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2mtz_peptidoglycan_his_removed

ID: 1505504917 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 169 (164)
Sequences: 1046 (595.9)
Seq/Len: 6.378
Nf(neff/√len): 46.5

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 6.378).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
82_Y152_E3.2531.00
102_N117_S2.9961.00
73_S78_V2.4991.00
98_F119_S2.3751.00
115_W124_G2.3351.00
111_F124_G2.1171.00
113_A151_I2.0661.00
64_S67_A1.9871.00
100_I116_L1.8761.00
68_K137_A1.7861.00
7_Y22_F1.7511.00
117_S124_G1.7311.00
67_A71_T1.6961.00
70_L84_I1.6941.00
90_L139_S1.6861.00
71_T78_V1.6731.00
97_E162_R1.6361.00
139_S142_C1.6241.00
60_H73_S1.5901.00
127_G153_L1.4850.99
103_R159_N1.4650.99
69_T81_T1.4530.99
85_A139_S1.4190.99
24_I49_P1.4070.99
112_G127_G1.3780.98
70_L125_I1.3650.98
29_L46_I1.3440.98
54_P166_N1.3380.98
151_I155_S1.3320.98
62_A73_S1.3260.98
87_G142_C1.3240.98
91_T140_K1.2920.97
61_I157_V1.2910.97
88_K91_T1.2810.97
103_R116_L1.2800.97
9_V12_G1.2730.97
105_R114_Y1.2720.97
133_S137_A1.2700.97
63_V84_I1.2630.96
97_E164_T1.2530.96
7_Y13_D1.2430.96
143_I165_I1.2420.96
152_E156_I1.2270.96
158_P161_T1.2170.95
116_L159_N1.2040.95
62_A166_N1.1960.95
64_S166_N1.1900.95
19_A29_L1.1840.94
9_V46_I1.1790.94
88_K92_Q1.1770.94
128_T131_P1.1490.93
126_H142_C1.1450.93
80_K152_E1.1430.93
72_L153_L1.1210.92
10_K13_D1.1210.92
61_I153_L1.1200.92
20_A148_K1.1200.92
145_M150_V1.1060.91
36_L49_P1.0960.91
91_T120_K1.0920.91
106_N113_A1.0920.91
20_A29_L1.0860.90
89_I139_S1.0740.90
87_G93_T1.0540.89
73_S166_N1.0540.89
16_N20_A1.0530.88
116_L125_I1.0520.88
103_R154_A1.0500.88
107_P112_G1.0490.88
134_I144_R1.0390.88
114_Y150_V1.0300.87
98_F120_K1.0160.86
85_A150_V1.0140.86
139_S144_R1.0130.86
41_T44_Q1.0010.85
117_S122_H1.0010.85
110_P128_T1.0000.85
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4lzhA10.94081000.227Contact Map
4a1kA10.97041000.233Contact Map
4jmnA10.98221000.382Contact Map
4xvoA30.97631000.383Contact Map
1zatA10.96451000.429Contact Map
4k73A10.95861000.445Contact Map
3vypA20.98221000.449Contact Map
4qtfA101000.45Contact Map
5bmqA101000.456Contact Map
4xxtA10.93491000.475Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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