GREMLIN Database
YADD - Uncharacterized protein YadD
UniProt: P31665 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11748
Length: 300 (282)
Sequences: 2597 (2266)
Seq/√Len: 134.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
254_E258_Q4.0121.00
244_L248_F3.8831.00
275_K284_E3.8551.00
261_R264_V3.6611.00
240_S244_L3.5131.00
275_K285_M3.4801.00
272_L285_M3.4751.00
253_I259_Q3.4461.00
278_S281_D3.2611.00
258_Q262_Q3.0851.00
249_E255_K3.0211.00
253_I257_I3.0041.00
250_E258_Q2.9951.00
254_E262_Q2.8441.00
262_Q266_Q2.7831.00
257_I261_R2.7371.00
257_I263_E2.4831.00
277_M281_D2.4441.00
248_F252_G2.4241.00
255_K259_Q2.3511.00
250_E254_E2.3121.00
245_A248_F2.2751.00
256_G260_G2.2541.00
245_A251_K2.2351.00
277_M285_M2.2231.00
288_L296_V2.2171.00
252_G256_G2.2141.00
236_T240_S2.1871.00
283_A290_L2.1791.00
289_P292_E2.1631.00
249_E257_I2.0811.00
264_V267_E2.0551.00
269_A288_L2.0001.00
275_K281_D1.9881.00
246_Q254_E1.9881.00
269_A286_A1.9711.00
259_Q263_E1.9381.00
45_H66_S1.9351.00
264_V268_F1.9341.00
240_S248_F1.9121.00
240_S243_T1.8511.00
272_L275_K1.8461.00
241_M247_W1.8351.00
268_F272_L1.8021.00
281_D285_M1.7951.00
271_R287_N1.7801.00
245_A249_E1.7691.00
271_R275_K1.7561.00
251_K255_K1.7501.00
282_V293_I1.7491.00
280_E290_L1.7311.00
290_L294_D1.7251.00
253_I261_R1.6981.00
269_A272_L1.6141.00
83_Q93_R1.6091.00
242_M248_F1.5891.00
272_L276_G1.5861.00
283_A293_I1.5731.00
260_G264_V1.5591.00
261_R265_S1.5391.00
249_E253_I1.5301.00
261_R267_E1.5251.00
251_K259_Q1.5091.00
245_A253_I1.5031.00
242_M246_Q1.4981.00
272_L277_M1.4951.00
24_R28_E1.4861.00
157_D160_I1.4851.00
269_A296_V1.4801.00
268_F286_A1.4531.00
282_V286_A1.4161.00
246_Q250_E1.4141.00
241_M244_L1.3881.00
244_L247_W1.3791.00
236_T239_E1.3681.00
225_D229_G1.3631.00
262_Q265_S1.3621.00
242_M245_A1.3551.00
271_R284_E1.3531.00
269_A287_N1.3491.00
237_G241_M1.3481.00
237_G240_S1.3431.00
271_R285_M1.3251.00
243_T248_F1.3051.00
286_A293_I1.2881.00
95_M99_I1.2771.00
269_A282_V1.2641.00
281_D284_E1.2491.00
265_S268_F1.2471.00
238_G241_M1.2471.00
211_M215_M1.2431.00
292_E295_K1.2391.00
276_G282_V1.2211.00
273_L282_V1.2131.00
227_F230_V1.2061.00
236_T244_L1.1830.99
266_Q270_Q1.1790.99
62_D65_Y1.1680.99
239_E242_M1.1660.99
276_G286_A1.1630.99
254_E257_I1.1610.99
237_G243_T1.1240.99
61_T64_L1.1170.99
205_G208_L1.1070.99
247_W255_K1.1000.99
238_G242_M1.0890.99
244_L249_E1.0800.99
262_Q292_E1.0750.99
283_A286_A1.0670.99
272_L281_D1.0620.99
83_Q90_M1.0580.99
94_M118_P1.0560.99
279_R290_L1.0550.99
243_T246_Q1.0550.99
191_L194_L1.0540.99
207_Q211_M1.0540.99
229_G233_D1.0490.99
279_R293_I1.0480.99
270_Q274_S1.0480.99
247_W251_K1.0460.99
239_E243_T1.0420.99
57_K62_D1.0380.99
239_E244_L1.0300.99
257_I265_S1.0300.99
92_F106_L1.0290.99
238_G244_L1.0250.98
240_S245_A1.0170.98
279_R289_P1.0100.98
277_M283_A1.0100.98
90_M93_R1.0070.98
98_S118_P1.0070.98
241_M245_A1.0040.98
276_G285_M1.0040.98
100_A103_H0.9910.98
291_A294_D0.9910.98
235_E240_S0.9850.98
279_R294_D0.9800.98
237_G244_L0.9720.98
59_H62_D0.9720.98
255_K263_E0.9670.98
203_T207_Q0.9520.98
57_K61_T0.9500.98
268_F271_R0.9500.98
230_V234_R0.9470.97
268_F285_M0.9460.97
272_L286_A0.9390.97
20_A43_T0.9330.97
271_R277_M0.9280.97
249_E252_G0.9270.97
229_G232_R0.9260.97
258_Q266_Q0.9250.97
67_V78_V0.9240.97
162_P165_E0.9190.97
25_D29_I0.9180.97
218_R221_T0.9170.97
61_T65_Y0.9170.97
273_L276_G0.9150.97
279_R282_V0.9000.97
242_M250_E0.8990.97
204_S207_Q0.8920.96
282_V288_L0.8870.96
246_Q249_E0.8810.96
276_G284_E0.8810.96
236_T245_A0.8810.96
248_F251_K0.8800.96
243_T247_W0.8720.96
14_K50_S0.8680.96
208_L212_Q0.8640.96
67_V71_G0.8550.95
244_L252_G0.8540.95
269_A276_G0.8530.95
248_F256_G0.8500.95
235_E238_G0.8440.95
276_G281_D0.8410.95
274_S285_M0.8390.95
246_Q258_Q0.8330.95
250_E262_Q0.8320.95
13_F82_H0.8310.95
98_S102_M0.8290.95
237_G242_M0.8280.95
293_I296_V0.8260.94
208_L211_M0.8200.94
258_Q261_R0.8200.94
211_M214_Y0.8170.94
282_V287_N0.8160.94
62_D67_V0.8130.94
241_M248_F0.8130.94
20_A24_R0.8120.94
98_S116_V0.8120.94
279_R283_A0.8070.94
208_L218_R0.8000.93
276_G283_A0.7950.93
271_R274_S0.7950.93
90_M120_L0.7860.93
208_L215_M0.7850.93
272_L287_N0.7840.93
268_F275_K0.7840.93
59_H64_L0.7830.93
288_L293_I0.7830.93
278_S283_A0.7770.92
235_E239_E0.7760.92
283_A294_D0.7750.92
244_L251_K0.7750.92
96_R103_H0.7710.92
132_S139_F0.7710.92
273_L296_V0.7680.92
26_F30_H0.7660.92
236_T243_T0.7610.92
257_I262_Q0.7600.92
209_V213_N0.7590.92
276_G293_I0.7590.92
217_Q221_T0.7580.91
51_F64_L0.7570.91
228_Y232_R0.7540.91
226_L230_V0.7510.91
230_V233_D0.7470.91
218_R222_E0.7460.91
40_D43_T0.7410.91
276_G279_R0.7400.90
201_G204_S0.7370.90
243_T249_E0.7370.90
271_R281_D0.7370.90
204_S208_L0.7330.90
64_L67_V0.7290.90
272_L282_V0.7290.90
255_K258_Q0.7260.90
272_L293_I0.7260.90
243_T251_K0.7200.89
10_D14_K0.7180.89
212_Q216_L0.7180.89
211_M217_Q0.7160.89
250_E253_I0.7150.89
286_A296_V0.7150.89
59_H100_A0.7140.89
284_E287_N0.7130.89
280_E284_E0.7130.89
251_K254_E0.7120.89
227_F231_L0.7110.89
35_L38_L0.7080.88
273_L293_I0.7070.88
203_T208_L0.7030.88
84_S123_Q0.7020.88
277_M286_A0.7020.88
132_S137_D0.6970.88
263_E267_E0.6940.87
165_E168_Q0.6940.87
17_L23_A0.6900.87
236_T241_M0.6890.87
282_V296_V0.6880.87
94_M120_L0.6850.87
207_Q221_T0.6850.87
202_Y208_L0.6850.87
79_V116_V0.6840.87
187_L191_L0.6840.87
192_E196_T0.6800.86
272_L278_S0.6800.86
62_D70_Q0.6800.86
134_C137_D0.6790.86
137_D140_Y0.6790.86
246_Q262_Q0.6780.86
286_A292_E0.6770.86
102_M116_V0.6740.86
240_S247_W0.6720.86
212_Q222_E0.6710.86
64_L101_A0.6710.86
211_M218_R0.6640.85
215_M218_R0.6600.85
268_F277_M0.6560.84
273_L279_R0.6510.84
46_L65_Y0.6510.84
239_E245_A0.6490.84
208_L217_Q0.6490.84
30_H119_I0.6460.83
51_F101_A0.6450.83
216_L219_G0.6430.83
268_F276_G0.6430.83
59_H65_Y0.6400.83
117_V154_P0.6380.83
191_L195_V0.6380.83
216_L220_H0.6370.83
271_R283_A0.6360.83
265_S272_L0.6350.82
163_D177_L0.6340.82
212_Q221_T0.6330.82
27_L78_V0.6300.82
194_L198_I0.6290.82
263_E274_S0.6290.82
57_K64_L0.6290.82
288_L292_E0.6280.82
274_S281_D0.6280.82
267_E271_R0.6270.82
266_Q269_A0.6260.82
275_K278_S0.6260.82
263_E266_Q0.6260.82
249_E259_Q0.6250.81
136_F140_Y0.6250.81
208_L219_G0.6240.81
209_V217_Q0.6230.81
237_G248_F0.6220.81
254_E266_Q0.6220.81
289_P294_D0.6200.81
46_L49_G0.6200.81
66_S77_H0.6200.81
273_L294_D0.6190.81
195_V198_I0.6180.81
205_G212_Q0.6170.81
25_D171_R0.6140.80
267_E275_K0.6130.80
92_F150_N0.6110.80
291_A295_K0.6110.80
183_R186_D0.6110.80
190_L193_Q0.6090.80
283_A289_P0.6090.80
175_L179_Q0.6080.80
22_T26_F0.6070.80
214_Y218_R0.6060.79
212_Q218_R0.6060.79
195_V227_F0.6040.79
261_R268_F0.6010.79
173_A177_L0.6000.79
79_V118_P0.5990.79
270_Q276_G0.5960.78
277_M288_L0.5950.78
190_L194_L0.5930.78
232_R235_E0.5930.78
236_T242_M0.5920.78
211_M216_L0.5900.78
214_Y219_G0.5900.78
242_M258_Q0.5890.77
228_Y233_D0.5880.77
277_M280_E0.5870.77
265_S276_G0.5830.77
57_K65_Y0.5830.77
265_S277_M0.5830.77
225_D228_Y0.5810.77
252_G255_K0.5810.77
226_L229_G0.5780.76
207_Q217_Q0.5720.75
112_K140_Y0.5710.75
105_H114_P0.5700.75
13_F17_L0.5690.75
35_L39_C0.5680.75
79_V101_A0.5670.75
279_R292_E0.5670.75
271_R276_G0.5660.75
125_E159_T0.5660.75
45_H68_Q0.5650.75
129_Y132_S0.5650.75
26_F31_L0.5640.74
269_A273_L0.5640.74
286_A289_P0.5610.74
242_M254_E0.5610.74
226_L231_L0.5610.74
235_E242_M0.5600.74
208_L221_T0.5590.74
186_D189_L0.5570.73
292_E296_V0.5560.73
283_A287_N0.5560.73
235_E244_L0.5520.73
101_A116_V0.5520.73
244_L250_E0.5510.73
279_R296_V0.5490.72
43_T68_Q0.5480.72
9_H12_V0.5480.72
276_G287_N0.5480.72
213_N217_Q0.5460.72
92_F99_I0.5450.72
201_G208_L0.5450.72
32_P35_L0.5440.72
200_E211_M0.5440.72
204_S212_Q0.5430.72
62_D68_Q0.5410.71
275_K292_E0.5410.71
133_M136_F0.5410.71
203_T212_Q0.5410.71
46_L50_S0.5400.71
274_S282_V0.5390.71
269_A293_I0.5380.71
208_L216_L0.5360.71
59_H96_R0.5350.70
205_G209_V0.5300.70
34_E37_E0.5300.70
60_S65_Y0.5290.70
281_D293_I0.5290.70
273_L277_M0.5280.69
82_H122_Y0.5270.69
252_G260_G0.5270.69
276_G288_L0.5270.69
270_Q285_M0.5270.69
245_A257_I0.5220.69
175_L178_L0.5210.68
271_R294_D0.5210.68
79_V94_M0.5190.68
268_F287_N0.5180.68
290_L295_K0.5180.68
56_L62_D0.5180.68
207_Q212_Q0.5180.68
186_D190_L0.5180.68
202_Y207_Q0.5180.68
289_P293_I0.5170.68
64_L94_M0.5170.68
281_D290_L0.5170.68
207_Q216_L0.5140.67
134_C152_P0.5140.67
98_S153_F0.5140.67
243_T252_G0.5130.67
28_E36_R0.5130.67
267_E270_Q0.5130.67
274_S278_S0.5130.67
227_F233_D0.5110.67
135_W139_F0.5110.67
219_G222_E0.5100.67
215_M219_G0.5100.67
205_G211_M0.5090.67
290_L293_I0.5070.66
135_W138_M0.5060.66
187_L193_Q0.5050.66
211_M221_T0.5040.66
272_L284_E0.5040.66
148_V152_P0.5030.66
61_T79_V0.5030.66
265_S271_R0.5030.66
172_I176_E0.5000.65
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  
4dyqA 5 0.1433 77.3 0.928 Contact Map
1jkoC 1 0.15 54 0.939 Contact Map
2jpcA 1 0.1233 40.2 0.943 Contact Map
2vldA 2 0.3967 35.7 0.945 Contact Map
1tc3C 1 0.15 34.8 0.945 Contact Map
2cobA 1 0.1767 33.4 0.946 Contact Map
3c1dA 2 0.3567 32.5 0.946 Contact Map
3e3vA 1 0.33 32.4 0.946 Contact Map
3iuoA 4 0.1533 30.5 0.947 Contact Map
2m8eA 1 0.16 27.6 0.948 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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