0271.00
132_R173_N2.0201.00
213_T219_V1.9771.00
125_K128_E1.9351.00
14_F49_I1.9241.00
8_N71_K1.8271.00
134_V149_M1.7591.00
38_A219_V1.7331.00
11_K22_P1.7321.00
51_S178_I1.6841.00
108_L112_E1.6521.00
9_N28_D1.6241.00
12_T58_V1.6031.00
115_T129_A1.5981.00
151_E155_R1.5971.00
227_I237_N1.5961.00
148_I156_L1.5561.00
14_F23_A1.5421.00
115_T133_A1.5421.00
7_V29_F1.5381.00
238_A242_D1.5211.00
135_E139_M1.5131.00
173_N205_F1.5121.00
111_G150_K1.4961.00
11_K62_G1.4931.00
199_K221_E1.4791.00
199_K202_C1.4751.00
130_R134_V1.4691.00
144_R147_Q1.4671.00
119_I129_A1.4571.00
12_T61_S1.4471.00
111_G149_M1.4341.00
10_L60_S1.4291.00
179_A209_I1.4261.00
11_K25_D1.4171.00
242_D246_E1.4171.00
73_E92_E1.4021.00
13_Y20_P1.3851.00
36_T202_C1.3721.00
134_V144_R1.3481.00
96_I179_A1.3451.00
35_E224_D1.3411.00
15_F20_P1.3381.00
101_M161_R1.3361.00
7_V54_I1.3331.00
143_S147_Q1.3331.00
156_L164_V1.3291.00
8_N30_H1.3201.00
139_M200_D1.3181.00
109_T112_E1.3051.00
195_L218_V1.3051.00
147_Q151_E1.2981.00
75_K80_F1.2921.00
31_I37_V1.2761.00
111_G115_T1.2661.00
114_I137_L1.2581.00
8_N28_D1.2311.00
36_T209_I1.2271.00
13_Y61_S1.2241.00
56_G59_Q1.2191.00
29_F227_I1.2041.00
250_P253_E1.2011.00
253_E257_T1.2001.00
55_M95_M1.1991.00
29_F50_T1.1941.00
130_R149_M1.1841.00
137_L149_M1.1761.00
37_V237_N1.1691.00
131_Q135_E1.1681.00
112_E115_T1.1591.00
39_L210_L1.1541.00
36_T223_A1.1521.00
71_K76_D1.1381.00
241_D245_L1.1351.00
109_T150_K1.1341.00
37_V225_R1.1331.00
27_V50_T1.1251.00
128_E131_Q1.1101.00
111_G130_R1.1011.00
32_S225_R1.0991.00
198_M209_I1.0991.00
113_Q168_I1.0861.00
53_S60_S1.0801.00
114_I171_S1.0791.00
226_V240_V1.0681.00
50_T229_M1.0661.00
111_G133_A1.0661.00
33_K206_N1.0661.00
33_K73_E1.0611.00
177_L207_T1.0601.00
58_V61_S1.0561.00
202_C209_I1.0551.00
127_K131_Q1.0521.00
129_A133_A1.0511.00
54_I210_L1.0431.00
24_V53_S1.0421.00
124_M129_A1.0371.00
107_V154_H1.0241.00
115_T119_I1.0201.00
141_G200_D1.0181.00
202_C224_D1.0151.00
31_I176_L1.0091.00
13_Y25_D1.0001.00
173_N207_T0.9961.00
138_Q143_S0.9951.00
186_L194_V0.9911.00
138_Q144_R0.9881.00
211_L222_A0.9791.00
177_L209_I0.9751.00
108_L116_E0.9661.00
143_S148_I0.9641.00
240_V244_F0.9581.00
55_M178_I0.9561.00
45_S229_M0.9551.00
191_Q218_V0.9511.00
32_S208_S0.9501.00
93_V176_L0.9391.00
12_T49_I0.9261.00
88_I93_V0.9251.00
115_T130_R0.9251.00
134_V138_Q0.9241.00
39_L227_I0.9221.00
94_S174_P0.9201.00
52_L57_L0.9131.00
135_E138_Q0.9111.00
118_L171_S0.9091.00
250_P254_G0.9031.00
254_G258_S0.8981.00
94_S169_A0.8921.00
242_D245_L0.8901.00
7_V70_I0.8891.00
110_I156_L0.8891.00
39_L50_T0.8861.00
75_K92_E0.8861.00
53_S70_I0.8751.00
244_F247_P0.8731.00
126_K129_A0.8711.00
12_T24_V0.8711.00
179_A198_M0.8701.00
15_F19_E0.8681.00
10_L53_S0.8621.00
24_V27_V0.8591.00
125_K129_A0.8551.00
218_V222_A0.8531.00
191_Q215_D0.8521.00
96_I166_I0.8511.00
109_T152_Y0.8511.00
23_A49_I0.8491.00
249_H252_T0.8471.00
279_P282_L0.8431.00
4_L73_E0.8391.00
108_L113_Q0.8301.00
142_F148_I0.8291.00
104_L161_R0.8281.00
132_R136_L0.8281.00
276_V279_P0.8251.00
243_L252_T0.8251.00
72_L92_E0.8231.00
9_N12_T0.8231.00
234_V237_N0.8231.00
4_L72_L0.8221.00
52_L58_V0.8191.00
136_L167_A0.8141.00
36_T199_K0.8131.00
128_E132_R0.8121.00
76_D80_F0.8111.00
110_I164_V0.8081.00
136_L139_M0.8031.00
124_M128_E0.7991.00
277_P283_P0.7991.00
152_Y155_R0.7951.00
58_V63_G0.7941.00
83_N87_K0.7871.00
5_L54_I0.7851.00
53_S58_V0.7841.00
261_V264_G0.7841.00
130_R150_K0.7831.00
176_L210_L0.7791.00
196_E221_E0.7791.00
141_G193_Q0.7791.00
223_A226_V0.7771.00
31_I208_S0.7741.00
26_G233_Q0.7741.00
133_A149_M0.7671.00
181_E214_H0.7671.00
40_V219_V0.7631.00
274_G277_P0.7611.00
254_G257_T0.7591.00
9_N62_G0.7591.00
117_V172_C0.7581.00
144_R149_M0.7551.00
263_D266_I0.7551.00
122_K132_R0.7541.00
156_L160_M0.7531.00
279_P283_P0.7531.00
27_V234_V0.7481.00
199_K222_A0.7481.00
104_L164_V0.7361.00
36_T222_A0.7351.00
96_I169_A0.7321.00
273_K276_V0.7311.00
272_I276_V0.7301.00
240_V243_L0.7271.00
271_A275_S0.7241.00
176_L208_S0.7241.00
140_V167_A0.7231.00
121_H172_C0.7191.00
77_L88_I0.7141.00
37_V210_L0.7101.00
153_P164_V0.7101.00
24_V50_T0.7071.00
82_E87_K0.7071.00
252_T256_L0.7071.00
274_G279_P0.7061.00
87_K91_N0.7061.00
36_T224_D0.7061.00
178_I210_L0.7051.00
197_L200_D0.7011.00
211_L223_A0.7011.00
119_I126_K0.7001.00
278_T283_P0.6991.00
183_T218_V0.6991.00
136_L170_L0.6981.00
278_T281_N0.6971.00
15_F18_K0.6971.00
91_N122_K0.6961.00
117_V120_Y0.6951.00
105_N108_L0.6921.00
196_E199_K0.6921.00
102_T161_R0.6921.00
144_R148_I0.6911.00
54_I70_I0.6901.00
274_G278_T0.6901.00
40_V228_V0.6891.00
117_V168_I0.6851.00
230_Y235_V0.6851.00
223_A240_V0.6841.00
173_N204_K0.6841.00
109_T113_Q0.6831.00
199_K203_Q0.6831.00
114_I133_A0.6821.00
216_L244_F0.6821.00
122_K129_A0.6811.00
4_L176_L0.6801.00
148_I160_M0.6761.00
77_L93_V0.6751.00
122_K125_K0.6751.00
278_T282_L0.6731.00
192_A196_E0.6721.00
201_L207_T0.6691.00
80_F88_I0.6681.00
5_L72_L0.6671.00
52_L95_M0.6631.00
243_L247_P0.6591.00
69_S78_T0.6581.00
258_S261_V0.6571.00
235_V249_H0.6551.00
31_I210_L0.6551.00
230_Y254_G0.6521.00
118_L123_N0.6521.00
72_L88_I0.6521.00
14_F58_V0.6511.00
72_L77_L0.6491.00
270_N274_G0.6481.00
228_V247_P0.6481.00
48_S52_L0.6481.00
111_G114_I0.6471.00
280_D283_P0.6441.00
272_I275_S0.6431.00
99_E102_T0.6421.00
111_G134_V0.6411.00
230_Y233_Q0.6381.00
251_Y254_G0.6381.00
241_D244_F0.6381.00
72_L176_L0.6331.00
57_L97_F0.6331.00
219_V226_V0.6321.00
71_K74_D0.6311.00
35_E237_N0.6301.00
33_K208_S0.6251.00
276_V283_P0.6241.00
104_L113_Q0.6241.00
34_G208_S0.6231.00
7_V50_T0.6201.00
196_E200_D0.6191.00
259_I263_D0.6181.00
42_E230_Y0.6171.00
5_L176_L0.6151.00
142_F160_M0.6151.00
69_S79_S0.6131.00
170_L207_T0.6071.00
158_G163_R0.6051.00
131_Q138_Q0.6031.00
228_V243_L0.6021.00
70_I78_T0.6011.00
55_M93_V0.6011.00
242_D248_L0.6011.00
276_V280_D0.6001.00
42_E251_Y0.5991.00
151_E156_L0.5991.00
98_Q158_G0.5961.00
118_L124_M0.5951.00
126_K130_R0.5931.00
275_S279_P0.5881.00
276_V282_L0.5871.00
271_A276_V0.5871.00
130_R133_A0.5851.00
275_S278_T0.5851.00
75_K88_I0.5841.00
274_G283_P0.5841.00
4_L208_S0.5801.00
238_A247_P0.5791.00
103_S165_M0.5781.00
43_S181_E0.5771.00
238_A244_F0.5771.00
132_R139_M0.5771.00
231_C279_P0.5741.00
166_I194_V0.5721.00
123_N129_A0.5701.00
29_F37_V0.5691.00
220_S240_V0.5671.00
230_Y249_H0.5671.00
183_T194_V0.5661.00
53_S61_S0.5661.00
251_Y255_L0.5641.00
195_L213_T0.5631.00
162_Q185_A0.5631.00
133_A171_S0.5631.00
201_L205_F0.5621.00
113_Q153_P0.5611.00
272_I279_P0.5601.00
140_V197_L0.5591.00
131_Q134_V0.5581.00
42_E45_S0.5581.00
22_P26_G0.5551.00
271_A274_G0.5541.00
114_I117_V0.5531.00
116_E120_Y0.5521.00
273_K277_P0.5491.00
56_G89_R0.5481.00
87_K92_E0.5461.00
110_I114_I0.5461.00
115_T149_M0.5421.00
197_L201_L0.5401.00
219_V223_A0.5391.00
269_L272_I0.5391.00
124_M132_R0.5351.00
265_E268_K0.5321.00
118_L122_K0.5291.00
277_P281_N0.5291.00
246_E249_H0.5271.00
13_Y23_A0.5221.00
277_P280_D0.5191.00
118_L121_H0.5181.00
202_C207_T0.5151.00
264_G267_D0.5141.00
255_L258_S0.5111.00
30_H237_N0.5111.00
118_L172_C0.5101.00
104_L165_M0.5081.00
77_L80_F0.5061.00
200_D203_Q0.5031.00
59_Q62_G0.5031.00
135_E173_N0.5031.00
250_P257_T0.5021.00
256_L260_P0.5021.00
136_L140_V0.5011.00
271_A279_P0.5001.00
265_E269_L0.5001.00
99_E161_R0.5001.00
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  
4fwiB 1 0.9299 100 0.213 Contact Map
3tuiC 2 0.9573 100 0.22 Contact Map
4u00A 1 0.7348 100 0.233 Contact Map
2oljA 2 0.7378 100 0.234 Contact Map
4ry2A 2 0.7287 100 0.235 Contact Map
4yerA 2 0.8567 100 0.242 Contact Map
4ymuJ 2 0.7317 100 0.244 Contact Map
1b0uA 2 0.753 100 0.245 Contact Map
4f4cA 1 0.7012 100 0.245 Contact Map
2yyzA 1 0.9299 100 0.246 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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