GREMLIN Database
YCIB - Putative L,D-transpeptidase YciB
UniProt: C0SP99 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 194 (167)
Sequences: 236 (203)
Seq/√Len: 15.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
115_E138_H4.0161.00
158_E172_R3.2400.99
131_Y178_A3.1160.99
130_E154_V3.0570.98
133_V181_V3.0290.98
69_W192_V2.9880.98
77_Q95_S2.9530.98
70_I81_I2.8670.98
149_T153_K2.7880.97
158_E161_K2.7820.97
167_S170_C2.7620.97
109_T190_K2.6080.96
179_K183_E2.5770.95
71_D82_K2.5550.95
79_A93_I2.3430.92
144_H170_C2.3290.92
144_H167_S2.3000.91
91_M173_L2.1450.88
69_W190_K2.1250.88
119_W148_M2.1210.88
81_I185_I2.0840.87
134_S138_H1.9910.84
142_L168_H1.8600.80
68_V189_T1.6730.72
134_S140_E1.6670.71
119_W130_E1.6570.71
23_H26_E1.6450.70
120_F168_H1.6430.70
185_I189_T1.6310.70
82_K87_T1.5930.68
133_V182_Y1.5880.68
81_I181_V1.5720.67
70_I181_V1.5500.66
161_K166_A1.4980.63
74_V107_K1.4920.62
113_E134_S1.4780.62
142_L170_C1.4730.61
115_E134_S1.4530.60
166_A172_R1.4160.58
135_W141_F1.4080.58
142_L167_S1.4020.58
22_D29_S1.3810.56
117_G132_W1.3410.54
117_G120_F1.3210.53
37_E126_Q1.3150.53
68_V185_I1.3110.52
79_A143_F1.2790.51
80_Y90_T1.2640.50
145_S185_I1.2600.49
115_E139_G1.2340.48
23_H28_A1.2320.48
113_E138_H1.2100.47
129_A147_P1.2080.46
27_H31_N1.1820.45
73_N183_E1.1780.45
158_E166_A1.1670.44
122_S125_Y1.1580.44
61_P89_Y1.1510.43
68_V181_V1.1150.41
109_T192_V1.1040.41
112_V185_I1.1030.41
23_H30_I1.1030.41
120_F142_L1.0990.40
24_A30_I1.0860.40
144_H168_H1.0790.39
128_G132_W1.0660.39
119_W154_V1.0580.38
51_D54_K1.0550.38
45_T71_D1.0530.38
148_M154_V1.0470.37
69_W109_T1.0390.37
50_I174_T1.0250.36
96_G172_R1.0180.36
110_F135_W1.0170.36
32_T35_T1.0010.35
120_F128_G0.9900.34
31_N34_K0.9880.34
154_V188_H0.9870.34
94_S147_P0.9800.34
63_I185_I0.9790.34
128_G147_P0.9710.33
25_E32_T0.9660.33
125_Y161_K0.9450.32
70_I175_I0.9240.31
52_W89_Y0.9230.31
106_P129_A0.9120.31
106_P147_P0.9030.30
122_S168_H0.8820.29
95_S112_V0.8800.29
25_E35_T0.8790.29
73_N135_W0.8730.29
94_S166_A0.8730.29
62_D193_I0.8720.29
79_A173_L0.8720.29
94_S191_V0.8630.28
55_P58_G0.8600.28
134_S159_A0.8530.28
31_N35_T0.8480.28
147_P191_V0.8450.27
44_K55_P0.8450.27
24_A32_T0.8400.27
78_K92_M0.8380.27
95_S168_H0.8330.27
56_S89_Y0.8310.27
68_V82_K0.8280.27
67_H84_G0.8270.27
105_T143_F0.8240.26
58_G97_L0.8230.26
22_D26_E0.8190.26
61_P91_M0.8180.26
47_K121_F0.8150.26
28_A39_I0.8110.26
27_H30_I0.8030.26
29_S38_N0.8000.25
55_P92_M0.7980.25
147_P180_W0.7970.25
52_W55_P0.7890.25
37_E40_T0.7860.25
57_G141_F0.7860.25
24_A31_N0.7860.25
140_E177_D0.7860.25
65_Q175_I0.7850.25
57_G92_M0.7830.25
46_A49_S0.7830.25
81_I136_K0.7810.25
96_G105_T0.7720.24
136_K140_E0.7630.24
117_G134_S0.7630.24
36_V41_D0.7580.24
106_P128_G0.7560.24
127_E168_H0.7560.24
121_F128_G0.7560.24
97_L181_V0.7520.23
90_T177_D0.7510.23
180_W191_V0.7500.23
105_T172_R0.7490.23
105_T167_S0.7470.23
112_V191_V0.7460.23
132_W147_P0.7440.23
169_G191_V0.7420.23
26_E34_K0.7380.23
91_M146_V0.7370.23
63_I88_I0.7350.23
25_E28_A0.7340.23
63_I68_V0.7330.23
136_K139_G0.7320.23
132_W185_I0.7310.22
98_D103_D0.7300.22
97_L166_A0.7280.22
52_W56_S0.7230.22
28_A33_K0.7200.22
60_Y134_S0.7180.22
66_K88_I0.7170.22
146_V166_A0.7160.22
181_V189_T0.7130.22
122_S154_V0.7130.22
28_A35_T0.7120.22
26_E33_K0.7060.22
88_I113_E0.7050.21
77_Q98_D0.7050.21
143_F173_L0.6990.21
95_S182_Y0.6980.21
24_A39_I0.6980.21
27_H33_K0.6960.21
50_I54_K0.6950.21
131_Y182_Y0.6900.21
33_K44_K0.6830.21
48_T70_I0.6820.21
115_E140_E0.6800.21
77_Q155_I0.6790.20
98_D104_A0.6790.20
24_A35_T0.6790.20
122_S140_E0.6760.20
22_D27_H0.6730.20
79_A146_V0.6710.20
105_T170_C0.6710.20
117_G128_G0.6690.20
78_K89_Y0.6660.20
33_K39_I0.6620.20
116_R132_W0.6620.20
31_N107_K0.6540.20
29_S33_K0.6540.20
63_I186_P0.6530.20
55_P60_Y0.6470.19
28_A36_V0.6470.19
153_K181_V0.6460.19
106_P180_W0.6400.19
122_S127_E0.6390.19
26_E36_V0.6360.19
130_E141_F0.6330.19
28_A31_N0.6300.19
62_D84_G0.6280.19
32_T40_T0.6280.19
79_A171_I0.6250.19
23_H36_V0.6200.18
146_V158_E0.6170.18
130_E148_M0.6160.18
154_V175_I0.6130.18
36_V151_D0.6070.18
105_T169_G0.6030.18
51_D55_P0.5990.18
28_A38_N0.5950.18
135_W191_V0.5950.18
61_P177_D0.5920.17
61_P159_A0.5910.17
22_D39_I0.5870.17
34_K39_I0.5870.17
122_S142_L0.5860.17
89_Y177_D0.5860.17
25_E37_E0.5830.17
33_K38_N0.5820.17
44_K49_S0.5820.17
125_Y148_M0.5800.17
52_W61_P0.5760.17
83_E193_I0.5750.17
42_V193_I0.5710.17
23_H29_S0.5660.17
84_G132_W0.5650.17
80_Y89_Y0.5640.17
79_A91_M0.5610.16
81_I126_Q0.5590.16
24_A28_A0.5560.16
25_E30_I0.5540.16
96_G170_C0.5540.16
22_D32_T0.5510.16
53_T175_I0.5510.16
77_Q132_W0.5460.16
52_W78_K0.5460.16
33_K37_E0.5450.16
121_F178_A0.5400.16
56_S90_T0.5280.15
167_S182_Y0.5280.15
76_E151_D0.5250.15
122_S128_G0.5200.15
47_K58_G0.5190.15
149_T193_I0.5180.15
98_D184_N0.5170.15
65_Q121_F0.5160.15
125_Y155_I0.5150.15
25_E34_K0.5130.15
93_I173_L0.5120.15
148_M158_E0.5110.15
73_N76_E0.5110.15
23_H35_T0.5060.15
33_K110_F0.5060.15
94_S106_P0.5050.15
128_G155_I0.5050.15
50_I53_T0.5020.15
56_S80_Y0.5000.15
96_G167_S0.5000.15
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  
4xxtA 1 0.8557 100 0.597 Contact Map
5bmqA 3 0.8969 99.9 0.648 Contact Map
4k73A 1 0.9278 99.9 0.651 Contact Map
4qtfA 2 0.9227 99.9 0.655 Contact Map
3vypA 1 0.9227 99.9 0.655 Contact Map
4jmnA 1 0.9227 99.9 0.659 Contact Map
4xvoA 1 0.8196 99.9 0.661 Contact Map
1zatA 1 0.8711 99.9 0.665 Contact Map
4a1kA 2 0.8299 99.9 0.678 Contact Map
4lpqA 1 0.8969 99.9 0.678 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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