GREMLIN Database
YPDA - Uncharacterized protein YpdA
UniProt: P50736 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 324 (282)
Sequences: 61213 (43461)
Seq/√Len: 2588.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
161_V243_N4.0861.00
159_D182_R3.4181.00
34_K96_M3.1281.00
184_T216_E3.0061.00
5_K28_D2.9091.00
182_R214_R2.7681.00
5_K120_P2.7321.00
225_T230_V2.7131.00
109_V116_T2.5061.00
223_K230_V2.4171.00
216_E239_I2.3471.00
161_V186_L2.3191.00
30_L92_N2.3161.00
108_F112_T2.3151.00
6_A22_L2.2941.00
133_N253_H2.2841.00
159_D244_D2.2671.00
18_A123_I2.2161.00
159_D184_T2.1891.00
230_V240_T2.1871.00
205_E209_R2.1571.00
276_N281_E2.1491.00
32_I117_Y2.1401.00
265_E274_F2.1371.00
222_E232_R2.1271.00
7_I32_I2.1231.00
111_E116_T2.0411.00
4_E30_L2.0341.00
123_I314_I2.0081.00
138_P223_K2.0031.00
108_F286_G1.9951.00
7_I110_I1.9441.00
220_C232_R1.9251.00
109_V118_T1.8311.00
99_K111_E1.7851.00
7_I117_Y1.7821.00
233_S239_I1.7711.00
188_R220_C1.7661.00
142_L226_E1.7581.00
225_T240_T1.7411.00
5_K30_L1.7381.00
102_K284_V1.7371.00
121_Y286_G1.7361.00
7_I119_T1.7211.00
186_L241_I1.7131.00
184_T214_R1.7091.00
159_D242_K1.7031.00
39_N42_Y1.6911.00
222_E230_V1.6401.00
112_T117_Y1.6321.00
131_H255_D1.6211.00
28_D90_R1.6191.00
119_T122_C1.6131.00
265_E283_N1.5991.00
131_H253_H1.5981.00
158_K244_D1.5961.00
267_D270_T1.5781.00
72_V75_Q1.5711.00
219_A233_S1.5571.00
14_C290_A1.5451.00
161_V229_V1.5381.00
145_V148_Y1.5291.00
81_R85_K1.4951.00
267_D272_R1.4861.00
8_I15_G1.4641.00
19_A31_V1.4441.00
219_A239_I1.4401.00
159_D181_A1.4321.00
276_N279_T1.4311.00
101_T104_Q1.4241.00
92_N95_E1.4231.00
95_E113_S1.3911.00
126_T293_I1.3871.00
131_H257_Q1.3861.00
7_I30_L1.3811.00
224_I246_V1.3791.00
123_I290_A1.3741.00
121_Y314_I1.3691.00
95_E112_T1.3621.00
190_N218_G1.3591.00
267_D295_A1.3531.00
184_T243_N1.3481.00
311_G315_A1.3471.00
216_E219_A1.3461.00
121_Y288_F1.3421.00
40_S43_N1.3201.00
11_G33_E1.3171.00
267_D274_F1.3081.00
59_I62_V1.3081.00
112_T115_E1.3011.00
160_V176_L1.3001.00
78_S82_E1.2981.00
288_F313_H1.2861.00
307_G311_G1.2711.00
36_N40_S1.2391.00
136_G140_E1.2211.00
281_E285_E1.2171.00
60_G63_A1.2161.00
21_H312_G1.1991.00
92_N115_E1.1981.00
95_E115_E1.1971.00
275_F294_A1.1891.00
6_A123_I1.1801.00
21_H24_Q1.1741.00
8_I19_A1.1721.00
165_G187_Y1.1711.00
310_H314_I1.1601.00
146_F149_F1.1561.00
101_T109_V1.1521.00
37_V40_S1.1491.00
207_L210_N1.1401.00
187_Y217_F1.1371.00
231_F241_I1.1311.00
101_T111_E1.1271.00
198_P202_P1.1221.00
156_F181_A1.1191.00
82_E86_R1.1101.00
30_L117_Y1.1091.00
160_V245_F1.1001.00
309_F313_H1.0951.00
83_V87_K1.0841.00
6_A27_I1.0821.00
75_Q78_S1.0801.00
284_V287_V1.0781.00
170_V185_V1.0761.00
82_E85_K1.0761.00
38_V42_Y1.0701.00
125_A290_A1.0631.00
4_E28_D1.0581.00
151_E155_Y1.0481.00
202_P205_E1.0461.00
157_D181_A1.0461.00
191_E201_L1.0431.00
177_V213_I1.0421.00
219_A231_F1.0361.00
100_V122_C1.0321.00
177_V182_R1.0251.00
14_C303_F1.0171.00
77_L81_R1.0101.00
173_A185_V1.0051.00
162_V173_A1.0031.00
160_V181_A1.0011.00
32_I97_V1.0011.00
273_P289_I0.9991.00
4_E7_I0.9981.00
99_K102_K0.9931.00
95_E98_R0.9931.00
163_I246_V0.9931.00
32_I112_T0.9931.00
6_A121_Y0.9911.00
97_V102_K0.9851.00
203_E207_L0.9841.00
273_P293_I0.9831.00
144_K226_E0.9831.00
39_N43_N0.9821.00
99_K261_K0.9821.00
102_K287_V0.9801.00
38_V41_I0.9771.00
145_V149_F0.9731.00
36_N81_R0.9701.00
78_S81_R0.9621.00
207_L211_G0.9621.00
79_Y82_E0.9611.00
20_I24_Q0.9601.00
178_K211_G0.9541.00
184_T241_I0.9521.00
9_I124_I0.9371.00
23_K89_I0.9351.00
227_N242_K0.9351.00
202_P206_A0.9311.00
290_A310_H0.9301.00
278_E281_E0.9281.00
32_I92_N0.9251.00
30_L119_T0.9221.00
98_R111_E0.9181.00
58_E61_D0.9161.00
4_E121_Y0.9101.00
9_I126_T0.9081.00
206_A209_R0.9051.00
30_L90_R0.9041.00
22_L311_G0.8961.00
206_A210_N0.8951.00
294_A306_N0.8911.00
92_N117_Y0.8891.00
302_I306_N0.8861.00
186_L231_F0.8861.00
38_V43_N0.8861.00
205_E217_F0.8831.00
169_S187_Y0.8811.00
161_V241_I0.8741.00
280_M309_F0.8741.00
257_Q260_E0.8731.00
275_F289_I0.8721.00
180_G183_V0.8701.00
22_L27_I0.8681.00
5_K118_T0.8671.00
95_E99_K0.8641.00
163_I250_T0.8641.00
80_Y83_V0.8631.00
103_T109_V0.8611.00
21_H308_R0.8591.00
289_I293_I0.8521.00
18_A290_A0.8461.00
8_I18_A0.8441.00
280_M294_A0.8431.00
23_K29_A0.8331.00
36_N41_I0.8321.00
214_R239_I0.8271.00
15_G125_A0.8251.00
216_E241_I0.8231.00
288_F314_I0.8231.00
303_F307_G0.8201.00
231_F239_I0.8191.00
19_A29_A0.8191.00
36_N39_N0.8191.00
139_G142_L0.8181.00
18_A307_G0.8161.00
97_V110_I0.8091.00
27_I315_A0.8051.00
5_K27_I0.8051.00
11_G31_V0.8011.00
306_N310_H0.8001.00
73_R80_Y0.7951.00
108_F284_V0.7931.00
161_V246_V0.7931.00
59_I63_A0.7901.00
292_V303_F0.7881.00
122_C287_V0.7861.00
225_T228_E0.7821.00
192_Y217_F0.7821.00
80_Y84_V0.7791.00
201_L205_E0.7791.00
163_I248_A0.7791.00
137_V140_E0.7751.00
74_I78_S0.7701.00
289_I294_A0.7691.00
79_Y83_V0.7691.00
191_E198_P0.7671.00
219_A232_R0.7651.00
32_I95_E0.7591.00
6_A314_I0.7551.00
37_V42_Y0.7551.00
73_R77_L0.7511.00
280_M310_H0.7501.00
134_Y140_E0.7491.00
18_A310_H0.7481.00
139_G223_K0.7471.00
128_Y252_Y0.7451.00
140_E248_A0.7401.00
203_E206_A0.7381.00
123_I310_H0.7381.00
36_N43_N0.7361.00
134_Y248_A0.7341.00
310_H313_H0.7341.00
22_L314_I0.7321.00
159_D243_N0.7281.00
25_I315_A0.7251.00
308_R312_G0.7241.00
279_T313_H0.7231.00
279_T282_T0.7221.00
204_F208_V0.7201.00
281_E286_G0.7201.00
163_I221_V0.7181.00
305_E308_R0.7131.00
99_K104_Q0.7131.00
19_A89_I0.7081.00
124_I293_I0.7031.00
32_I119_T0.7031.00
151_E154_P0.6991.00
15_G19_A0.6971.00
62_V86_R0.6951.00
243_N246_V0.6941.00
17_S21_H0.6921.00
135_M248_A0.6921.00
71_P75_Q0.6921.00
37_V93_A0.6901.00
8_I125_A0.6891.00
274_F283_N0.6871.00
150_K154_P0.6851.00
143_P226_E0.6851.00
266_I274_F0.6841.00
191_E194_P0.6841.00
174_L178_K0.6831.00
276_N280_M0.6831.00
281_E284_V0.6781.00
5_K117_Y0.6781.00
22_L29_A0.6761.00
172_A175_E0.6751.00
177_V212_T0.6711.00
83_V86_R0.6701.00
102_K108_F0.6691.00
221_V229_V0.6681.00
9_I97_V0.6671.00
153_H156_F0.6651.00
200_I203_E0.6651.00
186_L216_E0.6601.00
177_V211_G0.6581.00
305_E309_F0.6581.00
299_A302_I0.6581.00
77_L80_Y0.6561.00
228_E240_T0.6561.00
187_Y194_P0.6551.00
256_H266_I0.6511.00
25_I312_G0.6511.00
124_I258_F0.6501.00
198_P201_L0.6461.00
280_M313_H0.6441.00
155_Y245_F0.6431.00
259_L262_I0.6411.00
290_A307_G0.6301.00
158_K245_F0.6251.00
172_A249_M0.6241.00
99_K103_T0.6231.00
301_E304_I0.6221.00
290_A314_I0.6201.00
17_S20_I0.6201.00
172_A247_F0.6201.00
5_K119_T0.6191.00
27_I120_P0.6191.00
208_V215_M0.6191.00
272_R275_F0.6181.00
205_E215_M0.6171.00
199_W203_E0.6161.00
154_P157_D0.6151.00
98_R102_K0.6151.00
187_Y190_N0.6141.00
216_E231_F0.6141.00
8_I31_V0.6131.00
295_A306_N0.6091.00
84_V87_K0.6071.00
275_F280_M0.6071.00
134_Y141_D0.6071.00
186_L219_A0.6061.00
260_E266_I0.6061.00
150_K153_H0.6041.00
281_E313_H0.6031.00
150_K155_Y0.6031.00
282_T289_I0.6011.00
312_G316_A0.6001.00
108_F287_V0.5981.00
262_I266_I0.5961.00
161_V184_T0.5941.00
257_Q261_K0.5941.00
37_V41_I0.5921.00
133_N136_G0.5921.00
288_F310_H0.5911.00
166_K251_G0.5901.00
158_K181_A0.5871.00
191_E205_E0.5871.00
301_E305_E0.5861.00
165_G192_Y0.5861.00
104_Q109_V0.5861.00
23_K90_R0.5851.00
232_R236_K0.5801.00
224_I229_V0.5801.00
4_E120_P0.5791.00
21_H25_I0.5791.00
96_M99_K0.5781.00
74_I77_L0.5721.00
173_A183_V0.5671.00
200_I204_F0.5671.00
8_I29_A0.5661.00
140_E143_P0.5641.00
17_S304_I0.5631.00
175_E178_K0.5631.00
68_N75_Q0.5621.00
266_I273_P0.5621.00
136_G141_D0.5601.00
304_I308_R0.5591.00
23_K88_N0.5581.00
104_Q116_T0.5561.00
159_D241_I0.5561.00
97_V104_Q0.5551.00
299_A303_F0.5531.00
173_A213_I0.5521.00
209_R214_R0.5491.00
187_Y215_M0.5461.00
192_Y201_L0.5461.00
162_V169_S0.5451.00
28_D120_P0.5441.00
281_E288_F0.5441.00
14_C125_A0.5421.00
214_R241_I0.5411.00
18_A311_G0.5411.00
84_V89_I0.5401.00
300_N303_F0.5361.00
256_H293_I0.5361.00
29_A90_R0.5361.00
199_W202_P0.5351.00
186_L243_N0.5341.00
164_G251_G0.5331.00
20_I87_K0.5311.00
175_E179_S0.5291.00
135_M140_E0.5291.00
135_M250_T0.5281.00
153_H245_F0.5261.00
268_K274_F0.5251.00
109_V112_T0.5251.00
155_Y158_K0.5251.00
158_K182_R0.5241.00
138_P142_L0.5231.00
142_L223_K0.5181.00
111_E114_K0.5141.00
227_N240_T0.5141.00
6_A311_G0.5141.00
295_A298_N0.5131.00
176_L183_V0.5131.00
151_E157_D0.5121.00
230_V233_S0.5111.00
201_L204_F0.5091.00
75_Q79_Y0.5061.00
100_V110_I0.5061.00
169_S249_M0.5051.00
303_F306_N0.5041.00
146_F172_A0.5041.00
168_S249_M0.5041.00
70_K73_R0.5031.00
36_N42_Y0.5021.00
300_N304_I0.5011.00
156_F179_S0.5011.00
62_V87_K0.5011.00
110_I119_T0.5001.00
18_A22_L0.5001.00
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  
4c5oA 5 0.9475 100 0.261 Contact Map
4usrA 1 0.963 100 0.268 Contact Map
4usqA 3 0.9506 100 0.279 Contact Map
1lvlA 2 0.966 100 0.293 Contact Map
3d1cA 2 0.9506 100 0.296 Contact Map
2zbwA 2 0.9444 100 0.296 Contact Map
3ab1A 2 0.9444 100 0.301 Contact Map
3ctyA 2 0.9043 100 0.301 Contact Map
1vdcA 2 0.9105 100 0.302 Contact Map
3lzwA 2 0.9352 100 0.302 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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