GREMLIN Database
YRKA - UPF0053 protein YrkA
UniProt: P54428 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 434 (409)
Sequences: 8280 (5390)
Seq/√Len: 266.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
226_I329_L4.3781.00
400_D405_S3.9121.00
365_L429_I3.5461.00
408_E413_I3.5091.00
406_V413_I3.4441.00
406_V415_K3.3261.00
254_N259_S3.2021.00
296_V305_V3.1441.00
234_S237_T3.1361.00
394_F427_L3.0861.00
233_D237_T2.9831.00
268_E291_N2.9201.00
285_K288_N2.9091.00
364_I417_H2.8931.00
228_A253_L2.8861.00
359_N362_H2.8601.00
254_N287_E2.7861.00
130_K133_T2.6741.00
143_I147_R2.6671.00
252_V290_I2.6481.00
231_S254_N2.6171.00
154_W158_G2.5871.00
364_I426_Y2.5131.00
216_A305_V2.4751.00
318_I329_L2.4551.00
34_I48_A2.3701.00
113_F159_S2.3591.00
226_I326_T2.3411.00
300_V308_K2.2891.00
374_V378_L2.2531.00
162_F166_L2.2241.00
228_A257_K2.2161.00
231_S287_E2.1631.00
47_S143_I2.1531.00
393_W409_A2.1341.00
358_V362_H2.1041.00
231_S261_I2.0891.00
305_V330_V2.0751.00
229_I238_I2.0721.00
417_H428_E2.0671.00
263_F293_V2.0571.00
18_F141_P2.0561.00
390_I427_L2.0531.00
57_E150_F2.0501.00
47_S140_K2.0371.00
318_I326_T2.0281.00
362_H428_E2.0151.00
418_E426_Y1.9831.00
219_I330_V1.9701.00
374_V429_I1.9201.00
37_L136_L1.9041.00
229_I252_V1.8991.00
33_K132_E1.8801.00
219_I302_I1.8591.00
240_K244_T1.8551.00
38_I49_K1.8541.00
137_L141_P1.8051.00
369_V374_V1.8011.00
333_E337_E1.7861.00
42_K136_L1.7761.00
355_I369_V1.7731.00
420_V425_N1.7691.00
16_T70_A1.7671.00
253_L260_I1.7531.00
188_L205_V1.7451.00
233_D238_I1.7301.00
418_E425_N1.6941.00
248_T265_N1.6901.00
357_K363_Y1.6891.00
214_R218_E1.6851.00
50_K143_I1.6811.00
158_G162_F1.6761.00
369_V390_I1.6641.00
316_I329_L1.6391.00
208_I339_I1.6031.00
22_T138_T1.6001.00
415_K428_E1.5821.00
374_V390_I1.5791.00
204_Y208_I1.5651.00
230_S233_D1.5561.00
227_V241_I1.5461.00
298_E327_S1.5401.00
254_N261_I1.5371.00
133_T137_L1.5351.00
232_E254_N1.5271.00
394_F414_F1.5231.00
375_N380_T1.5181.00
365_L390_I1.5131.00
47_S139_A1.4801.00
302_I335_I1.4791.00
364_I428_E1.4781.00
256_D259_S1.4731.00
395_M424_I1.4651.00
284_F288_N1.4481.00
357_K360_D1.4461.00
300_V305_V1.4391.00
358_V364_I1.4381.00
48_A139_A1.4381.00
394_F416_V1.4361.00
16_T66_I1.4321.00
307_V310_Q1.4291.00
150_F154_W1.4251.00
365_L374_V1.4241.00
35_D39_L1.4241.00
147_R150_F1.4141.00
71_L74_G1.4011.00
263_F316_I1.3891.00
227_V247_Y1.3871.00
224_R325_G1.3861.00
82_E86_H1.3821.00
394_F407_I1.3711.00
7_I11_L1.3651.00
49_K53_T1.3611.00
345_D348_D1.3571.00
245_E250_Y1.3571.00
358_V428_E1.3551.00
6_L10_T1.3521.00
414_F427_L1.3521.00
37_L42_K1.3511.00
204_Y339_I1.3501.00
227_V250_Y1.3491.00
249_R315_H1.3471.00
409_A414_F1.3451.00
358_V361_N1.3331.00
21_A134_I1.3301.00
105_V109_V1.3271.00
101_V105_V1.3161.00
308_K312_E1.3121.00
38_I46_I1.3091.00
387_V396_T1.3051.00
61_A145_F1.3031.00
237_T240_K1.2991.00
35_D49_K1.2941.00
41_G45_A1.2891.00
227_V245_E1.2841.00
48_A135_T1.2831.00
138_T141_P1.2741.00
397_Q409_A1.2731.00
223_R258_D1.2671.00
158_G161_R1.2641.00
316_I331_T1.2591.00
394_F398_Q1.2571.00
141_P144_W1.2531.00
417_H426_Y1.2531.00
46_I50_K1.2521.00
258_D325_G1.2471.00
140_K144_W1.2321.00
258_D326_T1.2191.00
336_L340_V1.2181.00
63_Q66_I1.2081.00
44_G136_L1.2071.00
293_V318_I1.1991.00
412_Y429_I1.1941.00
233_D241_I1.1871.00
42_K45_A1.1841.00
355_I377_L1.1811.00
375_N382_L1.1801.00
86_H90_A1.1721.00
15_L69_T1.1721.00
223_R325_G1.1701.00
11_L15_L1.1681.00
371_I375_N1.1641.00
61_A153_I1.1621.00
19_F145_F1.1441.00
43_K46_I1.1411.00
216_A319_L1.1371.00
24_F27_V1.1261.00
260_I318_I1.1221.00
297_I300_V1.1211.00
122_A163_I1.1191.00
398_Q401_A1.1161.00
216_A296_V1.1151.00
126_L169_L1.1081.00
261_I290_I1.1041.00
236_E240_K1.1021.00
217_K298_E1.1001.00
407_I414_F1.0991.00
44_G140_K1.0981.00
19_F65_G1.0691.00
77_G111_A1.0681.00
333_E343_I1.0661.00
343_I348_D1.0611.00
391_G395_M1.0601.00
228_A326_T1.0541.00
162_F165_G1.0501.00
354_N366_D1.0471.00
356_R364_I1.0461.00
264_I289_H1.0441.00
378_L412_Y1.0431.00
408_E411_G1.0341.00
8_I76_V1.0331.00
144_W147_R1.0321.00
398_Q407_I1.0281.00
249_R333_E1.0271.00
230_S255_G1.0221.00
296_V319_L1.0111.00
18_F138_T1.0101.00
9_F111_A1.0091.00
70_A115_H1.0071.00
296_V317_A1.0031.00
192_Y202_L1.0021.00
16_T20_V0.9981.00
66_I70_A0.9961.00
294_I308_K0.9941.00
225_E423_H0.9941.00
13_I114_L0.9931.00
219_I335_I0.9921.00
255_G259_S0.9901.00
179_H187_L0.9891.00
61_A146_Y0.9791.00
34_I49_K0.9791.00
23_E124_K0.9761.00
81_F84_I0.9701.00
21_A127_A0.9671.00
309_M317_A0.9661.00
119_G124_K0.9581.00
393_W414_F0.9561.00
355_I363_Y0.9511.00
184_L191_S0.9501.00
403_V418_E0.9481.00
355_I365_L0.9441.00
191_S195_G0.9431.00
29_I131_A0.9331.00
272_A289_H0.9321.00
165_G170_K0.9291.00
370_L373_D0.9261.00
137_L140_K0.9251.00
51_V58_Y0.9231.00
50_K54_H0.9201.00
36_Q40_E0.9191.00
231_S290_I0.9181.00
54_H57_E0.9141.00
229_I286_L0.9121.00
45_A136_L0.9111.00
300_V304_D0.9091.00
243_K275_D0.9081.00
232_E287_E0.9081.00
366_D426_Y0.9081.00
284_F289_H0.9051.00
397_Q407_I0.9031.00
240_K243_K0.9031.00
230_S253_L0.9021.00
63_Q67_T0.9021.00
20_V24_F0.9021.00
375_N381_T0.9001.00
242_I250_Y0.8931.00
85_L88_L0.8921.00
71_L75_W0.8901.00
344_R351_E0.8861.00
367_S390_I0.8851.00
47_S50_K0.8831.00
151_P155_F0.8821.00
239_V243_K0.8821.00
51_V139_A0.8811.00
297_I322_E0.8801.00
44_G48_A0.8791.00
120_E124_K0.8791.00
74_G77_G0.8781.00
294_I317_A0.8701.00
9_F73_I0.8691.00
146_Y150_F0.8671.00
414_F429_I0.8661.00
226_I257_K0.8631.00
109_V113_F0.8611.00
88_L91_H0.8611.00
29_I34_I0.8561.00
251_P260_I0.8531.00
393_W397_Q0.8501.00
333_E346_E0.8491.00
38_I42_K0.8471.00
22_T142_I0.8461.00
211_F335_I0.8461.00
164_V169_L0.8441.00
391_G423_H0.8441.00
17_A21_A0.8431.00
155_F158_G0.8380.99
337_E342_E0.8370.99
71_L78_E0.8330.99
268_E347_F0.8320.99
34_I52_I0.8300.99
211_F306_L0.8290.99
235_Y284_F0.8260.99
161_R165_G0.8240.99
33_K37_L0.8200.99
315_H336_L0.8200.99
211_F303_H0.8190.99
321_D324_G0.8190.99
337_E345_D0.8170.99
333_E338_E0.8160.99
248_T267_K0.8150.99
305_V335_I0.8130.99
24_F127_A0.8130.99
333_E348_D0.8120.99
8_I11_L0.8120.99
333_E345_D0.8110.99
71_L112_T0.8100.99
75_W108_F0.8090.99
235_Y238_I0.8040.99
272_A277_D0.8030.99
382_L393_W0.8000.99
367_S391_G0.7970.99
12_L72_G0.7960.99
321_D327_S0.7960.99
70_A74_G0.7940.99
84_I87_P0.7940.99
253_L256_D0.7940.99
424_I427_L0.7900.99
223_R321_D0.7890.99
321_D325_G0.7860.99
170_K174_E0.7850.99
16_T115_H0.7800.99
56_D161_R0.7780.99
294_I312_E0.7780.99
103_I107_A0.7770.99
251_P318_I0.7770.99
241_I244_T0.7760.99
229_I250_Y0.7720.99
295_H320_V0.7650.99
333_E342_E0.7630.99
216_A330_V0.7630.99
229_I241_I0.7600.99
55_L58_Y0.7560.99
274_I277_D0.7530.99
64_L152_F0.7510.99
73_I111_A0.7510.99
44_G139_A0.7510.99
14_V17_A0.7490.99
287_E290_I0.7430.99
225_E368_K0.7430.99
371_I387_V0.7400.99
260_I326_T0.7390.99
320_V326_T0.7380.99
140_K143_I0.7370.99
383_A387_V0.7370.99
185_R210_E0.7340.99
231_S238_I0.7320.99
202_L206_N0.7300.99
243_K271_S0.7290.99
265_N268_E0.7280.99
18_F65_G0.7260.99
242_I266_A0.7250.99
66_I115_H0.7250.99
366_D369_V0.7230.98
67_T112_T0.7220.98
293_V316_I0.7220.98
31_S53_T0.7210.98
85_L89_F0.7200.98
181_E213_E0.7200.98
425_N428_E0.7180.98
387_V393_W0.7170.98
249_R265_N0.7170.98
242_I269_F0.7160.98
403_V419_T0.7100.98
215_I218_E0.7090.98
214_R338_E0.7080.98
51_V55_L0.7080.98
72_G76_V0.7080.98
102_L106_I0.7050.98
398_Q405_S0.7030.98
356_R426_Y0.7020.98
207_N339_I0.7020.98
21_A25_A0.7010.98
82_E100_H0.6990.98
338_E342_E0.6990.98
358_V418_E0.6980.98
380_T412_Y0.6980.98
308_K311_K0.6970.98
397_Q410_D0.6960.98
135_T139_A0.6950.98
37_L45_A0.6940.98
69_T73_I0.6940.98
367_S424_I0.6930.98
181_E185_R0.6920.98
374_V377_L0.6920.98
322_E392_G0.6900.98
332_A343_I0.6850.98
75_W116_V0.6830.98
391_G424_I0.6820.98
251_P263_F0.6770.98
381_T410_D0.6740.98
217_K327_S0.6740.98
66_I120_E0.6730.98
62_C66_I0.6720.98
33_K36_Q0.6700.98
261_I287_E0.6690.97
216_A300_V0.6670.97
148_I151_P0.6660.97
184_L197_I0.6660.97
357_K361_N0.6650.97
386_E396_T0.6640.97
37_L40_E0.6620.97
315_H333_E0.6620.97
189_S206_N0.6610.97
221_I344_R0.6610.97
167_F170_K0.6600.97
29_I132_E0.6600.97
20_V120_E0.6590.97
134_I138_T0.6560.97
223_R323_Y0.6560.97
73_I115_H0.6540.97
238_I286_L0.6540.97
8_I12_L0.6540.97
352_V356_R0.6540.97
229_I233_D0.6530.97
15_L19_F0.6520.97
227_V244_T0.6520.97
181_E212_D0.6520.97
265_N291_N0.6510.97
337_E348_D0.6500.97
272_A275_D0.6500.97
272_A276_T0.6490.97
204_Y211_F0.6460.97
229_I242_I0.6460.97
121_L156_L0.6450.97
66_I69_T0.6440.97
20_V115_H0.6400.97
10_T14_V0.6390.97
371_I382_L0.6390.97
23_E120_E0.6380.97
86_H103_I0.6380.97
355_I374_V0.6380.97
249_R346_E0.6380.97
181_E209_F0.6370.97
402_A405_S0.6370.97
354_N369_V0.6360.97
66_I121_L0.6360.97
236_E283_D0.6350.97
236_E282_E0.6340.97
71_L108_F0.6340.97
70_A76_V0.6290.96
249_R316_I0.6270.96
282_E285_K0.6260.96
306_L335_I0.6240.96
13_I119_G0.6240.96
185_R206_N0.6240.96
377_L380_T0.6230.96
337_E341_G0.6230.96
13_I16_T0.6230.96
237_T241_I0.6220.96
375_N385_D0.6210.96
62_C142_I0.6210.96
59_L63_Q0.6210.96
82_E103_I0.6200.96
223_R324_G0.6200.96
157_N161_R0.6190.96
25_A135_T0.6150.96
64_L71_L0.6150.96
306_L340_V0.6130.96
28_K128_I0.6130.96
16_T63_Q0.6120.96
56_D125_T0.6110.96
152_F156_L0.6100.96
44_G137_L0.6090.96
85_L103_I0.6090.96
118_V163_I0.6080.96
238_I242_I0.6070.96
86_H100_H0.6070.96
145_F149_L0.6070.96
16_T67_T0.6060.96
357_K362_H0.6060.96
212_D303_H0.6060.96
51_V146_Y0.6050.95
78_E83_V0.6010.95
164_V168_G0.5970.95
131_A134_I0.5970.95
294_I314_T0.5960.95
126_L134_I0.5950.95
419_T422_R0.5950.95
35_D38_I0.5940.95
54_H146_Y0.5930.95
180_S184_L0.5910.95
76_V80_T0.5910.95
76_V79_S0.5900.95
33_K45_A0.5900.95
5_N9_F0.5890.95
305_V309_M0.5890.95
62_C108_F0.5890.95
16_T69_T0.5880.95
82_E85_L0.5880.95
307_V311_K0.5870.95
61_A64_L0.5870.95
74_G79_S0.5840.95
59_L119_G0.5830.94
63_Q70_A0.5820.94
295_H318_I0.5820.94
210_E213_E0.5820.94
211_F301_P0.5800.94
29_I48_A0.5790.94
355_I359_N0.5770.94
365_L378_L0.5770.94
133_T136_L0.5760.94
413_I417_H0.5740.94
13_I73_I0.5740.94
27_V128_I0.5740.94
394_F401_A0.5720.94
205_V209_F0.5720.94
34_I45_A0.5710.94
67_T115_H0.5700.94
260_I295_H0.5690.94
69_T112_T0.5690.94
29_I136_L0.5680.94
64_L67_T0.5670.94
240_K275_D0.5670.94
48_A52_I0.5660.94
230_S259_S0.5650.94
20_V66_I0.5650.94
211_F339_I0.5650.94
58_Y64_L0.5640.93
50_K147_R0.5640.93
401_A405_S0.5640.93
306_L309_M0.5630.93
288_N292_P0.5630.93
263_F290_I0.5620.93
79_S83_V0.5620.93
253_L257_K0.5620.93
337_E343_I0.5610.93
20_V70_A0.5610.93
67_T108_F0.5600.93
203_K207_N0.5580.93
185_R205_V0.5580.93
65_G77_G0.5580.93
42_K46_I0.5580.93
25_A134_I0.5570.93
20_V63_Q0.5570.93
375_N384_S0.5560.93
89_F103_I0.5550.93
276_T282_E0.5540.93
257_K326_T0.5530.93
194_S197_I0.5530.93
50_K53_T0.5520.93
223_R322_E0.5520.93
70_A73_I0.5520.93
315_H332_A0.5510.93
398_Q406_V0.5500.93
383_A397_Q0.5490.93
253_L259_S0.5480.92
371_I374_V0.5480.92
46_I49_K0.5460.92
79_S82_E0.5440.92
265_N315_H0.5430.92
37_L41_G0.5410.92
44_G47_S0.5400.92
343_I346_E0.5390.92
217_K388_D0.5390.92
78_E82_E0.5380.92
12_L17_A0.5350.92
163_I167_F0.5350.92
393_W407_I0.5340.92
216_A301_P0.5320.91
104_L108_F0.5320.91
395_M405_S0.5320.91
180_S183_E0.5310.91
70_A75_W0.5310.91
89_F102_L0.5300.91
80_T107_A0.5300.91
70_A121_L0.5300.91
333_E340_V0.5290.91
419_T424_I0.5280.91
59_L62_C0.5280.91
60_S69_T0.5280.91
304_D307_V0.5270.91
63_Q115_H0.5270.91
363_Y378_L0.5270.91
30_R183_E0.5270.91
306_L332_A0.5270.91
371_I390_I0.5260.91
191_S196_E0.5250.91
60_S67_T0.5250.91
344_R350_D0.5250.91
315_H343_I0.5250.91
393_W410_D0.5250.91
125_T128_I0.5230.91
363_Y377_L0.5230.91
129_Q169_L0.5220.91
248_T345_D0.5220.91
365_L377_L0.5220.91
332_A340_V0.5210.91
262_G290_I0.5210.91
238_I285_K0.5200.90
21_A138_T0.5190.90
116_V120_E0.5190.90
378_L429_I0.5190.90
78_E100_H0.5180.90
322_E325_G0.5170.90
66_I119_G0.5170.90
298_E324_G0.5170.90
67_T120_E0.5150.90
32_S186_I0.5140.90
372_E376_D0.5140.90
57_E146_Y0.5130.90
218_E395_M0.5130.90
249_R263_F0.5120.90
83_V87_P0.5120.90
87_P103_I0.5110.90
241_I245_E0.5110.90
65_G74_G0.5110.90
75_W104_L0.5090.89
297_I320_V0.5090.89
301_P304_D0.5090.89
17_A119_G0.5080.89
26_I135_T0.5050.89
373_D377_L0.5050.89
144_W148_I0.5040.89
219_I338_E0.5040.89
252_V262_G0.5040.89
223_R327_S0.5040.89
218_E388_D0.5030.89
220_M328_G0.5030.89
272_A284_F0.5030.89
48_A51_V0.5020.89
290_I293_V0.5020.89
242_I270_L0.5010.89
223_R226_I0.5000.89
71_L107_A0.5000.89
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  
4hg0A 2 0.5323 100 0.5 Contact Map
3lhhA 1 0.288 100 0.762 Contact Map
3ocoA 2 0.3111 99.9 0.778 Contact Map
3oi8A 2 0.3594 99.9 0.779 Contact Map
3ocmA 5 0.3433 99.9 0.786 Contact Map
2v8qE 1 0.5138 99.9 0.788 Contact Map
3kxrA 3 0.371 99.9 0.788 Contact Map
3lv9A 2 0.2995 99.9 0.794 Contact Map
4iysA 2 0.3272 99.9 0.801 Contact Map
3t4nC 1 0.5276 99.9 0.807 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 0.0121 seconds.