GREMLIN Database
YBBE - UPF0214 protein YbbE
UniProt: O05213 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 441 (339)
Sequences: 5137 (4036)
Seq/√Len: 219.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
128_Q239_E4.2141.00
230_K238_Q3.8761.00
74_D395_N3.6011.00
134_Y161_I3.3521.00
124_R235_Y3.2561.00
105_T264_A3.2281.00
237_E242_K3.1931.00
135_E139_A3.0491.00
249_T311_S3.0021.00
121_A235_Y2.8891.00
127_S336_D2.8151.00
132_D135_E2.7341.00
235_Y239_E2.7251.00
53_D81_A2.4961.00
109_L311_S2.4941.00
101_M107_F2.4721.00
336_D339_T2.4611.00
231_P234_V2.3791.00
143_G226_K2.3771.00
127_S339_T2.3721.00
57_E61_A2.3551.00
82_A103_T2.3411.00
120_F319_L2.2441.00
86_S99_A2.2441.00
122_L220_L2.1971.00
124_R239_E2.1551.00
224_V235_Y2.1541.00
79_K83_Y2.1531.00
135_E140_Y2.1441.00
228_T235_Y2.1321.00
122_L131_L2.1211.00
328_S333_S2.1201.00
337_Q341_D2.0911.00
342_L345_A2.0081.00
248_H262_Q1.9981.00
80_K314_D1.9921.00
222_C225_E1.9651.00
233_D303_V1.9541.00
222_C226_K1.9291.00
87_K97_R1.9261.00
124_R128_Q1.9251.00
53_D83_Y1.8421.00
246_L249_T1.8401.00
87_K90_E1.8381.00
236_T241_Y1.8301.00
85_Y98_P1.7861.00
160_V223_I1.7421.00
238_Q242_K1.7271.00
70_V317_A1.7161.00
168_S216_G1.6791.00
159_R162_D1.6691.00
320_L397_G1.6241.00
121_A236_T1.6121.00
376_N393_A1.6111.00
68_V101_M1.6041.00
230_K239_E1.5861.00
234_V238_Q1.5641.00
119_N217_Y1.5491.00
161_I347_S1.5431.00
321_Q324_L1.5281.00
124_R334_L1.5271.00
53_D79_K1.5251.00
70_V77_I1.5171.00
125_L224_V1.5161.00
121_A224_V1.5021.00
344_T378_Y1.4831.00
374_S394_Y1.4771.00
72_V397_G1.4631.00
189_E192_K1.4541.00
126_V131_L1.4381.00
130_K227_L1.4381.00
58_R62_A1.4341.00
119_N164_L1.4321.00
162_D167_Q1.4301.00
320_L388_T1.4271.00
213_S216_G1.4121.00
85_Y97_R1.4081.00
86_S105_T1.4071.00
72_V317_A1.4011.00
122_L224_V1.3961.00
66_G101_M1.3831.00
326_K341_D1.3821.00
123_Q343_F1.3781.00
328_S331_N1.3691.00
111_S114_K1.3631.00
136_K139_A1.3551.00
119_N356_G1.3541.00
56_I69_L1.3531.00
80_K103_T1.3431.00
72_V77_I1.3401.00
110_A384_T1.3361.00
327_G333_S1.3311.00
69_L400_L1.3261.00
116_Y309_L1.3181.00
246_L315_D1.3131.00
126_V133_V1.3111.00
68_V107_F1.3081.00
53_D57_E1.3031.00
122_L164_L1.3021.00
232_L305_G1.3001.00
230_K235_Y1.2941.00
101_M105_T1.2771.00
249_T315_D1.2721.00
161_I355_L1.2711.00
112_N316_M1.2691.00
118_T305_G1.2671.00
162_D207_G1.2581.00
232_L236_T1.2511.00
54_Q58_R1.2441.00
68_V82_A1.2361.00
115_M319_L1.2291.00
143_G195_E1.2271.00
204_Y209_K1.2261.00
214_D306_H1.2261.00
56_I67_A1.2241.00
221_G232_L1.2231.00
102_K105_T1.2231.00
191_D195_E1.2201.00
113_T309_L1.2171.00
131_L223_I1.2161.00
320_L390_I1.2021.00
318_I330_R1.1941.00
313_A401_L1.1941.00
161_I342_L1.1931.00
120_F335_F1.1931.00
70_V313_A1.1821.00
82_A101_M1.1781.00
57_E83_Y1.1711.00
68_V313_A1.1671.00
241_Y246_L1.1631.00
246_L319_L1.1631.00
140_Y223_I1.1591.00
140_Y227_L1.1581.00
251_Y309_L1.1581.00
162_D165_Q1.1461.00
389_I398_I1.1411.00
224_V228_T1.1201.00
112_N388_T1.1171.00
354_A359_R1.1131.00
125_L228_T1.1111.00
131_L227_L1.1091.00
60_I83_Y1.1091.00
346_P349_T1.1061.00
304_S307_A1.1051.00
136_K157_K1.1041.00
123_Q133_V1.1041.00
217_Y220_L1.0991.00
135_E160_V1.0941.00
116_Y319_L1.0901.00
205_Q208_T1.0891.00
223_I227_L1.0861.00
115_M388_T1.0771.00
322_V327_G1.0711.00
192_K195_E1.0711.00
131_L160_V1.0711.00
103_T314_D1.0711.00
87_K99_A1.0691.00
318_I329_Y1.0571.00
335_F340_A1.0571.00
241_Y309_L1.0541.00
323_M344_T1.0511.00
254_L259_K1.0501.00
192_K196_Y1.0491.00
230_K234_V1.0451.00
118_T221_G1.0401.00
378_Y390_I1.0381.00
165_Q347_S1.0351.00
66_G107_F1.0331.00
114_K212_Y1.0281.00
194_I222_C1.0271.00
54_Q57_E1.0261.00
317_A397_G1.0251.00
224_V232_L1.0241.00
137_V163_V1.0221.00
126_V342_L1.0211.00
231_P303_V1.0111.00
125_L130_K1.0081.00
329_Y332_I1.0021.00
123_Q339_T0.9981.00
391_D394_Y0.9951.00
144_F158_I0.9801.00
156_D162_D0.9791.00
116_Y236_T0.9741.00
316_M399_A0.9711.00
106_M262_Q0.9651.00
67_A400_L0.9651.00
138_S145_K0.9611.00
73_K76_R0.9611.00
388_T399_A0.9601.00
86_S102_K0.9591.00
141_L226_K0.9591.00
124_R240_L0.9581.00
204_Y211_V0.9561.00
87_K265_A0.9551.00
324_L390_I0.9551.00
323_M378_Y0.9531.00
122_L227_L0.9481.00
338_K341_D0.9431.00
121_A239_E0.9391.00
316_M401_L0.9351.00
248_H312_N0.9331.00
322_V334_L0.9300.99
116_Y316_M0.9300.99
138_S157_K0.9290.99
109_L386_T0.9270.99
195_E199_K0.9260.99
321_Q325_N0.9230.99
121_A228_T0.9200.99
121_A240_L0.9200.99
343_F354_A0.9200.99
288_Q293_D0.9200.99
137_V223_I0.9170.99
244_L322_V0.9100.99
71_V398_I0.9070.99
228_T231_P0.9060.99
125_L227_L0.9050.99
112_N386_T0.9000.99
333_S337_Q0.9000.99
75_G321_Q0.8920.99
390_I397_G0.8910.99
137_V158_I0.8900.99
327_G332_I0.8810.99
375_E393_A0.8810.99
284_T288_Q0.8800.99
204_Y208_T0.8800.99
353_F358_R0.8790.99
107_F401_L0.8790.99
132_D140_Y0.8770.99
157_K205_Q0.8720.99
126_V339_T0.8660.99
172_S306_H0.8650.99
124_R127_S0.8550.99
140_Y160_V0.8550.99
85_Y100_K0.8540.99
324_L397_G0.8520.99
232_L251_Y0.8520.99
357_W388_T0.8480.99
190_R194_I0.8480.99
312_N315_D0.8470.99
116_Y241_Y0.8460.99
66_G403_N0.8440.99
85_Y99_A0.8420.99
125_L128_Q0.8420.99
246_L318_I0.8390.99
59_D64_F0.8390.99
44_F78_I0.8340.99
106_M310_F0.8330.99
70_V399_A0.8320.99
44_F49_L0.8310.99
69_L81_A0.8250.99
73_K396_L0.8250.99
166_H355_L0.8200.99
125_L235_Y0.8170.99
218_M306_H0.8150.99
70_V397_G0.8130.99
73_K395_N0.8120.99
123_Q126_V0.8090.99
246_L311_S0.8050.99
120_F323_M0.8040.99
358_R379_G0.8040.99
160_V227_L0.8020.99
323_M357_W0.8020.99
314_D318_I0.8000.98
323_M343_F0.8000.98
111_S212_Y0.7990.98
328_S332_I0.7970.98
307_A383_W0.7970.98
327_G331_N0.7890.98
136_K140_Y0.7870.98
347_S355_L0.7870.98
120_F124_R0.7850.98
87_K98_P0.7830.98
115_M320_L0.7820.98
56_I60_I0.7810.98
415_N418_V0.7800.98
104_R314_D0.7780.98
236_T240_L0.7780.98
245_R318_I0.7750.98
123_Q357_W0.7740.98
57_E81_A0.7730.98
248_H315_D0.7660.98
106_M248_H0.7650.98
343_F357_W0.7650.98
317_A399_A0.7620.98
381_T387_V0.7600.98
85_Y90_E0.7600.98
154_G158_I0.7600.98
228_T239_E0.7580.98
326_K337_Q0.7530.98
69_L79_K0.7530.98
378_Y392_P0.7530.98
166_H380_H0.7520.98
154_G205_Q0.7490.98
293_D296_A0.7460.98
118_T236_T0.7440.98
256_K259_K0.7430.98
43_Q49_L0.7410.98
240_L334_L0.7360.97
65_P404_K0.7350.97
383_W405_K0.7330.97
158_I162_D0.7320.97
237_E241_Y0.7310.97
45_S48_K0.7300.97
73_K78_I0.7300.97
168_S213_S0.7300.97
358_R380_H0.7290.97
137_V144_F0.7260.97
141_L222_C0.7240.97
289_G292_H0.7230.97
291_V294_E0.7220.97
221_G305_G0.7210.97
133_V161_I0.7210.97
342_L347_S0.7190.97
55_M59_D0.7160.97
285_N289_G0.7150.97
373_A377_A0.7100.97
233_D237_E0.7090.97
344_T392_P0.7080.97
113_T251_Y0.7070.97
341_D345_A0.7070.97
108_D310_F0.7050.97
137_V141_L0.7040.97
70_V80_K0.7020.97
311_S315_D0.7020.97
126_V132_D0.6980.96
109_L112_N0.6950.96
58_R61_A0.6930.96
90_E267_E0.6920.96
133_V355_L0.6920.96
116_Y246_L0.6900.96
110_A307_A0.6880.96
137_V140_Y0.6860.96
109_L316_M0.6790.96
156_D205_Q0.6780.96
64_F67_A0.6770.96
374_S391_D0.6770.96
225_E232_L0.6750.96
158_I168_S0.6740.96
286_T291_V0.6690.95
90_E97_R0.6680.95
50_R53_D0.6670.95
122_L223_I0.6660.95
90_E98_P0.6660.95
190_R222_C0.6650.95
236_T249_T0.6650.95
320_L399_A0.6630.95
408_P413_E0.6620.95
164_L220_L0.6590.95
68_V80_K0.6570.95
414_E418_V0.6550.95
249_T312_N0.6540.95
56_I400_L0.6540.95
287_L292_H0.6530.95
60_I63_G0.6500.95
317_A321_Q0.6480.95
285_N288_Q0.6460.95
359_R376_N0.6430.94
56_I83_Y0.6400.94
359_R377_A0.6390.94
329_Y333_S0.6380.94
304_S308_G0.6370.94
132_D139_A0.6370.94
120_F357_W0.6360.94
325_N328_S0.6360.94
45_S49_L0.6350.94
247_K250_L0.6350.94
241_Y249_T0.6330.94
240_L244_L0.6320.94
194_I198_T0.6290.94
47_K50_R0.6280.94
197_L219_L0.6260.94
72_V321_Q0.6260.94
113_T116_Y0.6250.94
374_S377_A0.6250.94
321_Q397_G0.6230.93
250_L253_P0.6220.93
108_D384_T0.6210.93
77_I321_Q0.6200.93
311_S316_M0.6190.93
77_I80_K0.6190.93
234_V237_E0.6170.93
134_Y159_R0.6150.93
144_F223_I0.6150.93
163_V168_S0.6130.93
286_T290_E0.6130.93
250_L259_K0.6110.93
56_I81_A0.6100.93
186_Y192_K0.6100.93
326_K395_N0.6100.93
292_H295_K0.6100.93
413_E416_P0.6070.93
259_K262_Q0.6070.93
141_L223_I0.6070.93
112_N115_M0.6060.92
291_V296_A0.6060.92
340_A343_F0.6050.92
292_H296_A0.6030.92
115_M357_W0.6020.92
126_V160_V0.6020.92
325_N333_S0.6010.92
86_S264_A0.6010.92
327_G334_L0.6010.92
160_V220_L0.6000.92
161_I165_Q0.5990.92
318_I321_Q0.5990.92
283_R286_T0.5980.92
191_D226_K0.5970.92
340_A344_T0.5960.92
99_A105_T0.5950.92
50_R54_Q0.5940.92
385_G404_K0.5940.92
282_I285_N0.5920.92
87_K267_E0.5850.91
143_G198_T0.5840.91
113_T232_L0.5830.91
320_L357_W0.5820.91
225_E228_T0.5820.91
253_P256_K0.5810.91
120_F240_L0.5770.91
289_G293_D0.5770.91
138_S142_P0.5750.90
353_F357_W0.5700.90
305_G308_G0.5690.90
42_A76_R0.5670.90
69_L83_Y0.5670.90
191_D222_C0.5670.90
67_A402_T0.5660.90
165_Q348_A0.5650.90
111_S382_G0.5650.90
158_I170_L0.5610.89
325_N332_I0.5600.89
322_V331_N0.5600.89
356_G403_N0.5600.89
287_L291_V0.5600.89
51_K54_Q0.5580.89
284_T287_L0.5560.89
266_T384_T0.5560.89
326_K340_A0.5550.89
164_L223_I0.5540.89
190_R193_T0.5540.89
57_E60_I0.5520.89
391_D396_L0.5520.89
126_V140_Y0.5500.88
322_V329_Y0.5490.88
190_R225_E0.5470.88
125_L131_L0.5470.88
347_S354_A0.5450.88
195_E198_T0.5450.88
109_L113_T0.5430.88
43_Q73_K0.5430.88
170_L215_I0.5420.88
290_E293_D0.5420.88
84_G403_N0.5420.88
233_D250_L0.5400.87
247_K315_D0.5390.87
146_D156_D0.5380.87
167_Q207_G0.5370.87
124_R335_F0.5360.87
326_K331_N0.5360.87
90_E265_A0.5360.87
123_Q323_M0.5340.87
89_Y267_E0.5330.87
284_T289_G0.5320.87
144_F219_L0.5320.87
144_F155_K0.5320.87
248_H259_K0.5310.87
250_L310_F0.5300.86
106_M250_L0.5300.86
227_L235_Y0.5290.86
145_K155_K0.5290.86
49_L73_K0.5280.86
412_P415_N0.5280.86
109_L401_L0.5270.86
127_S340_A0.5260.86
246_L312_N0.5260.86
167_Q348_A0.5250.86
294_E409_V0.5250.86
326_K392_P0.5240.86
172_S218_M0.5230.86
288_Q294_E0.5220.86
286_T289_G0.5200.85
242_K261_K0.5200.85
387_V400_L0.5190.85
328_S337_Q0.5190.85
412_P416_P0.5180.85
42_A46_T0.5180.85
237_E250_L0.5180.85
137_V160_V0.5160.85
119_N122_L0.5160.85
236_T309_L0.5130.85
326_K333_S0.5130.85
202_L207_G0.5120.85
166_H353_F0.5110.84
409_V413_E0.5100.84
357_W390_I0.5090.84
318_I322_V0.5080.84
166_H213_S0.5070.84
146_D199_K0.5070.84
108_D113_T0.5060.84
107_F313_A0.5050.84
327_G340_A0.5050.84
80_K313_A0.5040.84
357_W379_G0.5040.84
260_P263_F0.5040.84
65_P68_V0.5010.83
143_G146_D0.5000.83
73_K394_Y0.5000.83
106_M259_K0.5000.83
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  
4ivkA 4 0.839 100 0.314 Contact Map
4p6bA 5 0.805 100 0.323 Contact Map
3zytA 3 0.7959 100 0.341 Contact Map
1ci9A 1 0.7891 100 0.347 Contact Map
2drwA 3 0.7914 100 0.348 Contact Map
2qmiA 5 0.7823 100 0.349 Contact Map
4lclA 1 0.8254 100 0.352 Contact Map
1yqsA 1 0.7596 100 0.352 Contact Map
1ei5A 2 0.7619 100 0.361 Contact Map
2qz6A 1 0.7211 100 0.362 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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