GREMLIN Database
DDPD - Probable D,D-dipeptide transport ATP-binding protein DdpD
UniProt: P77268 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13787
Length: 328 (264)
Sequences: 54072 (33844)
Seq/√Len: 2082.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
36_E226_S4.0741.00
93_R176_Q3.4121.00
10_Q27_N3.2391.00
7_D31_Q3.1291.00
9_Q70_Q3.0571.00
23_H26_N2.8261.00
13_L54_L2.8051.00
38_V228_Y2.7921.00
70_Q77_D2.5251.00
39_G224_C2.4651.00
240_V243_D2.4571.00
33_N36_E2.3781.00
140_E206_S2.3741.00
74_L176_Q2.3731.00
226_S238_S2.3651.00
26_N234_S2.3551.00
14_S23_H2.3121.00
228_Y235_V2.3051.00
149_V152_R2.2961.00
7_D72_S2.2951.00
201_H205_A2.2151.00
8_I11_L2.1501.00
126_S129_E2.1421.00
12_H68_R2.1121.00
12_H27_N2.0721.00
133_K136_D2.0671.00
34_R176_Q2.0551.00
52_A213_I2.0271.00
221_S242_A2.0271.00
140_E205_A2.0111.00
77_D80_N1.9911.00
15_F50_V1.9451.00
82_R85_Q1.9351.00
133_K174_E1.9121.00
137_L172_S1.8871.00
239_G244_V1.8751.00
9_Q72_S1.8571.00
214_S220_V1.8331.00
135_I150_M1.8121.00
57_R86_L1.7861.00
12_H23_H1.7351.00
39_G220_V1.6991.00
109_R113_L1.6951.00
145_D148_E1.6771.00
15_F24_A1.6551.00
52_A179_I1.6441.00
116_M130_A1.6261.00
13_L59_L1.5991.00
152_R156_E1.5891.00
76_E85_Q1.5651.00
228_Y238_S1.5561.00
112_G151_S1.5501.00
174_E206_S1.5481.00
116_M134_A1.5431.00
239_G243_D1.5411.00
136_D140_E1.5111.00
13_L67_H1.5041.00
74_L93_R1.5021.00
14_S67_H1.4901.00
10_Q29_S1.4891.00
8_I30_L1.4851.00
112_G150_M1.4771.00
16_P21_D1.4751.00
200_K222_Q1.4631.00
131_R135_I1.4631.00
149_V157_L1.4601.00
14_S21_D1.4431.00
243_D247_H1.4401.00
120_R130_A1.4381.00
12_H26_N1.4141.00
144_P148_E1.4121.00
180_A210_V1.4111.00
200_K203_A1.3931.00
81_A85_Q1.3851.00
11_L66_V1.3791.00
115_M138_L1.3661.00
37_I203_A1.3441.00
140_E201_H1.3141.00
196_L219_V1.3101.00
97_I180_A1.2721.00
36_E225_D1.2691.00
9_Q31_Q1.2681.00
110_R113_L1.2681.00
102_M162_R1.2661.00
112_G116_M1.2461.00
32_I38_V1.2411.00
144_P149_V1.2381.00
8_I55_I1.2321.00
135_I145_D1.2211.00
148_E152_R1.2211.00
112_G131_R1.2131.00
37_I210_V1.2021.00
30_L51_T1.1931.00
9_Q29_S1.1891.00
157_L165_V1.1871.00
131_R150_M1.1791.00
110_R151_S1.1751.00
40_L211_L1.1661.00
30_L228_Y1.1621.00
199_L210_V1.1581.00
114_Q169_L1.1521.00
28_V51_T1.1491.00
38_V238_S1.1481.00
57_R65_C1.1471.00
113_L116_M1.1461.00
56_M96_M1.1371.00
72_S77_D1.1361.00
254_I258_Q1.1331.00
132_A136_D1.1241.00
76_E81_A1.1241.00
251_P254_I1.1211.00
54_L66_V1.1081.00
38_V226_S1.1071.00
242_A246_H1.1041.00
33_N226_S1.0991.00
108_T155_F1.0931.00
138_L150_M1.0901.00
34_R74_L1.0791.00
37_I224_C1.0741.00
81_A86_L1.0701.00
128_R132_A1.0601.00
112_G134_A1.0571.00
133_K137_L1.0431.00
145_D149_V1.0271.00
203_A225_D1.0161.00
34_R207_G1.0121.00
115_M172_S1.0111.00
187_L195_V1.0111.00
129_E132_A1.0081.00
227_V241_T1.0021.00
142_Q201_H0.9931.00
130_A134_A0.9911.00
178_I208_T0.9881.00
136_D139_E0.9851.00
55_I211_L0.9841.00
125_I129_E0.9781.00
203_A210_V0.9691.00
51_T230_M0.9661.00
109_R117_D0.9601.00
212_F223_L0.9551.00
243_D246_H0.9541.00
14_S26_N0.9531.00
25_L54_L0.9531.00
32_I177_L0.9511.00
10_Q68_R0.9501.00
178_I210_V0.9461.00
139_E144_P0.9431.00
174_E208_T0.9421.00
119_I172_S0.9371.00
116_M131_R0.9331.00
116_M120_R0.9131.00
53_M58_L0.9101.00
135_I139_E0.9091.00
137_L140_E0.9081.00
33_N209_A0.9071.00
5_V74_L0.9061.00
125_I130_A0.9001.00
40_L51_T0.9001.00
8_I71_I0.8971.00
13_L50_V0.8921.00
139_E145_D0.8841.00
95_A170_A0.8821.00
111_I157_L0.8781.00
262_E265_V0.8711.00
105_L162_R0.8711.00
192_Q219_V0.8681.00
143_I149_V0.8631.00
24_A50_V0.8611.00
280_L283_L0.8591.00
40_L228_Y0.8591.00
192_Q216_D0.8561.00
46_S230_M0.8501.00
16_P20_G0.8481.00
200_K223_L0.8451.00
53_M59_L0.8441.00
11_L54_L0.8421.00
94_V177_L0.8421.00
153_Y156_E0.8401.00
110_R153_Y0.8381.00
5_V73_L0.8381.00
97_I167_I0.8361.00
180_A199_L0.8351.00
111_I165_V0.8311.00
95_A175_P0.8311.00
123_Q133_K0.8291.00
56_M179_I0.8281.00
250_H253_T0.8271.00
54_L71_I0.8261.00
202_K208_T0.8261.00
251_P255_G0.8241.00
137_L168_A0.8181.00
219_V223_L0.8151.00
73_L93_R0.8141.00
255_G259_C0.8131.00
37_I200_K0.8131.00
76_E93_R0.8131.00
244_V253_T0.8131.00
13_L25_L0.8091.00
54_L59_L0.8071.00
41_V220_V0.8041.00
245_I248_P0.8011.00
83_E86_L0.7991.00
6_L55_I0.7981.00
127_R130_A0.7901.00
197_R222_Q0.7901.00
198_L201_H0.7881.00
109_R114_Q0.7841.00
118_V173_C0.7811.00
134_A150_M0.7791.00
77_D81_A0.7781.00
142_Q194_Q0.7771.00
92_A123_Q0.7751.00
84_K87_R0.7741.00
126_S130_A0.7711.00
157_L161_M0.7701.00
241_T245_I0.7681.00
224_C227_V0.7591.00
131_R151_S0.7591.00
118_V169_L0.7581.00
255_G258_Q0.7571.00
235_V238_S0.7561.00
25_L28_V0.7521.00
177_L211_L0.7511.00
10_Q13_L0.7491.00
32_I209_A0.7481.00
278_P284_P0.7451.00
27_N234_S0.7431.00
258_Q271_P0.7401.00
141_M168_A0.7381.00
132_A135_I0.7381.00
259_C262_E0.7321.00
122_H173_C0.7321.00
179_I211_L0.7311.00
37_I223_L0.7301.00
196_L222_Q0.7271.00
145_D150_M0.7261.00
123_Q126_S0.7261.00
277_V280_L0.7241.00
28_V235_V0.7211.00
280_L284_P0.7201.00
120_R127_R0.7191.00
137_L171_F0.7171.00
193_L197_R0.7161.00
182_E215_H0.7161.00
212_F224_C0.7121.00
279_N283_L0.7101.00
217_M245_I0.7081.00
154_P165_V0.7071.00
224_C241_T0.7031.00
149_V161_M0.7031.00
279_N282_H0.7011.00
279_N284_P0.7001.00
231_Y234_S0.7001.00
15_F59_L0.6981.00
106_N109_R0.6951.00
59_L65_C0.6951.00
37_I225_D0.6911.00
197_R200_K0.6881.00
184_T219_V0.6871.00
253_T257_L0.6851.00
275_G278_P0.6841.00
97_I170_A0.6841.00
25_L51_T0.6811.00
229_V248_P0.6791.00
131_R134_A0.6791.00
177_L209_A0.6771.00
272_A276_T0.6771.00
115_M134_A0.6771.00
105_L165_V0.6741.00
231_Y255_G0.6741.00
41_V229_V0.6731.00
105_L114_Q0.6691.00
112_G135_I0.6661.00
271_P275_G0.6641.00
38_V211_L0.6591.00
197_R201_H0.6571.00
66_V79_L0.6511.00
58_L98_F0.6461.00
110_R114_Q0.6451.00
236_I250_H0.6451.00
123_Q130_A0.6451.00
273_I277_V0.6441.00
27_N68_R0.6441.00
70_Q79_L0.6431.00
53_M96_M0.6401.00
49_S53_M0.6401.00
32_I211_L0.6401.00
129_E133_K0.6391.00
274_P277_V0.6371.00
247_H250_H0.6351.00
270_L273_I0.6331.00
54_L67_H0.6321.00
73_L78_V0.6301.00
202_K206_S0.6291.00
14_S68_R0.6261.00
276_T279_N0.6231.00
174_E205_A0.6231.00
8_I51_T0.6211.00
114_Q154_P0.6201.00
5_V177_L0.6201.00
56_M94_V0.6181.00
78_V94_V0.6161.00
72_S75_G0.6161.00
281_T284_P0.6141.00
70_Q80_N0.6141.00
275_G279_N0.6121.00
43_E231_Y0.6111.00
34_R209_A0.6111.00
55_I71_I0.6091.00
73_L177_L0.6081.00
143_I161_M0.6071.00
229_V244_V0.6061.00
220_V227_V0.6051.00
132_A139_E0.6051.00
277_V281_T0.6031.00
82_R86_L0.6021.00
167_I195_V0.6021.00
142_Q149_V0.5991.00
231_Y236_I0.5991.00
152_R157_L0.5971.00
277_V284_P0.5971.00
6_L177_L0.5941.00
10_Q69_G0.5941.00
275_G280_L0.5931.00
127_R131_R0.5921.00
273_I276_T0.5891.00
43_E46_S0.5871.00
112_G115_M0.5851.00
278_P281_T0.5831.00
282_H285_D0.5821.00
171_F208_T0.5731.00
115_M118_V0.5721.00
78_V81_A0.5691.00
203_A206_S0.5691.00
31_Q238_S0.5681.00
83_E87_R0.5681.00
36_E238_S0.5671.00
243_D249_R0.5671.00
116_M150_M0.5661.00
6_L73_L0.5661.00
134_A137_L0.5651.00
241_T252_Y0.5621.00
268_Q271_P0.5611.00
260_A264_G0.5581.00
13_L66_V0.5571.00
163_Q186_A0.5561.00
43_E252_Y0.5531.00
35_G209_A0.5531.00
119_I125_I0.5521.00
280_L285_D0.5521.00
184_T195_V0.5501.00
159_G164_R0.5481.00
252_Y255_G0.5481.00
119_I124_P0.5471.00
99_Q159_G0.5471.00
244_V248_P0.5471.00
231_Y250_H0.5461.00
5_V209_A0.5461.00
71_I79_L0.5441.00
272_A277_V0.5441.00
220_V224_C0.5441.00
44_S182_E0.5431.00
138_L149_V0.5411.00
252_Y256_L0.5411.00
237_E248_P0.5401.00
276_T280_L0.5391.00
105_L166_M0.5391.00
133_K140_E0.5381.00
59_L66_V0.5351.00
221_S241_T0.5341.00
232_A280_L0.5341.00
239_G248_P0.5331.00
100_E162_R0.5261.00
158_S161_M0.5261.00
119_I123_Q0.5251.00
16_P65_C0.5231.00
125_I133_K0.5221.00
196_L223_L0.5211.00
137_L141_M0.5191.00
281_T285_D0.5181.00
14_S24_A0.5151.00
239_G245_I0.5121.00
123_Q127_R0.5121.00
275_G284_P0.5111.00
269_L272_A0.5111.00
241_T244_V0.5091.00
23_H27_N0.5091.00
220_V241_T0.5081.00
123_Q174_E0.5081.00
254_I257_L0.5071.00
278_P283_L0.5051.00
124_P130_A0.5041.00
228_Y236_I0.5041.00
111_I115_M0.5021.00
273_I280_L0.5011.00
119_I173_C0.5001.00
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 0.9268 100 0.207 Contact Map
3tuiC 2 0.9299 100 0.208 Contact Map
1oxxK 1 0.9482 100 0.234 Contact Map
1g291 4 0.9024 100 0.235 Contact Map
1v43A 2 0.8963 100 0.236 Contact Map
2it1A 1 0.8537 100 0.236 Contact Map
2yyzA 1 0.9238 100 0.236 Contact Map
4mkiB 2 0.8598 100 0.238 Contact Map
1b0uA 2 0.753 100 0.238 Contact Map
3rlfA 2 0.9268 100 0.239 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.

Page generated in 0.0128 seconds.