GREMLIN Database
YQJB - Putative L,D-transpeptidase YqjB
UniProt: P54539 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 176 (134)
Sequences: 1772 (1039)
Seq/√Len: 89.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
137_H141_T3.7691.00
36_N122_F3.2731.00
68_V96_I3.1401.00
32_N35_T3.0841.00
93_A136_V3.0531.00
98_F148_V3.0421.00
50_Y137_H3.0051.00
35_T39_A2.7631.00
65_E147_R2.6111.00
110_I130_M2.5681.00
17_P46_V2.4711.00
130_M135_V2.4041.00
48_G137_H2.3451.00
95_W109_G2.3071.00
71_K139_F2.0331.00
36_N54_T1.9951.00
40_V141_T1.8871.00
37_E49_V1.8871.00
31_V128_I1.8791.00
70_V97_G1.8241.00
28_Y149_L1.8011.00
29_V142_I1.7761.00
97_G109_G1.7701.00
53_A123_V1.7261.00
52_V130_M1.7021.00
20_E23_L1.6951.00
19_G46_V1.6921.00
94_R140_Q1.6441.00
76_Y84_G1.6271.00
38_L52_V1.6021.00
66_F99_D1.5511.00
83_E86_S1.5351.00
67_S145_G1.4951.00
52_V128_I1.4941.00
91_L109_G1.4210.99
33_K63_E1.4160.99
69_T99_D1.4000.99
118_S123_V1.3390.99
110_I148_V1.3340.99
65_E149_L1.3030.99
58_D124_S1.2990.99
98_F128_I1.2910.99
38_L110_I1.2570.98
60_L125_N1.2200.98
40_V48_G1.1870.98
94_R136_V1.1850.98
32_N151_T1.1640.97
51_S134_E1.1440.97
16_W37_E1.1280.97
53_A118_S1.1130.97
42_L48_G1.1130.97
39_A46_V1.1110.97
94_R139_F1.1040.96
17_P42_L1.0980.96
51_S119_V1.0970.96
37_E51_S1.0900.96
143_P146_T1.0710.96
21_N25_G1.0470.95
22_P41_I1.0280.95
57_T61_T1.0240.95
40_V142_I1.0220.95
76_Y82_I1.0130.94
71_K143_P1.0060.94
53_A119_V1.0030.94
73_E140_Q1.0010.94
100_A107_I0.9920.94
75_P90_P0.9880.93
98_F110_I0.9850.93
24_P149_L0.9740.93
71_K96_I0.9700.93
70_V99_D0.9610.93
53_A124_S0.9560.92
66_F100_A0.9470.92
78_R82_I0.9360.92
40_V137_H0.9360.92
30_I41_I0.9240.91
33_K54_T0.9150.91
39_A49_V0.9050.90
81_N84_G0.8950.90
73_E139_F0.8940.90
96_I135_V0.8830.89
38_L130_M0.8640.88
76_Y85_G0.8410.86
48_G141_T0.8370.86
54_T148_V0.8300.86
75_P89_N0.8160.85
113_T116_E0.8100.84
80_K83_E0.8000.84
67_S147_R0.7880.83
107_I125_N0.7880.83
94_R135_V0.7850.82
74_N97_G0.7670.81
96_I143_P0.7630.81
56_K60_L0.7620.81
62_P150_I0.7550.80
29_V140_Q0.7550.80
112_G132_N0.7520.80
95_W135_V0.7450.79
24_P41_I0.7450.79
50_Y134_E0.7430.79
99_D106_R0.7430.79
41_I46_V0.7360.78
29_V110_I0.7320.78
69_T101_K0.7300.78
68_V148_V0.7300.78
110_I135_V0.7270.77
34_R152_D0.7250.77
74_N93_A0.7170.76
118_S121_K0.7170.76
76_Y81_N0.7140.76
19_G23_L0.7010.75
54_T122_F0.6990.75
28_Y147_R0.6910.74
73_E94_R0.6850.73
54_T77_Y0.6840.73
57_T60_L0.6830.73
85_G90_P0.6830.73
72_A99_D0.6750.72
61_T128_I0.6720.72
31_V81_N0.6700.71
77_Y92_G0.6700.71
128_I132_N0.6690.71
36_N124_S0.6690.71
96_I147_R0.6660.71
29_V135_V0.6600.70
72_A97_G0.6580.70
33_K150_I0.6580.70
113_T119_V0.6580.70
33_K55_G0.6570.70
34_R151_T0.6570.70
22_P25_G0.6530.69
116_E119_V0.6490.69
116_E131_H0.6300.67
16_W19_G0.6290.67
31_V52_V0.6250.66
55_G108_Y0.6220.66
99_D105_G0.6190.65
75_P95_W0.6180.65
86_S90_P0.6180.65
67_S144_V0.6160.65
19_G22_P0.6090.64
116_E123_V0.6010.63
77_Y120_G0.6000.63
92_G132_N0.6000.63
64_G116_E0.5970.63
75_P91_L0.5960.62
80_K99_D0.5940.62
116_E133_D0.5930.62
17_P21_N0.5870.61
24_P151_T0.5860.61
25_G42_L0.5850.61
91_L95_W0.5840.61
27_P41_I0.5820.61
56_K131_H0.5750.60
20_E24_P0.5720.59
27_P42_L0.5710.59
53_A129_R0.5700.59
115_R123_V0.5690.59
70_V144_V0.5650.58
49_V133_D0.5630.58
66_F148_V0.5630.58
63_E152_D0.5620.58
75_P92_G0.5580.57
122_F152_D0.5580.57
50_Y130_M0.5530.57
62_P108_Y0.5510.56
125_N134_E0.5500.56
29_V40_V0.5500.56
67_S101_K0.5470.56
28_Y134_E0.5440.56
96_I138_L0.5420.55
61_T66_F0.5420.55
53_A58_D0.5410.55
30_I39_A0.5390.55
18_L47_E0.5390.55
101_K106_R0.5390.55
108_Y128_I0.5370.55
34_R63_E0.5340.54
82_I99_D0.5330.54
28_Y41_I0.5320.54
79_K83_E0.5320.54
98_F150_I0.5320.54
27_P47_E0.5300.54
92_G116_E0.5290.53
61_T122_F0.5270.53
120_G148_V0.5270.53
53_A80_K0.5260.53
142_I146_T0.5240.53
129_R135_V0.5210.52
33_K108_Y0.5200.52
30_I151_T0.5180.52
112_G129_R0.5170.52
82_I85_G0.5170.52
33_K61_T0.5140.51
18_L22_P0.5120.51
40_V146_T0.5100.51
87_P90_P0.5090.51
64_G100_A0.5080.51
37_E121_K0.5080.51
131_H134_E0.5040.50
30_I147_R0.5000.50
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  
4lzhA 1 0.9261 100 0.34 Contact Map
1zatA 1 0.8125 100 0.434 Contact Map
4jmnA 1 0.8182 100 0.44 Contact Map
4xvoA 1 0.8295 100 0.444 Contact Map
4a1kA 2 0.7557 100 0.463 Contact Map
4k73A 1 0.7727 100 0.464 Contact Map
5bmqA 3 0.7841 100 0.468 Contact Map
4qtfA 2 0.9375 100 0.47 Contact Map
3vypA 1 0.9432 100 0.477 Contact Map
4xxtA 1 0.7443 100 0.492 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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