GREMLIN Database
MURF - UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
UniProt: P11880 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10622
Length: 452 (380)
Sequences: 18166 (13237)
Seq/√Len: 679.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
180_L292_L3.5711.00
239_F288_A2.9271.00
252_N263_T2.7081.00
80_V83_T2.6161.00
124_Q309_N2.5271.00
299_T302_A2.5221.00
101_R177_E2.5051.00
407_F416_R2.4891.00
290_A303_I2.4861.00
180_L288_A2.4531.00
178_A292_L2.4371.00
416_R420_L2.4201.00
194_S197_G2.3901.00
409_D412_A2.3751.00
251_T265_Q2.3741.00
319_P327_L2.3281.00
274_L308_A2.2911.00
386_R420_L2.2301.00
219_A246_S2.2181.00
121_I289_A2.2151.00
263_T272_D2.1931.00
56_Q60_G2.1901.00
248_F291_A2.1811.00
356_L384_I2.1771.00
121_I293_S2.1681.00
199_A226_N2.1451.00
214_I295_S2.1391.00
124_Q306_G2.1371.00
80_V84_R2.1331.00
275_L286_A2.1231.00
58_K75_L2.1071.00
341_T345_Q1.9911.00
193_G197_G1.9421.00
124_Q305_A1.9421.00
41_V66_L1.9351.00
261_E272_D1.9181.00
206_F215_A1.9061.00
421_I429_I1.9051.00
125_C302_A1.8851.00
177_E213_G1.8641.00
104_A176_P1.8551.00
127_N153_D1.8501.00
416_R419_L1.8471.00
120_A309_N1.8251.00
353_Y427_I1.8201.00
388_L420_L1.8161.00
203_G230_V1.8141.00
56_Q59_A1.8061.00
104_A159_L1.7751.00
118_T289_A1.7751.00
263_T270_S1.7691.00
262_F286_A1.7611.00
185_A338_G1.7431.00
103_V296_V1.7231.00
118_T292_L1.6791.00
388_L416_R1.6721.00
286_A307_L1.6561.00
197_G200_K1.6521.00
119_A123_S1.6401.00
265_Q270_S1.6331.00
119_A131_T1.6321.00
250_A287_L1.6301.00
118_T293_S1.6261.00
241_P280_R1.6261.00
201_A204_E1.6251.00
319_P329_L1.6231.00
249_T265_Q1.6221.00
378_A382_A1.6191.00
199_A223_D1.6131.00
55_D59_A1.6081.00
261_E274_L1.6041.00
250_A253_I1.6021.00
367_E396_A1.5911.00
280_R345_Q1.5851.00
294_M300_L1.5811.00
161_A192_F1.5801.00
407_F412_A1.5441.00
109_S336_N1.5431.00
178_A296_V1.5421.00
266_T294_M1.5401.00
179_A205_I1.5401.00
102_V174_T1.5321.00
105_L118_T1.5271.00
113_S282_N1.5231.00
125_C298_A1.5211.00
219_A238_R1.5101.00
101_R154_Y1.5071.00
293_S303_I1.4731.00
304_K308_A1.4711.00
44_K68_S1.4461.00
354_R359_G1.4391.00
48_F52_D1.4391.00
214_I237_W1.4341.00
322_L327_L1.4311.00
120_A306_G1.4281.00
342_A345_Q1.4251.00
355_V420_L1.4141.00
248_F294_M1.4131.00
103_V118_T1.4131.00
105_L115_K1.4121.00
154_Y296_V1.4111.00
368_S393_Q1.4061.00
262_F283_I1.4051.00
216_I295_S1.3951.00
217_M236_V1.3901.00
266_T269_G1.3881.00
357_V390_V1.3801.00
276_P311_K1.3751.00
328_L418_K1.3611.00
326_Q421_I1.3591.00
280_R349_E1.3561.00
254_H261_E1.3551.00
214_I235_K1.3501.00
367_E370_A1.3491.00
122_L156_V1.3291.00
390_V413_L1.3251.00
345_Q378_A1.3211.00
114_V182_N1.3201.00
345_Q383_G1.3161.00
122_L296_V1.3151.00
112_T313_V1.3041.00
251_T263_T1.3001.00
305_A309_N1.2981.00
217_M238_R1.2871.00
302_A305_A1.2841.00
117_M310_L1.2841.00
355_V386_R1.2761.00
271_V304_K1.2731.00
117_M277_L1.2731.00
293_S298_A1.2711.00
264_L290_A1.2711.00
184_L199_A1.2681.00
178_A295_S1.2641.00
108_S187_A1.2621.00
217_M224_W1.2521.00
412_A415_T1.2481.00
95_R98_V1.2451.00
203_G227_W1.2331.00
389_S398_S1.2321.00
68_S83_T1.2301.00
200_K230_V1.2241.00
101_R153_D1.2191.00
175_R213_G1.2161.00
218_N284_A1.2151.00
235_K295_S1.2131.00
178_A216_I1.2091.00
186_A189_L1.2081.00
85_L89_E1.2081.00
388_L413_L1.2041.00
196_A200_K1.2011.00
122_L154_Y1.1851.00
181_V184_L1.1741.00
128_T153_D1.1711.00
317_L347_L1.1691.00
395_H399_T1.1611.00
305_A308_A1.1611.00
186_A371_C1.1591.00
54_A65_L1.1501.00
319_P322_L1.1441.00
282_N285_N1.1371.00
238_R247_D1.1371.00
259_G274_L1.1331.00
340_M432_K1.1311.00
317_L329_L1.1311.00
314_P318_F1.1291.00
389_S406_H1.1251.00
415_T419_L1.1231.00
251_T270_S1.1211.00
79_I82_D1.1201.00
248_F266_T1.1171.00
353_Y422_A1.1121.00
373_V377_E1.1121.00
237_W291_A1.1041.00
394_S397_I1.1021.00
341_T378_A1.1001.00
355_V388_L1.0961.00
177_E210_P1.0951.00
118_T180_L1.0851.00
159_L171_V1.0831.00
204_E207_S1.0771.00
369_E373_V1.0751.00
142_P145_L1.0741.00
262_F273_V1.0721.00
280_R284_A1.0681.00
301_D305_A1.0661.00
217_M228_Q1.0641.00
237_W295_S1.0641.00
223_D226_N1.0611.00
103_V292_L1.0581.00
242_N280_R1.0561.00
169_W201_A1.0551.00
186_A195_L1.0551.00
70_P79_I1.0521.00
99_P148_L1.0511.00
226_N229_S1.0441.00
371_C374_Q1.0431.00
391_G408_A1.0391.00
109_S338_G1.0351.00
106_T202_K1.0331.00
318_F330_D1.0311.00
325_N423_E1.0291.00
216_I291_A1.0281.00
200_K204_E1.0281.00
219_A225_L1.0281.00
89_E93_W1.0231.00
343_A430_L1.0191.00
354_R360_D1.0171.00
196_A223_D1.0091.00
335_A340_M1.0071.00
89_E92_A1.0051.00
169_W172_S1.0011.00
117_M286_A1.0001.00
142_P146_L0.9981.00
411_T415_T0.9951.00
182_N288_A0.9951.00
181_V206_F0.9941.00
298_A302_A0.9911.00
220_D284_A0.9841.00
195_L223_D0.9841.00
256_T261_E0.9821.00
388_L407_F0.9791.00
240_S284_A0.9781.00
90_L94_V0.9681.00
322_L326_Q0.9661.00
125_C306_G0.9651.00
241_P284_A0.9641.00
356_L359_G0.9641.00
353_Y385_D0.9631.00
122_L298_A0.9631.00
187_A336_N0.9631.00
90_L93_W0.9621.00
58_K65_L0.9601.00
178_A214_I0.9591.00
44_K69_R0.9561.00
347_L354_R0.9441.00
207_S230_V0.9411.00
241_P250_A0.9351.00
356_L360_D0.9351.00
353_Y386_R0.9341.00
121_I303_I0.9311.00
199_A203_G0.9301.00
124_Q302_A0.9301.00
355_V427_I0.9291.00
48_F53_F0.9271.00
412_A416_R0.9171.00
127_N154_Y0.9161.00
121_I306_G0.9141.00
120_A123_S0.9141.00
256_T259_G0.9141.00
120_A310_L0.9121.00
45_G50_A0.9121.00
374_Q377_E0.9111.00
341_T382_A0.9101.00
292_L296_V0.9091.00
250_A283_I0.9011.00
408_A412_A0.8961.00
372_H376_G0.8951.00
340_M358_V0.8951.00
102_V155_A0.8941.00
225_L229_S0.8881.00
181_V227_W0.8861.00
395_H406_H0.8831.00
366_A392_K0.8821.00
294_M303_I0.8821.00
141_V145_L0.8781.00
329_L347_L0.8751.00
367_E372_H0.8741.00
162_N191_G0.8731.00
218_N221_N0.8671.00
238_R246_S0.8641.00
326_Q424_Q0.8611.00
338_G342_A0.8611.00
41_V83_T0.8601.00
78_L82_D0.8591.00
101_R296_V0.8581.00
242_N245_N0.8571.00
315_G330_D0.8551.00
388_L417_L0.8521.00
424_Q427_I0.8511.00
125_C299_T0.8491.00
141_V147_R0.8471.00
42_A67_V0.8451.00
92_A95_R0.8431.00
197_G201_A0.8401.00
91_A94_V0.8401.00
422_A427_I0.8401.00
119_A130_Y0.8391.00
271_V300_L0.8381.00
221_N284_A0.8361.00
220_D240_S0.8351.00
204_E208_G0.8311.00
273_V304_K0.8271.00
222_N226_N0.8251.00
348_A383_G0.8241.00
49_D69_R0.8181.00
203_G207_S0.8161.00
417_L421_I0.8141.00
401_S405_E0.8101.00
143_M146_L0.8071.00
104_A205_I0.8041.00
57_A62_A0.8031.00
290_A294_M0.8021.00
67_V77_Q0.7991.00
281_H342_A0.7991.00
407_F413_L0.7981.00
120_A124_Q0.7981.00
175_R210_P0.7961.00
327_L428_T0.7941.00
40_F63_G0.7921.00
169_W191_G0.7911.00
114_V289_A0.7911.00
65_L75_L0.7901.00
85_L169_W0.7881.00
228_Q238_R0.7871.00
398_S406_H0.7871.00
91_A173_L0.7861.00
303_I306_G0.7851.00
65_L68_S0.7841.00
119_A129_L0.7841.00
127_N151_E0.7791.00
143_M147_R0.7791.00
254_H272_D0.7781.00
79_I83_T0.7771.00
317_L346_V0.7761.00
225_L238_R0.7711.00
413_L417_L0.7711.00
42_A54_A0.7701.00
88_G173_L0.7691.00
396_A399_T0.7611.00
373_V400_A0.7591.00
260_T283_I0.7591.00
88_G169_W0.7581.00
161_A201_A0.7571.00
216_I292_L0.7561.00
114_V288_A0.7551.00
368_S371_C0.7541.00
354_R358_V0.7531.00
41_V87_F0.7531.00
164_Q200_K0.7531.00
88_G92_A0.7521.00
185_A195_L0.7501.00
300_L304_K0.7501.00
358_V389_S0.7491.00
182_N239_F0.7451.00
215_A231_I0.7411.00
343_A432_K0.7411.00
51_H54_A0.7411.00
393_Q396_A0.7401.00
269_G300_L0.7371.00
334_N432_K0.7361.00
371_C375_V0.7301.00
322_L325_N0.7281.00
116_E135_L0.7281.00
125_C293_S0.7271.00
51_H68_S0.7251.00
195_L199_A0.7251.00
116_E313_V0.7251.00
341_T374_Q0.7251.00
218_N239_F0.7241.00
196_A199_A0.7231.00
102_V157_I0.7231.00
247_D267_P0.7201.00
50_A53_F0.7191.00
159_L176_P0.7181.00
119_A156_V0.7141.00
171_V174_T0.7141.00
195_L198_V0.7141.00
109_S339_S0.7101.00
290_A300_L0.7081.00
264_L287_L0.7071.00
115_K131_T0.7071.00
142_P147_R0.7061.00
148_L155_A0.7041.00
54_A58_K0.7031.00
253_I283_I0.7031.00
192_F201_A0.7031.00
87_F92_A0.7011.00
277_L310_L0.7001.00
196_A226_N0.7001.00
367_E371_C0.6991.00
149_T152_Y0.6991.00
49_D52_D0.6951.00
359_G433_G0.6951.00
360_D393_Q0.6921.00
49_D53_F0.6911.00
255_V260_T0.6901.00
186_A338_G0.6891.00
219_A224_W0.6841.00
360_D437_A0.6791.00
376_G380_K0.6791.00
164_Q201_A0.6781.00
199_A227_W0.6781.00
366_A369_E0.6771.00
115_K156_V0.6761.00
368_S372_H0.6731.00
301_D304_K0.6731.00
246_S249_T0.6711.00
390_V410_K0.6651.00
324_E423_E0.6641.00
148_L152_Y0.6641.00
414_I418_K0.6641.00
298_A303_I0.6641.00
344_V382_A0.6641.00
43_L84_R0.6621.00
88_G91_A0.6621.00
164_Q197_G0.6611.00
367_E376_G0.6611.00
370_A374_Q0.6591.00
100_A148_L0.6581.00
397_I400_A0.6581.00
273_V286_A0.6561.00
369_E372_H0.6561.00
226_N230_V0.6551.00
315_G435_R0.6551.00
184_L195_L0.6531.00
433_G437_A0.6521.00
373_V376_G0.6501.00
277_L282_N0.6501.00
325_N424_Q0.6481.00
141_V146_L0.6461.00
241_P253_I0.6461.00
279_G282_N0.6431.00
109_S185_A0.6401.00
100_A155_A0.6391.00
329_L428_T0.6381.00
224_W228_Q0.6361.00
255_V280_R0.6361.00
357_V360_D0.6351.00
170_T173_L0.6351.00
369_E396_A0.6351.00
73_I82_D0.6351.00
256_T274_L0.6331.00
336_N339_S0.6291.00
384_I387_V0.6291.00
216_I237_W0.6281.00
244_A249_T0.6271.00
87_F91_A0.6261.00
46_E66_L0.6251.00
334_N343_A0.6241.00
410_K414_I0.6221.00
96_Q175_R0.6211.00
200_K203_G0.6201.00
328_L429_I0.6191.00
112_T134_N0.6181.00
92_A96_Q0.6181.00
290_A304_K0.6181.00
435_R438_A0.6151.00
116_E120_A0.6121.00
271_V301_D0.6121.00
86_A89_E0.6121.00
118_T156_V0.6111.00
52_D69_R0.6101.00
347_L430_L0.6061.00
252_N272_D0.6051.00
163_H191_G0.6051.00
321_Q327_L0.6031.00
253_I262_F0.6031.00
266_T300_L0.6021.00
219_A240_S0.6001.00
220_D241_P0.5991.00
354_R385_D0.5991.00
132_A147_R0.5981.00
103_V122_L0.5971.00
181_V199_A0.5971.00
386_R416_R0.5941.00
390_V437_A0.5921.00
86_A91_A0.5921.00
121_I125_C0.5911.00
253_I256_T0.5911.00
189_L193_G0.5911.00
50_A54_A0.5891.00
290_A307_L0.5871.00
390_V407_F0.5851.00
129_L148_L0.5841.00
105_L180_L0.5841.00
352_G427_I0.5841.00
225_L228_Q0.5831.00
287_L291_A0.5811.00
300_L303_I0.5811.00
240_S246_S0.5801.00
345_Q349_E0.5781.00
345_Q382_A0.5761.00
170_T174_T0.5761.00
129_L132_A0.5751.00
283_I287_L0.5741.00
42_A51_H0.5731.00
159_L174_T0.5701.00
395_H398_S0.5681.00
51_H83_T0.5681.00
245_N249_T0.5661.00
86_A90_L0.5661.00
171_V208_G0.5651.00
65_L77_Q0.5651.00
344_V384_I0.5631.00
42_A65_L0.5621.00
131_T134_N0.5611.00
410_K413_L0.5601.00
375_V378_A0.5581.00
70_P73_I0.5581.00
113_S117_M0.5571.00
368_S373_V0.5541.00
237_W248_F0.5541.00
291_A295_S0.5531.00
421_I427_I0.5531.00
385_D422_A0.5521.00
103_V154_Y0.5511.00
130_Y152_Y0.5511.00
280_R283_I0.5511.00
175_R208_G0.5491.00
393_Q397_I0.5491.00
129_L152_Y0.5491.00
122_L293_S0.5471.00
187_A202_K0.5471.00
224_W227_W0.5461.00
269_G294_M0.5461.00
248_F267_P0.5461.00
252_N255_V0.5451.00
128_T152_Y0.5451.00
54_A66_L0.5441.00
131_T136_N0.5421.00
241_P287_L0.5381.00
302_A306_G0.5381.00
116_E314_P0.5371.00
123_S128_T0.5371.00
113_S310_L0.5371.00
117_M289_A0.5351.00
323_A326_Q0.5341.00
43_L57_A0.5341.00
356_L387_V0.5341.00
85_L92_A0.5331.00
116_E136_N0.5321.00
288_A292_L0.5301.00
88_G94_V0.5291.00
292_L295_S0.5291.00
340_M375_V0.5291.00
58_K63_G0.5291.00
275_L307_L0.5251.00
330_D431_V0.5241.00
49_D68_S0.5220.99
385_D427_I0.5220.99
162_N190_E0.5200.99
53_F57_A0.5200.99
177_E212_N0.5200.99
344_V356_L0.5180.99
317_L343_A0.5180.99
400_A408_A0.5170.99
357_V432_K0.5170.99
98_V175_R0.5160.99
328_L431_V0.5150.99
105_L114_V0.5150.99
160_G163_H0.5150.99
44_K48_F0.5140.99
121_I307_L0.5130.99
240_S249_T0.5110.99
74_D79_I0.5100.99
57_A61_G0.5090.99
346_V350_M0.5090.99
324_E418_K0.5090.99
352_G428_T0.5080.99
231_I236_V0.5080.99
47_R52_D0.5070.99
200_K207_S0.5070.99
85_L88_G0.5050.99
228_Q236_V0.5030.99
129_L156_V0.5030.99
92_A175_R0.5020.99
433_G438_A0.5010.99
121_I298_A0.5010.99
357_V431_V0.5000.99
45_G48_F0.5000.99
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  
1gg4A 1 0.9668 100 0.128 Contact Map
4cvkA 1 0.9513 100 0.134 Contact Map
4qdiA 1 0.9801 100 0.135 Contact Map
3zm6A 1 0.9624 100 0.175 Contact Map
3zl8A 1 0.9292 100 0.202 Contact Map
4c12A 2 0.9668 100 0.221 Contact Map
2wtzA 1 0.9646 100 0.227 Contact Map
4bubA 1 0.9513 100 0.239 Contact Map
1e8cA 1 0.969 100 0.255 Contact Map
1p3dA 1 0.9159 100 0.377 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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