GREMLIN Database
MURF - UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
UniProt: P96613 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 457 (395)
Sequences: 17941 (13180)
Seq/√Len: 663.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
186_V291_A3.4631.00
253_D264_T2.7021.00
241_Y287_A2.7001.00
412_S423_A2.6871.00
387_R412_S2.6311.00
130_T308_G2.5581.00
357_L385_I2.5461.00
107_R183_D2.5451.00
414_Y423_A2.5391.00
298_A301_D2.5221.00
289_I302_A2.4881.00
423_A427_N2.4201.00
184_A291_A2.4041.00
186_V287_A2.3901.00
318_L326_S2.3841.00
416_E419_D2.3671.00
200_S203_G2.3581.00
387_R427_N2.3471.00
252_Q266_K2.3291.00
127_V288_A2.2541.00
59_Q63_A2.2381.00
127_V292_G2.2241.00
264_T271_T2.1971.00
273_F307_S2.1871.00
130_T305_G2.1821.00
220_V294_Y2.1781.00
249_Y290_A2.1411.00
225_G247_N2.1381.00
205_A232_N2.1241.00
340_K344_Q2.1001.00
354_K432_D2.0061.00
423_A426_E1.9861.00
85_L88_D1.9761.00
274_I285_A1.9751.00
130_T304_K1.9701.00
199_G203_G1.9671.00
396_A400_E1.9441.00
389_F427_N1.9331.00
44_I69_L1.8991.00
133_R159_E1.8811.00
131_Q301_D1.8791.00
183_D219_G1.8571.00
428_A434_I1.8501.00
61_F81_H1.8211.00
110_G182_P1.8201.00
126_A308_G1.8071.00
440_R445_E1.7931.00
212_I221_L1.7931.00
109_I295_F1.7741.00
110_G165_M1.7651.00
356_M427_N1.7511.00
59_Q62_E1.7501.00
124_I288_A1.7351.00
125_H137_T1.7231.00
124_I291_A1.7131.00
262_H271_T1.7121.00
356_M387_R1.6981.00
251_L286_M1.6881.00
267_G270_N1.6721.00
397_F400_E1.6721.00
285_A306_L1.6711.00
354_K387_R1.6581.00
293_A299_P1.6481.00
191_G337_T1.6421.00
389_F423_A1.6321.00
124_I292_G1.6321.00
399_A413_H1.6311.00
125_H129_G1.6251.00
251_L254_V1.6211.00
318_L328_I1.6181.00
58_E62_E1.6151.00
131_Q297_I1.5941.00
203_G206_E1.5841.00
205_A229_L1.5771.00
321_T326_S1.5761.00
263_F285_A1.5741.00
111_V124_I1.5641.00
262_H273_F1.5601.00
250_Q266_K1.5571.00
207_A210_E1.5421.00
279_K344_Q1.5401.00
185_A211_I1.5391.00
243_T279_K1.5381.00
107_R160_I1.5371.00
340_K379_V1.5261.00
249_Y293_A1.5121.00
108_V180_A1.4911.00
184_A295_F1.4891.00
119_T281_N1.4821.00
225_G240_T1.4811.00
47_K71_D1.4721.00
374_K401_G1.4701.00
267_G293_A1.4691.00
167_M198_L1.4691.00
303_A307_S1.4651.00
115_N335_S1.4631.00
390_T399_A1.4631.00
185_A215_L1.4451.00
220_V237_Q1.4441.00
396_A413_H1.4391.00
341_A344_Q1.4271.00
414_Y419_D1.4201.00
344_Q379_V1.4201.00
292_G302_A1.4191.00
394_L397_F1.4031.00
126_A305_G1.3971.00
358_V391_Y1.3881.00
417_K446_E1.3881.00
171_G207_A1.3881.00
128_L162_V1.3881.00
275_P310_K1.3851.00
160_I295_F1.3831.00
109_I124_I1.3821.00
327_I425_K1.3741.00
142_N146_G1.3711.00
220_V239_K1.3691.00
369_E394_L1.3681.00
378_A383_D1.3631.00
184_A294_Y1.3461.00
111_V121_K1.3461.00
85_L89_T1.3441.00
301_D304_K1.3381.00
73_S85_L1.3321.00
344_Q384_K1.3311.00
304_K308_G1.3301.00
325_L428_A1.3291.00
128_L295_F1.3271.00
399_A403_L1.3151.00
51_F55_S1.3111.00
356_M389_F1.3011.00
120_T188_T1.2991.00
215_L219_G1.2951.00
71_D89_T1.2911.00
240_T248_D1.2901.00
171_G197_D1.2891.00
123_M276_I1.2851.00
255_S262_H1.2831.00
279_K348_S1.2801.00
389_F420_L1.2721.00
123_M309_L1.2631.00
95_Q98_K1.2601.00
265_I289_I1.2591.00
184_A222_I1.2591.00
292_G297_I1.2591.00
223_Y238_T1.2571.00
419_D422_Q1.2501.00
118_T312_T1.2291.00
222_I294_Y1.2281.00
190_I205_A1.2221.00
354_K429_S1.2141.00
223_Y240_T1.2121.00
368_L371_T1.2061.00
391_Y420_L1.2041.00
387_R410_R1.2041.00
263_F282_V1.2021.00
304_K307_S1.1981.00
224_I283_M1.1971.00
99_A103_E1.1951.00
151_V155_P1.1911.00
187_I190_I1.1881.00
181_N219_G1.1881.00
91_T95_Q1.1861.00
324_G430_K1.1821.00
114_S193_S1.1771.00
124_I186_V1.1771.00
318_L321_T1.1741.00
422_Q426_E1.1701.00
202_E206_E1.1621.00
209_L233_A1.1601.00
223_Y230_L1.1531.00
260_G273_F1.1531.00
354_K386_D1.1471.00
107_R159_E1.1471.00
252_Q264_T1.1461.00
316_L328_I1.1401.00
377_G402_A1.1331.00
192_E371_T1.1331.00
237_Q294_Y1.1271.00
281_N284_N1.1271.00
192_E195_M1.1241.00
123_M285_A1.1161.00
251_L282_V1.1121.00
134_V159_E1.1111.00
210_E213_N1.1091.00
128_L297_I1.1081.00
249_Y267_G1.1061.00
339_M437_K1.1041.00
313_G317_E1.0931.00
356_M432_D1.0901.00
239_K290_A1.0901.00
47_K72_R1.0891.00
316_L346_T1.0881.00
128_L160_I1.0871.00
300_E304_K1.0851.00
175_L178_R1.0831.00
226_D283_M1.0811.00
418_K422_Q1.0811.00
57_V68_V1.0801.00
438_A444_L1.0751.00
346_T355_K1.0741.00
165_M177_S1.0731.00
372_F375_E1.0651.00
229_L232_N1.0631.00
222_I290_A1.0591.00
183_D216_K1.0571.00
390_T413_H1.0551.00
388_V402_A1.0471.00
53_G57_V1.0421.00
279_K283_M1.0361.00
429_S432_D1.0331.00
225_G231_Q1.0331.00
151_V154_M1.0331.00
375_E378_A1.0321.00
317_E329_N1.0311.00
239_K294_Y1.0241.00
202_E229_L1.0231.00
206_E210_E1.0191.00
187_I212_I1.0181.00
396_A415_T1.0131.00
342_A435_L1.0071.00
397_F401_G1.0021.00
187_I233_A1.0001.00
400_E404_K0.9971.00
334_A339_M0.9961.00
192_E201_R0.9951.00
389_F414_Y0.9941.00
205_A209_L0.9911.00
108_V161_A0.9871.00
127_V305_G0.9871.00
127_V302_A0.9861.00
243_T283_M0.9851.00
419_D423_A0.9761.00
350_E355_K0.9731.00
392_G415_T0.9721.00
340_K383_D0.9701.00
61_F68_V0.9681.00
272_F303_A0.9621.00
115_N337_T0.9611.00
201_R229_L0.9601.00
257_S262_H0.9601.00
94_Q98_K0.9581.00
109_I291_A0.9561.00
297_I301_D0.9531.00
89_T92_A0.9511.00
57_V61_F0.9471.00
188_T287_A0.9451.00
377_G381_S0.9401.00
395_G413_H0.9391.00
126_A129_G0.9391.00
339_M359_L0.9351.00
370_E397_F0.9301.00
43_F66_A0.9241.00
133_R160_I0.9241.00
244_G279_K0.9211.00
263_F272_F0.9201.00
412_S427_N0.9201.00
291_A295_F0.9191.00
131_Q305_G0.9171.00
321_T325_L0.9131.00
367_D393_K0.9081.00
215_L221_L0.9011.00
227_E283_M0.9001.00
184_A220_V0.8981.00
112_T208_K0.8901.00
403_L411_V0.8891.00
350_E353_G0.8891.00
389_F424_V0.8881.00
126_A309_L0.8861.00
203_G207_A0.8811.00
100_Y104_L0.8801.00
328_I346_T0.8791.00
193_S335_S0.8781.00
91_T175_L0.8751.00
224_I227_E0.8721.00
101_L104_L0.8661.00
374_K378_A0.8651.00
107_R295_F0.8641.00
48_G53_G0.8631.00
45_P70_W0.8591.00
98_K102_Q0.8551.00
401_G404_K0.8541.00
125_H136_K0.8541.00
357_L437_K0.8511.00
92_A96_L0.8511.00
242_G283_M0.8501.00
153_A156_E0.8501.00
325_L431_G0.8501.00
74_V77_P0.8491.00
299_P303_A0.8491.00
44_I89_T0.8481.00
400_E403_L0.8481.00
424_V428_A0.8471.00
395_G398_I0.8461.00
84_I87_D0.8441.00
79_E82_A0.8431.00
210_E214_G0.8431.00
316_L345_L0.8411.00
293_A302_A0.8391.00
125_H135_H0.8361.00
181_N216_K0.8341.00
289_I293_A0.8341.00
350_E433_L0.8331.00
209_L213_N0.8331.00
372_F376_C0.8321.00
243_T251_L0.8311.00
168_S197_D0.8271.00
51_F56_F0.8261.00
152_L156_E0.8261.00
415_T419_D0.8191.00
150_T153_A0.8161.00
247_N250_Q0.8161.00
337_T341_A0.8141.00
60_A65_V0.8131.00
131_Q298_A0.8111.00
120_T287_A0.8091.00
126_A130_T0.8091.00
130_T301_D0.8081.00
370_E374_K0.8061.00
371_T375_E0.7991.00
122_D312_T0.7981.00
399_A411_V0.7961.00
228_P232_N0.7951.00
379_V383_D0.7891.00
226_D242_G0.7871.00
120_T288_A0.7871.00
377_G401_G0.7801.00
280_H341_A0.7791.00
90_L94_Q0.7781.00
147_L150_T0.7781.00
396_A399_A0.7771.00
94_Q175_L0.7771.00
133_R157_N0.7751.00
44_I93_L0.7751.00
353_G432_D0.7731.00
170_K207_A0.7721.00
225_G230_L0.7721.00
80_N83_V0.7701.00
152_L155_P0.7691.00
170_K203_G0.7661.00
389_F412_S0.7661.00
326_S433_L0.7651.00
110_G211_I0.7631.00
202_E205_A0.7611.00
420_L424_V0.7611.00
314_M329_N0.7591.00
333_N437_K0.7591.00
414_Y420_L0.7521.00
52_D72_R0.7501.00
402_A406_F0.7461.00
347_E384_K0.7451.00
54_H57_V0.7431.00
167_M207_A0.7411.00
142_N145_I0.7411.00
343_I357_L0.7391.00
240_T247_N0.7351.00
125_H162_V0.7331.00
257_S260_G0.7281.00
92_A97_A0.7281.00
421_L425_K0.7271.00
242_G245_T0.7251.00
155_P158_T0.7211.00
276_I309_L0.7211.00
289_I299_P0.7201.00
256_Q261_T0.7161.00
191_G201_R0.7161.00
265_I286_M0.7131.00
356_M428_A0.7091.00
201_R205_A0.7091.00
443_K446_E0.7081.00
171_G203_G0.7081.00
52_D55_S0.7061.00
190_I201_R0.7051.00
358_V424_V0.7051.00
224_I241_Y0.7031.00
302_A305_G0.7031.00
131_Q292_G0.7021.00
327_I434_I0.7001.00
353_G433_L0.6991.00
92_A95_Q0.6971.00
84_I88_D0.6951.00
321_T324_G0.6941.00
328_I433_L0.6931.00
170_K206_E0.6931.00
94_Q179_L0.6931.00
205_A233_A0.6931.00
390_T402_A0.6921.00
70_W83_V0.6911.00
222_I291_A0.6901.00
239_K249_Y0.6891.00
147_L155_P0.6841.00
255_S271_T0.6831.00
165_M182_P0.6821.00
261_T282_V0.6811.00
57_V69_L0.6811.00
246_H250_Q0.6811.00
230_L233_A0.6801.00
324_G431_G0.6791.00
192_E337_T0.6761.00
54_H71_D0.6731.00
231_Q240_T0.6721.00
198_L207_A0.6711.00
68_V81_H0.6701.00
221_L236_C0.6691.00
360_G438_A0.6681.00
98_K103_E0.6631.00
45_P57_V0.6621.00
46_L90_L0.6611.00
358_V434_I0.6581.00
401_G405_H0.6581.00
83_V87_D0.6581.00
206_E209_L0.6541.00
53_G61_F0.6541.00
336_P375_E0.6541.00
121_K137_T0.6521.00
108_V163_L0.6491.00
78_P87_D0.6491.00
177_S180_A0.6481.00
323_S430_K0.6471.00
118_T140_N0.6461.00
82_A85_L0.6451.00
234_Y238_T0.6451.00
201_R204_I0.6441.00
299_P302_A0.6431.00
278_G281_N0.6421.00
378_A405_H0.6411.00
395_G402_A0.6411.00
115_N338_S0.6411.00
49_E69_L0.6411.00
88_D91_T0.6401.00
342_A437_K0.6371.00
53_G56_F0.6371.00
98_K181_N0.6341.00
52_D56_F0.6331.00
253_D256_Q0.6331.00
391_Y417_K0.6321.00
154_M158_T0.6291.00
195_M199_G0.6291.00
369_E372_F0.6281.00
202_E232_N0.6241.00
390_T411_V0.6241.00
385_I388_V0.6231.00
276_I281_N0.6211.00
55_S72_R0.6211.00
300_E303_A0.6191.00
253_D271_T0.6181.00
147_L156_E0.6181.00
297_I302_A0.6161.00
356_M424_V0.6161.00
121_K162_V0.6161.00
134_V158_T0.6151.00
361_D442_M0.6141.00
344_Q348_S0.6141.00
335_S338_S0.6141.00
368_L373_H0.6131.00
256_Q279_K0.6121.00
102_Q181_N0.6111.00
188_T241_Y0.6111.00
257_S273_F0.6101.00
340_K375_E0.6091.00
358_V420_L0.6071.00
417_K421_L0.6071.00
124_I162_V0.6051.00
394_L398_I0.6051.00
60_A64_G0.6051.00
359_L390_T0.6041.00
358_V436_F0.6041.00
320_K326_S0.6031.00
58_E61_F0.6031.00
61_F66_A0.6021.00
109_I128_L0.6011.00
347_E350_E0.6001.00
94_Q97_A0.5991.00
222_I239_K0.5981.00
391_Y414_Y0.5981.00
279_K282_V0.5971.00
225_G242_G0.5971.00
187_I205_A0.5971.00
105_G154_M0.5971.00
127_V131_Q0.5971.00
151_V156_E0.5961.00
370_E401_G0.5951.00
333_N342_A0.5941.00
417_K447_I0.5921.00
122_D126_A0.5921.00
386_D429_S0.5911.00
343_I383_D0.5891.00
82_A86_V0.5871.00
286_M290_A0.5851.00
119_T123_M0.5851.00
242_G250_Q0.5831.00
248_D268_I0.5831.00
267_G299_P0.5821.00
111_V186_V0.5811.00
355_K386_D0.5801.00
217_E235_S0.5801.00
403_L413_H0.5791.00
143_N146_G0.5791.00
339_M376_C0.5791.00
263_F266_K0.5781.00
374_K404_K0.5781.00
380_I388_V0.5781.00
169_A197_D0.5771.00
98_K179_L0.5761.00
357_L388_V0.5761.00
171_G210_E0.5761.00
128_L292_G0.5751.00
282_V286_M0.5751.00
70_W74_V0.5751.00
192_E375_E0.5741.00
91_T97_A0.5731.00
378_A381_S0.5721.00
177_S214_G0.5721.00
115_N191_G0.5711.00
359_L402_A0.5711.00
392_G395_G0.5711.00
266_K269_E0.5691.00
346_T435_L0.5681.00
252_Q256_Q0.5681.00
344_Q383_D0.5681.00
165_M180_A0.5671.00
99_A102_Q0.5661.00
243_T286_M0.5651.00
261_T264_T0.5621.00
254_V282_V0.5621.00
122_D313_G0.5581.00
72_R75_P0.5571.00
45_P68_V0.5561.00
391_Y446_E0.5541.00
289_I306_L0.5511.00
289_I303_A0.5511.00
136_K158_T0.5501.00
138_G153_A0.5501.00
141_F144_H0.5501.00
147_L153_A0.5491.00
91_T94_Q0.5491.00
375_E379_V0.5471.00
242_G247_N0.5451.00
154_M161_A0.5451.00
347_E355_K0.5441.00
45_P54_H0.5441.00
78_P81_H0.5431.00
65_V69_L0.5431.00
391_Y442_M0.5421.00
183_D218_D0.5421.00
243_T254_V0.5401.00
92_A98_K0.5381.00
357_L380_I0.5381.00
129_G134_V0.5381.00
176_L179_L0.5371.00
274_I306_L0.5371.00
343_I380_I0.5371.00
272_F285_A0.5361.00
109_I160_I0.5351.00
373_H377_G0.5341.00
422_Q425_K0.5341.00
395_G399_A0.5331.00
418_K446_E0.5331.00
314_M440_R0.5311.00
96_L99_A0.5301.00
301_D305_G0.5291.00
322_D425_K0.5291.00
424_V434_I0.5280.99
79_E84_I0.5250.99
181_N214_G0.5240.99
135_H154_M0.5230.99
377_G398_I0.5210.99
339_M379_V0.5210.99
368_L372_F0.5200.99
387_R423_A0.5200.99
291_A294_Y0.5200.99
290_A294_Y0.5190.99
54_H89_T0.5190.99
111_V120_T0.5190.99
390_T395_G0.5180.99
106_T161_A0.5180.99
147_L151_V0.5170.99
373_H401_G0.5160.99
398_I402_A0.5160.99
377_G405_H0.5140.99
322_D325_L0.5130.99
135_H162_V0.5090.99
90_L96_L0.5080.99
135_H158_T0.5050.99
287_A291_A0.5050.99
234_Y237_Q0.5040.99
168_S196_Q0.5020.99
175_L179_L0.5010.99
57_V71_D0.5010.99
325_L429_S0.5010.99
261_T267_G0.5000.99
352_Y431_G0.5000.99
316_L342_A0.5000.99
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  
3zm6A 1 0.9716 100 0.161 Contact Map
4qdiA 1 0.965 100 0.165 Contact Map
4cvkA 1 0.93 100 0.166 Contact Map
1gg4A 1 0.9409 100 0.174 Contact Map
3zl8A 1 0.9147 100 0.205 Contact Map
4c12A 2 0.9694 100 0.208 Contact Map
4bubA 1 0.9562 100 0.22 Contact Map
2wtzA 1 0.9781 100 0.221 Contact Map
1e8cA 1 0.965 100 0.258 Contact Map
2x5oA 1 0.8512 100 0.354 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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